Starting phenix.real_space_refine on Thu Jun 19 05:46:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rfg_19119/06_2025/8rfg_19119.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rfg_19119/06_2025/8rfg_19119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rfg_19119/06_2025/8rfg_19119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rfg_19119/06_2025/8rfg_19119.map" model { file = "/net/cci-nas-00/data/ceres_data/8rfg_19119/06_2025/8rfg_19119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rfg_19119/06_2025/8rfg_19119.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 13786 2.51 5 N 3858 2.21 5 O 4167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21879 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 21580 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2765, 21558 Classifications: {'peptide': 2765} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 114, 'TRANS': 2650} Chain breaks: 5 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 9, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 158 Conformer: "B" Number of residues, atoms: 2765, 21558 Classifications: {'peptide': 2765} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 114, 'TRANS': 2650} Chain breaks: 5 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 9, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 158 bond proxies already assigned to first conformer: 22028 Chain: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 99 Unusual residues: {'BGC': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 143 Unusual residues: {'BGC': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 55 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 194 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG A 194 " occ=0.40 residue: pdb=" N AARG A1355 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A1355 " occ=0.50 Time building chain proxies: 22.26, per 1000 atoms: 1.02 Number of scatterers: 21879 At special positions: 0 Unit cell: (102.496, 120.433, 208.836, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 4167 8.00 N 3858 7.00 C 13786 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-2 " BGC B 1 " - " BGC B 2 " " BGC B 2 " - " BGC B 3 " " BGC B 3 " - " BGC B 4 " " BGC B 4 " - " BGC B 5 " " BGC B 5 " - " BGC B 6 " " BGC B 6 " - " BGC B 7 " " BGC B 7 " - " BGC B 8 " " BGC B 8 " - " BGC B 9 " " BGC C 1 " - " BGC C 2 " " BGC C 2 " - " BGC C 3 " " BGC C 3 " - " BGC C 4 " " BGC C 4 " - " BGC C 5 " " BGC C 5 " - " BGC C 6 " " BGC C 6 " - " BGC C 7 " " BGC C 7 " - " BGC C 8 " " BGC C 8 " - " BGC C 9 " " BGC C 9 " - " BGC C 10 " " BGC C 10 " - " BGC C 11 " " BGC C 11 " - " BGC C 12 " " BGC C 12 " - " BGC C 13 " " BGC D 1 " - " BGC D 2 " " BGC D 2 " - " BGC D 3 " " BGC D 3 " - " BGC D 4 " " BGC D 4 " - " BGC D 5 " Time building additional restraints: 5.75 Conformation dependent library (CDL) restraints added in 5.4 seconds 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5142 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 21 sheets defined 46.5% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.04 Creating SS restraints... Processing helix chain 'A' and resid 34 through 46 Processing helix chain 'A' and resid 57 through 79 removed outlier: 5.672A pdb=" N THR A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 95 removed outlier: 3.712A pdb=" N TRP A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 105 removed outlier: 3.596A pdb=" N GLN A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 123 through 127 removed outlier: 4.265A pdb=" N GLY A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 removed outlier: 3.578A pdb=" N TYR A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 168 through 212 Proline residue: A 174 - end of helix Processing helix chain 'A' and resid 215 through 226 removed outlier: 3.822A pdb=" N ALA A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 231 through 244 removed outlier: 3.818A pdb=" N ALA A 235 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLN A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 267 through 274 removed outlier: 3.664A pdb=" N GLU A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 298 Processing helix chain 'A' and resid 301 through 308 Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 323 through 341 removed outlier: 4.032A pdb=" N SER A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 373 through 378 removed outlier: 3.700A pdb=" N LEU A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 394 through 406 Processing helix chain 'A' and resid 408 through 430 Proline residue: A 414 - end of helix Processing helix chain 'A' and resid 438 through 467 removed outlier: 3.567A pdb=" N ALA A 442 " --> pdb=" O TYR A 438 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Proline residue: A 450 - end of helix Processing helix chain 'A' and resid 499 through 515 removed outlier: 4.213A pdb=" N GLU A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 557 Processing helix chain 'A' and resid 586 through 599 removed outlier: 3.531A pdb=" N ARG A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 643 removed outlier: 4.043A pdb=" N LYS A 636 " --> pdb=" O ASP A 632 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 637 " --> pdb=" O ALA A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 647 Processing helix chain 'A' and resid 702 through 707 Processing helix chain 'A' and resid 719 through 728 Processing helix chain 'A' and resid 737 through 746 removed outlier: 3.675A pdb=" N LEU A 741 " --> pdb=" O SER A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 780 removed outlier: 4.147A pdb=" N GLU A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 787 removed outlier: 3.777A pdb=" N ILE A 785 " --> pdb=" O LEU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 823 removed outlier: 3.626A pdb=" N TRP A 798 " --> pdb=" O ALA A 794 " (cutoff:3.500A) Proline residue: A 810 - end of helix Processing helix chain 'A' and resid 828 through 851 removed outlier: 4.278A pdb=" N TRP A 832 " --> pdb=" O GLY A 828 " (cutoff:3.500A) Proline residue: A 844 - end of helix removed outlier: 4.468A pdb=" N SER A 847 " --> pdb=" O ALA A 843 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 906 removed outlier: 5.377A pdb=" N ALA A 887 " --> pdb=" O ILE A 883 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASP A 888 " --> pdb=" O VAL A 884 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LEU A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 935 Processing helix chain 'A' and resid 937 through 951 removed outlier: 3.946A pdb=" N LEU A 951 " --> pdb=" O LEU A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 969 Proline residue: A 962 - end of helix Processing helix chain 'A' and resid 969 through 979 removed outlier: 3.951A pdb=" N VAL A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1005 Processing helix chain 'A' and resid 1005 through 1011 Processing helix chain 'A' and resid 1037 through 1055 Processing helix chain 'A' and resid 1058 through 1075 Processing helix chain 'A' and resid 1102 through 1124 Processing helix chain 'A' and resid 1135 through 1150 removed outlier: 3.587A pdb=" N LYS A1149 " --> pdb=" O ARG A1145 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA A1150 " --> pdb=" O GLU A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1182 Processing helix chain 'A' and resid 1188 through 1211 removed outlier: 3.556A pdb=" N ASN A1192 " --> pdb=" O ILE A1188 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A1210 " --> pdb=" O ASN A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1237 removed outlier: 3.737A pdb=" N VAL A1219 " --> pdb=" O GLN A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1264 Processing helix chain 'A' and resid 1300 through 1312 Processing helix chain 'A' and resid 1316 through 1322 removed outlier: 3.978A pdb=" N TYR A1320 " --> pdb=" O THR A1316 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A1322 " --> pdb=" O HIS A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1351 Processing helix chain 'A' and resid 1358 through 1379 removed outlier: 3.954A pdb=" N GLN A1362 " --> pdb=" O GLY A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1409 removed outlier: 3.906A pdb=" N GLY A1409 " --> pdb=" O PRO A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1421 through 1428 removed outlier: 4.202A pdb=" N SER A1425 " --> pdb=" O ALA A1421 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A1426 " --> pdb=" O PRO A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1429 through 1431 No H-bonds generated for 'chain 'A' and resid 1429 through 1431' Processing helix chain 'A' and resid 1432 through 1445 Processing helix chain 'A' and resid 1461 through 1465 removed outlier: 3.512A pdb=" N VAL A1465 " --> pdb=" O PRO A1462 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1494 Processing helix chain 'A' and resid 1496 through 1504 removed outlier: 3.556A pdb=" N GLU A1500 " --> pdb=" O GLY A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1513 removed outlier: 3.609A pdb=" N ALA A1511 " --> pdb=" O VAL A1507 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU A1513 " --> pdb=" O GLU A1509 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1541 Processing helix chain 'A' and resid 1690 through 1696 removed outlier: 3.814A pdb=" N HIS A1696 " --> pdb=" O ASP A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1696 through 1703 removed outlier: 3.574A pdb=" N SER A1700 " --> pdb=" O HIS A1696 " (cutoff:3.500A) Processing helix chain 'A' and resid 1760 through 1768 removed outlier: 3.766A pdb=" N ALA A1764 " --> pdb=" O LEU A1761 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA A1765 " --> pdb=" O ARG A1762 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA A1766 " --> pdb=" O GLU A1763 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A1767 " --> pdb=" O ALA A1764 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A1768 " --> pdb=" O ALA A1765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1810 through 1823 removed outlier: 3.744A pdb=" N VAL A1814 " --> pdb=" O SER A1810 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP A1815 " --> pdb=" O ARG A1811 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS A1816 " --> pdb=" O GLU A1812 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG A1820 " --> pdb=" O LYS A1816 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS A1823 " --> pdb=" O ASP A1819 " (cutoff:3.500A) Processing helix chain 'A' and resid 1830 through 1845 removed outlier: 3.542A pdb=" N VAL A1845 " --> pdb=" O GLN A1841 " (cutoff:3.500A) Processing helix chain 'A' and resid 1848 through 1864 Processing helix chain 'A' and resid 1872 through 1878 removed outlier: 3.618A pdb=" N THR A1878 " --> pdb=" O GLU A1874 " (cutoff:3.500A) Processing helix chain 'A' and resid 1909 through 1925 Processing helix chain 'A' and resid 1940 through 1957 removed outlier: 4.753A pdb=" N THR A1954 " --> pdb=" O HIS A1950 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLN A1955 " --> pdb=" O ILE A1951 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A1957 " --> pdb=" O GLU A1953 " (cutoff:3.500A) Processing helix chain 'A' and resid 1977 through 1988 Processing helix chain 'A' and resid 2001 through 2010 removed outlier: 3.601A pdb=" N SER A2008 " --> pdb=" O ASN A2004 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2139 removed outlier: 3.600A pdb=" N SER A2139 " --> pdb=" O ALA A2136 " (cutoff:3.500A) Processing helix chain 'A' and resid 2256 through 2261 Processing helix chain 'A' and resid 2316 through 2330 Processing helix chain 'A' and resid 2332 through 2348 Processing helix chain 'A' and resid 2356 through 2364 removed outlier: 3.747A pdb=" N HIS A2361 " --> pdb=" O ALA A2357 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET A2362 " --> pdb=" O GLY A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2365 through 2376 removed outlier: 3.592A pdb=" N TYR A2369 " --> pdb=" O ASN A2365 " (cutoff:3.500A) Processing helix chain 'A' and resid 2391 through 2398 removed outlier: 3.836A pdb=" N THR A2398 " --> pdb=" O GLN A2394 " (cutoff:3.500A) Processing helix chain 'A' and resid 2407 through 2418 Processing helix chain 'A' and resid 2444 through 2460 removed outlier: 3.595A pdb=" N TRP A2448 " --> pdb=" O ASP A2444 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU A2449 " --> pdb=" O ASP A2445 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA A2450 " --> pdb=" O VAL A2446 " (cutoff:3.500A) Processing helix chain 'A' and resid 2462 through 2467 Processing helix chain 'A' and resid 2497 through 2512 Processing helix chain 'A' and resid 2542 through 2563 removed outlier: 3.824A pdb=" N ASP A2554 " --> pdb=" O GLY A2550 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU A2557 " --> pdb=" O ARG A2553 " (cutoff:3.500A) Processing helix chain 'A' and resid 2564 through 2585 Processing helix chain 'A' and resid 2615 through 2624 removed outlier: 3.988A pdb=" N VAL A2622 " --> pdb=" O GLN A2618 " (cutoff:3.500A) Processing helix chain 'A' and resid 2628 through 2644 removed outlier: 3.604A pdb=" N MET A2640 " --> pdb=" O MET A2636 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU A2641 " --> pdb=" O ASP A2637 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N HIS A2642 " --> pdb=" O ALA A2638 " (cutoff:3.500A) Processing helix chain 'A' and resid 2666 through 2671 removed outlier: 3.915A pdb=" N LYS A2669 " --> pdb=" O GLY A2666 " (cutoff:3.500A) Processing helix chain 'A' and resid 2683 through 2697 removed outlier: 3.942A pdb=" N TRP A2688 " --> pdb=" O HIS A2684 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A2697 " --> pdb=" O LEU A2693 " (cutoff:3.500A) Processing helix chain 'A' and resid 2698 through 2710 removed outlier: 3.582A pdb=" N ALA A2702 " --> pdb=" O ARG A2698 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A2708 " --> pdb=" O ASN A2704 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A2709 " --> pdb=" O CYS A2705 " (cutoff:3.500A) Processing helix chain 'A' and resid 2752 through 2764 removed outlier: 4.355A pdb=" N TRP A2756 " --> pdb=" O GLY A2752 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 568 through 569 removed outlier: 8.043A pdb=" N LEU A 568 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU A 524 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL A 491 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 525 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 488 " --> pdb=" O TYR A 619 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG A 667 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP A 753 " --> pdb=" O ARG A 667 " (cutoff:3.500A) removed outlier: 9.925A pdb=" N THR A 669 " --> pdb=" O ASP A 753 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N GLU A 755 " --> pdb=" O THR A 669 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 574 through 576 removed outlier: 7.372A pdb=" N CYS A 580 " --> pdb=" O ASN A 575 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1035 through 1036 Processing sheet with id=AA4, first strand: chain 'A' and resid 1099 through 1101 removed outlier: 3.540A pdb=" N GLU A1288 " --> pdb=" O ARG A1283 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1327 through 1329 Processing sheet with id=AA6, first strand: chain 'A' and resid 1419 through 1420 Processing sheet with id=AA7, first strand: chain 'A' and resid 1548 through 1550 removed outlier: 3.503A pdb=" N LYS A1629 " --> pdb=" O HIS A1640 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS A1652 " --> pdb=" O ALA A1637 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1548 through 1550 removed outlier: 3.503A pdb=" N LYS A1629 " --> pdb=" O HIS A1640 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS A1652 " --> pdb=" O ALA A1637 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER A1800 " --> pdb=" O ASN A1738 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN A1738 " --> pdb=" O SER A1800 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1560 through 1564 removed outlier: 6.816A pdb=" N SER A1580 " --> pdb=" O ILE A1587 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLN A1585 " --> pdb=" O ALA A1688 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ALA A1688 " --> pdb=" O GLN A1585 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A1587 " --> pdb=" O VAL A1686 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1613 through 1615 removed outlier: 3.627A pdb=" N LEU A1787 " --> pdb=" O SER A1681 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1968 through 1969 removed outlier: 6.278A pdb=" N LEU A1930 " --> pdb=" O PHE A1969 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A1992 " --> pdb=" O SER A1899 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2051 through 2053 removed outlier: 3.535A pdb=" N HIS A2150 " --> pdb=" O TYR A2060 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY A2312 " --> pdb=" O PHE A2243 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A2227 " --> pdb=" O LEU A2244 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A2226 " --> pdb=" O ASP A2221 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2051 through 2053 removed outlier: 3.535A pdb=" N HIS A2150 " --> pdb=" O TYR A2060 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A2305 " --> pdb=" O VAL A2185 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2076 through 2080 removed outlier: 3.822A pdb=" N PHE A2083 " --> pdb=" O ASN A2080 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A2084 " --> pdb=" O TRP A2096 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2119 through 2122 removed outlier: 3.853A pdb=" N ALA A2199 " --> pdb=" O LEU A2293 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2350 through 2352 Processing sheet with id=AB8, first strand: chain 'A' and resid 2389 through 2390 removed outlier: 4.525A pdb=" N TRP A2429 " --> pdb=" O VAL A2438 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2470 through 2474 removed outlier: 6.755A pdb=" N ARG A2494 " --> pdb=" O PHE A2472 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LYS A2474 " --> pdb=" O SER A2492 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N SER A2492 " --> pdb=" O LYS A2474 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2595 through 2596 Processing sheet with id=AC2, first strand: chain 'A' and resid 2681 through 2682 removed outlier: 6.863A pdb=" N THR A2732 " --> pdb=" O SER A2748 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER A2748 " --> pdb=" O THR A2732 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP A2734 " --> pdb=" O GLY A2746 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2768 through 2770 1048 hydrogen bonds defined for protein. 3019 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: 13.37 Time building geometry restraints manager: 6.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7324 1.34 - 1.46: 5080 1.46 - 1.58: 9848 1.58 - 1.69: 0 1.69 - 1.81: 121 Bond restraints: 22373 Sorted by residual: bond pdb=" C1 BGC C 11 " pdb=" O5 BGC C 11 " ideal model delta sigma weight residual 1.408 1.472 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C1 BGC C 12 " pdb=" O5 BGC C 12 " ideal model delta sigma weight residual 1.408 1.467 -0.059 2.00e-02 2.50e+03 8.68e+00 bond pdb=" C1 BGC B 9 " pdb=" O5 BGC B 9 " ideal model delta sigma weight residual 1.408 1.461 -0.053 2.00e-02 2.50e+03 6.93e+00 bond pdb=" N GLU A1228 " pdb=" CA GLU A1228 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.81e+00 bond pdb=" N ASN A1996 " pdb=" CA ASN A1996 " ideal model delta sigma weight residual 1.456 1.482 -0.025 1.31e-02 5.83e+03 3.66e+00 ... (remaining 22368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 29593 2.17 - 4.33: 726 4.33 - 6.50: 68 6.50 - 8.67: 12 8.67 - 10.83: 4 Bond angle restraints: 30403 Sorted by residual: angle pdb=" N PRO A2030 " pdb=" CA PRO A2030 " pdb=" CB PRO A2030 " ideal model delta sigma weight residual 102.81 109.96 -7.15 6.70e-01 2.23e+00 1.14e+02 angle pdb=" N PRO A1524 " pdb=" CA PRO A1524 " pdb=" CB PRO A1524 " ideal model delta sigma weight residual 103.33 110.52 -7.19 9.30e-01 1.16e+00 5.97e+01 angle pdb=" N PRO A1520 " pdb=" CA PRO A1520 " pdb=" CB PRO A1520 " ideal model delta sigma weight residual 103.20 110.48 -7.28 9.50e-01 1.11e+00 5.88e+01 angle pdb=" N PRO A2033 " pdb=" CA PRO A2033 " pdb=" CB PRO A2033 " ideal model delta sigma weight residual 103.25 110.99 -7.74 1.05e+00 9.07e-01 5.44e+01 angle pdb=" N PRO A1888 " pdb=" CA PRO A1888 " pdb=" CB PRO A1888 " ideal model delta sigma weight residual 103.25 110.74 -7.49 1.05e+00 9.07e-01 5.09e+01 ... (remaining 30398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.71: 12664 25.71 - 51.42: 677 51.42 - 77.13: 102 77.13 - 102.83: 72 102.83 - 128.54: 65 Dihedral angle restraints: 13580 sinusoidal: 5591 harmonic: 7989 Sorted by residual: dihedral pdb=" CA VAL A 72 " pdb=" C VAL A 72 " pdb=" N TYR A 73 " pdb=" CA TYR A 73 " ideal model delta harmonic sigma weight residual 180.00 145.52 34.48 0 5.00e+00 4.00e-02 4.76e+01 dihedral pdb=" CA ALA A1519 " pdb=" C ALA A1519 " pdb=" N PRO A1520 " pdb=" CA PRO A1520 " ideal model delta harmonic sigma weight residual -180.00 -154.14 -25.86 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" C2 BGC B 1 " pdb=" C1 BGC B 1 " pdb=" O5 BGC B 1 " pdb=" C5 BGC B 1 " ideal model delta sinusoidal sigma weight residual -65.02 63.52 -128.54 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 13577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2875 0.057 - 0.113: 494 0.113 - 0.170: 49 0.170 - 0.226: 4 0.226 - 0.283: 6 Chirality restraints: 3428 Sorted by residual: chirality pdb=" CB ILE A1643 " pdb=" CA ILE A1643 " pdb=" CG1 ILE A1643 " pdb=" CG2 ILE A1643 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA PRO A1520 " pdb=" N PRO A1520 " pdb=" C PRO A1520 " pdb=" CB PRO A1520 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA PRO A2030 " pdb=" N PRO A2030 " pdb=" C PRO A2030 " pdb=" CB PRO A2030 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 3425 not shown) Planarity restraints: 3926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 613 " 0.095 5.00e-02 4.00e+02 1.43e-01 3.25e+01 pdb=" N PRO A 614 " -0.247 5.00e-02 4.00e+02 pdb=" CA PRO A 614 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO A 614 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A1519 " 0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C ALA A1519 " -0.061 2.00e-02 2.50e+03 pdb=" O ALA A1519 " 0.023 2.00e-02 2.50e+03 pdb=" N PRO A1520 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1227 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C VAL A1227 " -0.058 2.00e-02 2.50e+03 pdb=" O VAL A1227 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU A1228 " 0.020 2.00e-02 2.50e+03 ... (remaining 3923 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 236 2.58 - 3.16: 18507 3.16 - 3.74: 33550 3.74 - 4.32: 44690 4.32 - 4.90: 75754 Nonbonded interactions: 172737 Sorted by model distance: nonbonded pdb=" OH TYR A2200 " pdb=" OE2 GLU A2202 " model vdw 2.000 3.040 nonbonded pdb=" O ASN A1417 " pdb=" OG1 THR A1461 " model vdw 2.097 3.040 nonbonded pdb=" OH TYR A 694 " pdb=" O3 BGC B 1 " model vdw 2.103 3.040 nonbonded pdb=" OD2 ASP A1208 " pdb=" OG1 THR A1220 " model vdw 2.120 3.040 nonbonded pdb=" OE2 GLU A 102 " pdb=" NE2 GLN A1325 " model vdw 2.137 3.120 ... (remaining 172732 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.40 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 70.770 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22397 Z= 0.215 Angle : 0.761 10.834 30475 Z= 0.445 Chirality : 0.044 0.283 3428 Planarity : 0.005 0.143 3926 Dihedral : 19.693 128.542 8438 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.84 % Allowed : 8.86 % Favored : 90.30 % Rotamer: Outliers : 0.14 % Allowed : 0.18 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.16), residues: 2759 helix: 0.82 (0.16), residues: 1215 sheet: -1.38 (0.28), residues: 335 loop : -3.03 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 821 HIS 0.008 0.001 HIS A1833 PHE 0.026 0.002 PHE A2555 TYR 0.018 0.002 TYR A 98 ARG 0.007 0.000 ARG A1321 Details of bonding type rmsd link_BETA1-2 : bond 0.00557 ( 24) link_BETA1-2 : angle 1.69222 ( 72) hydrogen bonds : bond 0.17223 ( 995) hydrogen bonds : angle 6.32908 ( 3019) covalent geometry : bond 0.00434 (22373) covalent geometry : angle 0.75701 (30403) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 2.395 Fit side-chains revert: symmetry clash REVERT: A 830 LEU cc_start: 0.7020 (pt) cc_final: 0.6650 (tt) REVERT: A 1906 MET cc_start: 0.7447 (pmm) cc_final: 0.7037 (pmm) REVERT: A 2790 ILE cc_start: 0.8788 (tt) cc_final: 0.8412 (mt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.3603 time to fit residues: 110.3944 Evaluate side-chains 145 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 3.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 141 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN A 515 ASN A1353 GLN A1364 ASN ** A1394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 HIS ** A2642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.101557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.076325 restraints weight = 84443.442| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 4.40 r_work: 0.3021 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 22397 Z= 0.220 Angle : 0.734 10.661 30475 Z= 0.366 Chirality : 0.047 0.250 3428 Planarity : 0.005 0.108 3926 Dihedral : 16.440 123.330 3571 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.79 % Favored : 90.41 % Rotamer: Outliers : 0.63 % Allowed : 5.48 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.16), residues: 2759 helix: 0.88 (0.16), residues: 1214 sheet: -1.29 (0.28), residues: 346 loop : -2.97 (0.16), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 821 HIS 0.009 0.001 HIS A2086 PHE 0.032 0.002 PHE A 957 TYR 0.019 0.002 TYR A1864 ARG 0.010 0.001 ARG A 117 Details of bonding type rmsd link_BETA1-2 : bond 0.00577 ( 24) link_BETA1-2 : angle 2.25315 ( 72) hydrogen bonds : bond 0.04749 ( 995) hydrogen bonds : angle 4.76008 ( 3019) covalent geometry : bond 0.00501 (22373) covalent geometry : angle 0.72660 (30403) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 3.285 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.7855 (tpt) cc_final: 0.7641 (tpp) REVERT: A 320 TYR cc_start: 0.8301 (t80) cc_final: 0.7951 (t80) REVERT: A 515 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8484 (p0) REVERT: A 965 LEU cc_start: 0.8211 (mt) cc_final: 0.7989 (mt) REVERT: A 1690 GLU cc_start: 0.8687 (tp30) cc_final: 0.8262 (tm-30) REVERT: A 2783 GLU cc_start: 0.8739 (mp0) cc_final: 0.8516 (mp0) REVERT: A 2790 ILE cc_start: 0.8181 (tt) cc_final: 0.7909 (mt) outliers start: 11 outliers final: 8 residues processed: 161 average time/residue: 0.4156 time to fit residues: 116.4101 Evaluate side-chains 153 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1461 THR Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 2453 ILE Chi-restraints excluded: chain A residue 2730 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 203 optimal weight: 0.8980 chunk 257 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 230 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN A1233 HIS ** A1395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.103108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.078593 restraints weight = 68976.405| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.98 r_work: 0.3072 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22397 Z= 0.142 Angle : 0.665 10.403 30475 Z= 0.324 Chirality : 0.043 0.238 3428 Planarity : 0.004 0.090 3926 Dihedral : 12.962 128.683 3571 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.14 % Favored : 91.06 % Rotamer: Outliers : 0.86 % Allowed : 7.42 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.16), residues: 2759 helix: 1.04 (0.16), residues: 1227 sheet: -1.11 (0.28), residues: 358 loop : -2.92 (0.16), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 821 HIS 0.009 0.001 HIS A1394 PHE 0.025 0.001 PHE A 957 TYR 0.013 0.001 TYR A2103 ARG 0.005 0.000 ARG A1321 Details of bonding type rmsd link_BETA1-2 : bond 0.00531 ( 24) link_BETA1-2 : angle 2.45840 ( 72) hydrogen bonds : bond 0.04209 ( 995) hydrogen bonds : angle 4.44170 ( 3019) covalent geometry : bond 0.00316 (22373) covalent geometry : angle 0.65491 (30403) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7896 (tpt) cc_final: 0.7545 (tpp) REVERT: A 54 MET cc_start: 0.8163 (ppp) cc_final: 0.7441 (ppp) REVERT: A 320 TYR cc_start: 0.8231 (t80) cc_final: 0.7936 (t80) REVERT: A 750 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8400 (tp) REVERT: A 991 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7325 (tm-30) REVERT: A 2423 GLU cc_start: 0.8749 (tt0) cc_final: 0.8544 (tt0) REVERT: A 2479 MET cc_start: 0.7804 (pmm) cc_final: 0.7099 (pmm) REVERT: A 2561 LYS cc_start: 0.9020 (tppt) cc_final: 0.8480 (ttmm) REVERT: A 2751 THR cc_start: 0.8649 (p) cc_final: 0.8314 (t) REVERT: A 2783 GLU cc_start: 0.8737 (mp0) cc_final: 0.8501 (mp0) REVERT: A 2790 ILE cc_start: 0.8127 (tt) cc_final: 0.7875 (mt) outliers start: 16 outliers final: 11 residues processed: 169 average time/residue: 0.3984 time to fit residues: 114.9856 Evaluate side-chains 163 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1287 LYS Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1461 THR Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain A residue 2453 ILE Chi-restraints excluded: chain A residue 2730 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 179 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 112 optimal weight: 0.3980 chunk 183 optimal weight: 9.9990 chunk 275 optimal weight: 0.3980 chunk 199 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1480 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.103201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.077535 restraints weight = 95665.960| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 4.70 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22397 Z= 0.138 Angle : 0.636 9.523 30475 Z= 0.312 Chirality : 0.043 0.242 3428 Planarity : 0.004 0.082 3926 Dihedral : 10.044 118.101 3571 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.39 % Favored : 90.85 % Rotamer: Outliers : 1.09 % Allowed : 8.42 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2759 helix: 1.19 (0.16), residues: 1227 sheet: -0.93 (0.28), residues: 354 loop : -2.88 (0.16), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 821 HIS 0.011 0.001 HIS A1394 PHE 0.022 0.001 PHE A 957 TYR 0.015 0.001 TYR A1087 ARG 0.005 0.000 ARG A 117 Details of bonding type rmsd link_BETA1-2 : bond 0.00592 ( 24) link_BETA1-2 : angle 2.76466 ( 72) hydrogen bonds : bond 0.03857 ( 995) hydrogen bonds : angle 4.24444 ( 3019) covalent geometry : bond 0.00307 (22373) covalent geometry : angle 0.62258 (30403) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.7756 (ppp) cc_final: 0.7125 (ppp) REVERT: A 272 MET cc_start: 0.7613 (tpp) cc_final: 0.7352 (ttp) REVERT: A 320 TYR cc_start: 0.8121 (t80) cc_final: 0.7760 (t80) REVERT: A 509 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6613 (pm20) REVERT: A 2423 GLU cc_start: 0.8487 (tt0) cc_final: 0.8277 (tt0) REVERT: A 2479 MET cc_start: 0.7733 (pmm) cc_final: 0.7108 (pmm) REVERT: A 2561 LYS cc_start: 0.9043 (tppt) cc_final: 0.8490 (ttmm) REVERT: A 2654 PHE cc_start: 0.7271 (m-10) cc_final: 0.6969 (m-80) REVERT: A 2751 THR cc_start: 0.8554 (p) cc_final: 0.8254 (t) REVERT: A 2783 GLU cc_start: 0.8726 (mp0) cc_final: 0.8403 (mp0) REVERT: A 2790 ILE cc_start: 0.8137 (tt) cc_final: 0.7891 (mt) outliers start: 21 outliers final: 15 residues processed: 173 average time/residue: 0.3118 time to fit residues: 90.7807 Evaluate side-chains 169 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1287 LYS Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1461 THR Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain A residue 2453 ILE Chi-restraints excluded: chain A residue 2555 PHE Chi-restraints excluded: chain A residue 2730 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 53 optimal weight: 0.8980 chunk 59 optimal weight: 0.0870 chunk 251 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 HIS ** A1395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2776 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.101223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.075811 restraints weight = 88657.579| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 4.48 r_work: 0.3010 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22397 Z= 0.184 Angle : 0.673 10.934 30475 Z= 0.332 Chirality : 0.043 0.243 3428 Planarity : 0.004 0.079 3926 Dihedral : 8.688 95.697 3571 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.83 % Favored : 90.45 % Rotamer: Outliers : 1.00 % Allowed : 9.28 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.16), residues: 2759 helix: 1.16 (0.16), residues: 1228 sheet: -0.94 (0.29), residues: 339 loop : -2.87 (0.16), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 821 HIS 0.009 0.001 HIS A1394 PHE 0.018 0.001 PHE A 957 TYR 0.017 0.001 TYR A2103 ARG 0.005 0.000 ARG A 529 Details of bonding type rmsd link_BETA1-2 : bond 0.00584 ( 24) link_BETA1-2 : angle 2.88187 ( 72) hydrogen bonds : bond 0.04156 ( 995) hydrogen bonds : angle 4.27881 ( 3019) covalent geometry : bond 0.00419 (22373) covalent geometry : angle 0.65893 (30403) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8248 (ppp) cc_final: 0.7558 (ppp) REVERT: A 320 TYR cc_start: 0.8314 (t80) cc_final: 0.8032 (t80) REVERT: A 628 ARG cc_start: 0.8218 (ttm-80) cc_final: 0.7948 (ttm-80) REVERT: A 2362 MET cc_start: 0.9242 (mmt) cc_final: 0.8996 (mmm) REVERT: A 2654 PHE cc_start: 0.7671 (m-10) cc_final: 0.7454 (m-80) REVERT: A 2751 THR cc_start: 0.8924 (p) cc_final: 0.8571 (t) REVERT: A 2783 GLU cc_start: 0.8723 (mp0) cc_final: 0.8319 (mp0) REVERT: A 2790 ILE cc_start: 0.8193 (tt) cc_final: 0.7936 (mt) outliers start: 19 outliers final: 18 residues processed: 163 average time/residue: 0.3154 time to fit residues: 84.1889 Evaluate side-chains 166 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1287 LYS Chi-restraints excluded: chain A residue 1461 THR Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain A residue 2429 TRP Chi-restraints excluded: chain A residue 2453 ILE Chi-restraints excluded: chain A residue 2555 PHE Chi-restraints excluded: chain A residue 2730 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 193 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 203 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 182 optimal weight: 0.3980 chunk 160 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 HIS ** A1934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2713 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.102298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.077909 restraints weight = 68461.309| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.93 r_work: 0.3061 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22397 Z= 0.138 Angle : 0.642 10.550 30475 Z= 0.313 Chirality : 0.042 0.237 3428 Planarity : 0.004 0.081 3926 Dihedral : 7.753 94.056 3571 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.10 % Favored : 91.17 % Rotamer: Outliers : 1.04 % Allowed : 9.82 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.16), residues: 2759 helix: 1.27 (0.16), residues: 1227 sheet: -0.80 (0.29), residues: 336 loop : -2.80 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 821 HIS 0.008 0.001 HIS A1394 PHE 0.018 0.001 PHE A 957 TYR 0.029 0.001 TYR A 764 ARG 0.009 0.000 ARG A 805 Details of bonding type rmsd link_BETA1-2 : bond 0.00618 ( 24) link_BETA1-2 : angle 2.94476 ( 72) hydrogen bonds : bond 0.03804 ( 995) hydrogen bonds : angle 4.16473 ( 3019) covalent geometry : bond 0.00307 (22373) covalent geometry : angle 0.62620 (30403) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8289 (ppp) cc_final: 0.7727 (ppp) REVERT: A 320 TYR cc_start: 0.8247 (t80) cc_final: 0.7916 (t80) REVERT: A 509 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6997 (pm20) REVERT: A 596 MET cc_start: 0.8311 (mtt) cc_final: 0.8021 (mmt) REVERT: A 628 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7881 (ttm-80) REVERT: A 1005 TRP cc_start: 0.8660 (t60) cc_final: 0.8117 (t-100) REVERT: A 1699 PHE cc_start: 0.6918 (OUTLIER) cc_final: 0.6627 (m-10) REVERT: A 2362 MET cc_start: 0.9245 (mmt) cc_final: 0.8984 (mmm) REVERT: A 2561 LYS cc_start: 0.9039 (tppt) cc_final: 0.8452 (ttmm) REVERT: A 2654 PHE cc_start: 0.7579 (m-10) cc_final: 0.7148 (m-80) REVERT: A 2722 GLU cc_start: 0.7478 (tp30) cc_final: 0.7278 (tp30) REVERT: A 2751 THR cc_start: 0.8793 (p) cc_final: 0.8529 (t) REVERT: A 2783 GLU cc_start: 0.8733 (mp0) cc_final: 0.8330 (mp0) REVERT: A 2790 ILE cc_start: 0.8138 (tt) cc_final: 0.7897 (mt) outliers start: 20 outliers final: 15 residues processed: 173 average time/residue: 0.3275 time to fit residues: 93.7067 Evaluate side-chains 168 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1287 LYS Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1461 THR Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1699 PHE Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain A residue 2429 TRP Chi-restraints excluded: chain A residue 2453 ILE Chi-restraints excluded: chain A residue 2555 PHE Chi-restraints excluded: chain A residue 2730 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 134 optimal weight: 0.0070 chunk 119 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 237 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 271 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 HIS A2713 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.103879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.078207 restraints weight = 87663.943| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 4.59 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22397 Z= 0.123 Angle : 0.624 10.046 30475 Z= 0.304 Chirality : 0.041 0.242 3428 Planarity : 0.004 0.079 3926 Dihedral : 6.986 92.119 3571 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.32 % Favored : 90.96 % Rotamer: Outliers : 0.91 % Allowed : 10.64 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.17), residues: 2759 helix: 1.35 (0.16), residues: 1227 sheet: -0.72 (0.29), residues: 352 loop : -2.80 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 821 HIS 0.006 0.001 HIS A1394 PHE 0.017 0.001 PHE A 957 TYR 0.025 0.001 TYR A 764 ARG 0.004 0.000 ARG A 529 Details of bonding type rmsd link_BETA1-2 : bond 0.00597 ( 24) link_BETA1-2 : angle 2.92561 ( 72) hydrogen bonds : bond 0.03620 ( 995) hydrogen bonds : angle 4.07446 ( 3019) covalent geometry : bond 0.00271 (22373) covalent geometry : angle 0.60866 (30403) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 2.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7825 (tpp) cc_final: 0.7343 (tpt) REVERT: A 54 MET cc_start: 0.7937 (ppp) cc_final: 0.7396 (ppp) REVERT: A 320 TYR cc_start: 0.8124 (t80) cc_final: 0.7820 (t80) REVERT: A 509 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6637 (pm20) REVERT: A 932 TYR cc_start: 0.8544 (m-80) cc_final: 0.8007 (m-80) REVERT: A 1005 TRP cc_start: 0.8430 (t60) cc_final: 0.7946 (t-100) REVERT: A 1699 PHE cc_start: 0.6655 (OUTLIER) cc_final: 0.6328 (m-10) REVERT: A 2307 MET cc_start: 0.7553 (mtt) cc_final: 0.7290 (mtt) REVERT: A 2362 MET cc_start: 0.9145 (mmt) cc_final: 0.8879 (mmm) REVERT: A 2557 GLU cc_start: 0.8693 (tt0) cc_final: 0.8113 (tm-30) REVERT: A 2561 LYS cc_start: 0.9133 (tppt) cc_final: 0.8330 (ttmm) REVERT: A 2654 PHE cc_start: 0.7182 (m-10) cc_final: 0.6924 (m-80) REVERT: A 2751 THR cc_start: 0.8642 (p) cc_final: 0.8393 (t) REVERT: A 2783 GLU cc_start: 0.8763 (mp0) cc_final: 0.8316 (mp0) REVERT: A 2790 ILE cc_start: 0.8121 (tt) cc_final: 0.7901 (mt) outliers start: 17 outliers final: 13 residues processed: 177 average time/residue: 0.3250 time to fit residues: 95.7202 Evaluate side-chains 171 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1287 LYS Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1699 PHE Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain A residue 2429 TRP Chi-restraints excluded: chain A residue 2453 ILE Chi-restraints excluded: chain A residue 2555 PHE Chi-restraints excluded: chain A residue 2730 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 121 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 chunk 242 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 185 optimal weight: 0.0040 chunk 89 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 260 optimal weight: 0.5980 chunk 221 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2713 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.104215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.077859 restraints weight = 108151.917| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 5.10 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22397 Z= 0.120 Angle : 0.622 11.307 30475 Z= 0.303 Chirality : 0.041 0.289 3428 Planarity : 0.004 0.084 3926 Dihedral : 6.456 90.919 3571 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.81 % Favored : 91.46 % Rotamer: Outliers : 1.04 % Allowed : 11.00 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.17), residues: 2759 helix: 1.40 (0.16), residues: 1229 sheet: -0.66 (0.29), residues: 337 loop : -2.75 (0.16), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 821 HIS 0.005 0.001 HIS A2086 PHE 0.018 0.001 PHE A 838 TYR 0.025 0.001 TYR A 764 ARG 0.005 0.000 ARG A 529 Details of bonding type rmsd link_BETA1-2 : bond 0.00609 ( 24) link_BETA1-2 : angle 2.94231 ( 72) hydrogen bonds : bond 0.03567 ( 995) hydrogen bonds : angle 4.03896 ( 3019) covalent geometry : bond 0.00262 (22373) covalent geometry : angle 0.60634 (30403) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7881 (tpp) cc_final: 0.7367 (tpt) REVERT: A 54 MET cc_start: 0.7920 (ppp) cc_final: 0.7383 (ppp) REVERT: A 320 TYR cc_start: 0.8124 (t80) cc_final: 0.7833 (t80) REVERT: A 932 TYR cc_start: 0.8558 (m-80) cc_final: 0.8026 (m-80) REVERT: A 1005 TRP cc_start: 0.8428 (t60) cc_final: 0.7951 (t-100) REVERT: A 1699 PHE cc_start: 0.6613 (OUTLIER) cc_final: 0.6303 (m-10) REVERT: A 1737 ASP cc_start: 0.8543 (t0) cc_final: 0.8177 (t0) REVERT: A 2362 MET cc_start: 0.9147 (mmt) cc_final: 0.8881 (mmm) REVERT: A 2557 GLU cc_start: 0.8697 (tt0) cc_final: 0.8098 (tm-30) REVERT: A 2561 LYS cc_start: 0.9064 (tppt) cc_final: 0.8234 (ttmm) REVERT: A 2751 THR cc_start: 0.8604 (p) cc_final: 0.8350 (t) REVERT: A 2783 GLU cc_start: 0.8822 (mp0) cc_final: 0.8364 (mp0) REVERT: A 2790 ILE cc_start: 0.8127 (tt) cc_final: 0.7894 (mt) outliers start: 20 outliers final: 15 residues processed: 179 average time/residue: 0.3105 time to fit residues: 93.3843 Evaluate side-chains 172 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1287 LYS Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1699 PHE Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain A residue 2429 TRP Chi-restraints excluded: chain A residue 2453 ILE Chi-restraints excluded: chain A residue 2555 PHE Chi-restraints excluded: chain A residue 2730 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 193 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 206 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 236 optimal weight: 0.0670 chunk 167 optimal weight: 0.8980 chunk 214 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2713 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.104317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.078219 restraints weight = 103609.469| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 4.97 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22397 Z= 0.120 Angle : 0.615 11.133 30475 Z= 0.301 Chirality : 0.041 0.279 3428 Planarity : 0.004 0.085 3926 Dihedral : 6.049 89.671 3571 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.92 % Favored : 91.35 % Rotamer: Outliers : 0.91 % Allowed : 11.05 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.17), residues: 2759 helix: 1.43 (0.16), residues: 1230 sheet: -0.56 (0.29), residues: 344 loop : -2.77 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 255 HIS 0.005 0.001 HIS A2086 PHE 0.016 0.001 PHE A2547 TYR 0.025 0.001 TYR A 764 ARG 0.005 0.000 ARG A 529 Details of bonding type rmsd link_BETA1-2 : bond 0.00626 ( 24) link_BETA1-2 : angle 2.89380 ( 72) hydrogen bonds : bond 0.03503 ( 995) hydrogen bonds : angle 4.01937 ( 3019) covalent geometry : bond 0.00265 (22373) covalent geometry : angle 0.59929 (30403) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7835 (tpp) cc_final: 0.7351 (tpt) REVERT: A 54 MET cc_start: 0.7893 (ppp) cc_final: 0.7334 (ppp) REVERT: A 320 TYR cc_start: 0.8126 (t80) cc_final: 0.7830 (t80) REVERT: A 932 TYR cc_start: 0.8557 (m-80) cc_final: 0.8017 (m-80) REVERT: A 1005 TRP cc_start: 0.8440 (t60) cc_final: 0.7972 (t-100) REVERT: A 1029 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7549 (tp30) REVERT: A 1699 PHE cc_start: 0.6956 (OUTLIER) cc_final: 0.6594 (m-10) REVERT: A 1737 ASP cc_start: 0.8502 (t0) cc_final: 0.8185 (t0) REVERT: A 2362 MET cc_start: 0.9149 (mmt) cc_final: 0.8888 (mmm) REVERT: A 2557 GLU cc_start: 0.8706 (tt0) cc_final: 0.8097 (tm-30) REVERT: A 2561 LYS cc_start: 0.9046 (tppt) cc_final: 0.8209 (ttmm) REVERT: A 2751 THR cc_start: 0.8603 (p) cc_final: 0.8355 (t) REVERT: A 2783 GLU cc_start: 0.8766 (mp0) cc_final: 0.8240 (mp0) REVERT: A 2790 ILE cc_start: 0.8179 (tt) cc_final: 0.7915 (mt) outliers start: 17 outliers final: 16 residues processed: 170 average time/residue: 0.3048 time to fit residues: 87.0619 Evaluate side-chains 172 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1287 LYS Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1699 PHE Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain A residue 2429 TRP Chi-restraints excluded: chain A residue 2453 ILE Chi-restraints excluded: chain A residue 2544 LEU Chi-restraints excluded: chain A residue 2555 PHE Chi-restraints excluded: chain A residue 2730 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 6 optimal weight: 0.9990 chunk 256 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 269 optimal weight: 3.9990 chunk 271 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2713 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.099630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.073066 restraints weight = 114342.792| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 5.14 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 22397 Z= 0.239 Angle : 0.721 11.988 30475 Z= 0.360 Chirality : 0.045 0.275 3428 Planarity : 0.005 0.092 3926 Dihedral : 6.430 90.757 3571 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.55 % Favored : 89.72 % Rotamer: Outliers : 1.00 % Allowed : 11.14 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.16), residues: 2759 helix: 1.15 (0.15), residues: 1235 sheet: -0.65 (0.30), residues: 320 loop : -2.74 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 821 HIS 0.008 0.001 HIS A2086 PHE 0.023 0.002 PHE A2547 TYR 0.024 0.002 TYR A 764 ARG 0.005 0.001 ARG A 332 Details of bonding type rmsd link_BETA1-2 : bond 0.00643 ( 24) link_BETA1-2 : angle 2.98332 ( 72) hydrogen bonds : bond 0.04495 ( 995) hydrogen bonds : angle 4.34575 ( 3019) covalent geometry : bond 0.00552 (22373) covalent geometry : angle 0.70665 (30403) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7791 (tpp) cc_final: 0.7428 (tpt) REVERT: A 240 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.7636 (t80) REVERT: A 320 TYR cc_start: 0.8286 (t80) cc_final: 0.7914 (t80) REVERT: A 509 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6765 (pm20) REVERT: A 1699 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.7034 (m-10) REVERT: A 1737 ASP cc_start: 0.8519 (t0) cc_final: 0.8220 (t0) REVERT: A 2557 GLU cc_start: 0.8691 (tt0) cc_final: 0.8109 (tm-30) REVERT: A 2561 LYS cc_start: 0.9075 (tppt) cc_final: 0.8253 (ttmm) REVERT: A 2790 ILE cc_start: 0.8330 (tt) cc_final: 0.8077 (mt) outliers start: 19 outliers final: 16 residues processed: 161 average time/residue: 0.3192 time to fit residues: 84.4494 Evaluate side-chains 161 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1287 LYS Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1699 PHE Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain A residue 2429 TRP Chi-restraints excluded: chain A residue 2453 ILE Chi-restraints excluded: chain A residue 2544 LEU Chi-restraints excluded: chain A residue 2555 PHE Chi-restraints excluded: chain A residue 2730 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 225 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 chunk 159 optimal weight: 0.7980 chunk 173 optimal weight: 0.0040 chunk 268 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 47 optimal weight: 0.1980 chunk 152 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1844 HIS ** A1934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2713 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.103071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.077478 restraints weight = 82797.035| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 4.46 r_work: 0.3064 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22397 Z= 0.125 Angle : 0.627 11.626 30475 Z= 0.309 Chirality : 0.042 0.262 3428 Planarity : 0.004 0.093 3926 Dihedral : 6.013 91.086 3571 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.81 % Favored : 91.54 % Rotamer: Outliers : 0.95 % Allowed : 11.18 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.17), residues: 2759 helix: 1.35 (0.16), residues: 1234 sheet: -0.62 (0.29), residues: 332 loop : -2.64 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 255 HIS 0.005 0.001 HIS A2086 PHE 0.018 0.001 PHE A2547 TYR 0.025 0.001 TYR A 764 ARG 0.005 0.000 ARG A 529 Details of bonding type rmsd link_BETA1-2 : bond 0.00607 ( 24) link_BETA1-2 : angle 2.78928 ( 72) hydrogen bonds : bond 0.03705 ( 995) hydrogen bonds : angle 4.11740 ( 3019) covalent geometry : bond 0.00275 (22373) covalent geometry : angle 0.61328 (30403) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10118.65 seconds wall clock time: 176 minutes 6.30 seconds (10566.30 seconds total)