Starting phenix.real_space_refine on Sun Oct 25 05:43:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jac_6343/10_2026/3jac_6343.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jac_6343/10_2026/3jac_6343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/3jac_6343/10_2026/3jac_6343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jac_6343/10_2026/3jac_6343.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jac_6343/10_2026/3jac_6343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jac_6343/10_2026/3jac_6343.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 18 5.16 5 C 9624 2.51 5 N 2985 2.21 5 O 3114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15741 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 5247 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 653} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 884} Chain breaks: 11 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1898 Unresolved non-hydrogen angles: 2596 Unresolved non-hydrogen dihedrals: 1385 Unresolved non-hydrogen chiralities: 122 Planarities with less than four sites: {'UNK:plan-1': 346, 'PHE:plan': 31, 'HIS:plan': 6, 'ASP:plan': 13, 'TYR:plan': 15, 'ARG:plan': 16, 'TRP:plan': 8, 'GLN:plan1': 11, 'GLU:plan': 15, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 980 Chain: "B" Number of atoms: 5247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 5247 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 653} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 885} Chain breaks: 11 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1898 Unresolved non-hydrogen angles: 2596 Unresolved non-hydrogen dihedrals: 1385 Unresolved non-hydrogen chiralities: 122 Planarities with less than four sites: {'UNK:plan-1': 346, 'PHE:plan': 31, 'HIS:plan': 6, 'ASP:plan': 13, 'TYR:plan': 15, 'ARG:plan': 16, 'TRP:plan': 8, 'GLN:plan1': 11, 'GLU:plan': 15, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 980 Chain: "C" Number of atoms: 5247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 5247 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 653} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 885} Chain breaks: 11 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1898 Unresolved non-hydrogen angles: 2596 Unresolved non-hydrogen dihedrals: 1385 Unresolved non-hydrogen chiralities: 122 Planarities with less than four sites: {'UNK:plan-1': 346, 'PHE:plan': 31, 'HIS:plan': 6, 'ASP:plan': 13, 'TYR:plan': 15, 'ARG:plan': 16, 'TRP:plan': 8, 'GLN:plan1': 11, 'GLU:plan': 15, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 980 Time building chain proxies: 3.72, per 1000 atoms: 0.24 Number of scatterers: 15741 At special positions: 0 Unit cell: (192.72, 171.6, 158.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 3114 8.00 N 2985 7.00 C 9624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A2437 " - pdb=" SG CYS A2441 " distance=2.05 Simple disulfide: pdb=" SG CYS B2437 " - pdb=" SG CYS B2441 " distance=2.05 Simple disulfide: pdb=" SG CYS C2437 " - pdb=" SG CYS C2441 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 516.5 milliseconds 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5334 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 9 sheets defined 123.2% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 201 through 240 removed outlier: 3.924A pdb=" N UNK A 205 " --> pdb=" O UNK A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 296 removed outlier: 4.364A pdb=" N UNK A 250 " --> pdb=" O UNK A 246 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N UNK A 251 " --> pdb=" O UNK A 247 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N UNK A 255 " --> pdb=" O UNK A 251 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N UNK A 256 " --> pdb=" O UNK A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 471 Processing helix chain 'A' and resid 563 through 576 removed outlier: 4.789A pdb=" N UNK A 569 " --> pdb=" O UNK A 565 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N UNK A 571 " --> pdb=" O UNK A 567 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N UNK A 572 " --> pdb=" O UNK A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 896 removed outlier: 4.313A pdb=" N UNK A 886 " --> pdb=" O UNK A 882 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N UNK A 887 " --> pdb=" O UNK A 883 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N UNK A 890 " --> pdb=" O UNK A 886 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N UNK A 894 " --> pdb=" O UNK A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1019 Processing helix chain 'A' and resid 1121 through 1136 removed outlier: 3.694A pdb=" N UNK A1126 " --> pdb=" O UNK A1122 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N UNK A1133 " --> pdb=" O UNK A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1145 removed outlier: 3.665A pdb=" N UNK A1142 " --> pdb=" O UNK A1138 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N UNK A1143 " --> pdb=" O UNK A1139 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N UNK A1144 " --> pdb=" O UNK A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1263 Processing helix chain 'A' and resid 1365 through 1386 removed outlier: 3.923A pdb=" N UNK A1373 " --> pdb=" O UNK A1369 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N UNK A1374 " --> pdb=" O UNK A1370 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N UNK A1378 " --> pdb=" O UNK A1374 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N UNK A1379 " --> pdb=" O UNK A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1505 removed outlier: 3.693A pdb=" N UNK A1493 " --> pdb=" O UNK A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1509 through 1514 removed outlier: 3.895A pdb=" N UNK A1513 " --> pdb=" O UNK A1509 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N UNK A1514 " --> pdb=" O UNK A1510 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1509 through 1514' Processing helix chain 'A' and resid 1740 through 1759 Processing helix chain 'A' and resid 1759 through 1780 removed outlier: 3.505A pdb=" N UNK A1778 " --> pdb=" O UNK A1774 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N UNK A1779 " --> pdb=" O UNK A1775 " (cutoff:3.500A) Processing helix chain 'A' and resid 1782 through 1804 removed outlier: 3.658A pdb=" N UNK A1786 " --> pdb=" O UNK A1782 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N UNK A1788 " --> pdb=" O UNK A1784 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N UNK A1789 " --> pdb=" O UNK A1785 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N UNK A1790 " --> pdb=" O UNK A1786 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N UNK A1799 " --> pdb=" O UNK A1795 " (cutoff:3.500A) Processing helix chain 'A' and resid 1962 through 1969 removed outlier: 3.521A pdb=" N LYS A1969 " --> pdb=" O ILE A1965 " (cutoff:3.500A) Processing helix chain 'A' and resid 1969 through 1974 removed outlier: 3.846A pdb=" N ALA A1973 " --> pdb=" O LYS A1969 " (cutoff:3.500A) Processing helix chain 'A' and resid 1975 through 1989 Processing helix chain 'A' and resid 1991 through 2021 removed outlier: 3.525A pdb=" N PHE A1995 " --> pdb=" O ILE A1991 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TRP A1996 " --> pdb=" O ILE A1992 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA A1997 " --> pdb=" O PHE A1993 " (cutoff:3.500A) Proline residue: A2017 - end of helix removed outlier: 4.286A pdb=" N LEU A2021 " --> pdb=" O PRO A2017 " (cutoff:3.500A) Processing helix chain 'A' and resid 2025 through 2047 Processing helix chain 'A' and resid 2055 through 2078 removed outlier: 4.177A pdb=" N PHE A2062 " --> pdb=" O HIS A2058 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A2063 " --> pdb=" O ILE A2059 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A2065 " --> pdb=" O MET A2061 " (cutoff:3.500A) Proline residue: A2066 - end of helix removed outlier: 5.835A pdb=" N THR A2069 " --> pdb=" O LEU A2065 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A2078 " --> pdb=" O SER A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2082 through 2105 removed outlier: 3.958A pdb=" N LYS A2086 " --> pdb=" O TRP A2082 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR A2089 " --> pdb=" O VAL A2085 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A2090 " --> pdb=" O LYS A2086 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A2091 " --> pdb=" O CYS A2087 " (cutoff:3.500A) Proline residue: A2102 - end of helix Processing helix chain 'A' and resid 2106 through 2111 Processing helix chain 'A' and resid 2111 through 2123 removed outlier: 3.579A pdb=" N ASN A2115 " --> pdb=" O THR A2111 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS A2116 " --> pdb=" O LYS A2112 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A2119 " --> pdb=" O ASN A2115 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2149 Proline residue: A2129 - end of helix removed outlier: 3.934A pdb=" N LEU A2134 " --> pdb=" O PHE A2130 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ARG A2135 " --> pdb=" O LEU A2131 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ALA A2136 " --> pdb=" O VAL A2132 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL A2137 " --> pdb=" O GLU A2133 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET A2138 " --> pdb=" O LEU A2134 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP A2144 " --> pdb=" O TRP A2140 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A2149 " --> pdb=" O THR A2145 " (cutoff:3.500A) Processing helix chain 'A' and resid 2149 through 2175 removed outlier: 3.991A pdb=" N VAL A2155 " --> pdb=" O ASN A2151 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE A2158 " --> pdb=" O CYS A2154 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A2159 " --> pdb=" O VAL A2155 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A2175 " --> pdb=" O THR A2171 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2180 Processing helix chain 'A' and resid 2186 through 2212 removed outlier: 3.505A pdb=" N GLY A2190 " --> pdb=" O ILE A2186 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A2193 " --> pdb=" O TYR A2189 " (cutoff:3.500A) Proline residue: A2206 - end of helix removed outlier: 4.098A pdb=" N LEU A2212 " --> pdb=" O LEU A2208 " (cutoff:3.500A) Processing helix chain 'A' and resid 2252 through 2264 Processing helix chain 'A' and resid 2266 through 2274 Processing helix chain 'A' and resid 2275 through 2276 No H-bonds generated for 'chain 'A' and resid 2275 through 2276' Processing helix chain 'A' and resid 2277 through 2279 No H-bonds generated for 'chain 'A' and resid 2277 through 2279' Processing helix chain 'A' and resid 2297 through 2311 Processing helix chain 'A' and resid 2326 through 2330 Processing helix chain 'A' and resid 2348 through 2358 removed outlier: 3.898A pdb=" N LEU A2358 " --> pdb=" O LEU A2354 " (cutoff:3.500A) Processing helix chain 'A' and resid 2393 through 2398 Processing helix chain 'A' and resid 2461 through 2484 removed outlier: 3.705A pdb=" N GLY A2483 " --> pdb=" O LYS A2479 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE A2484 " --> pdb=" O PHE A2480 " (cutoff:3.500A) Processing helix chain 'A' and resid 2486 through 2497 removed outlier: 3.590A pdb=" N ILE A2492 " --> pdb=" O ILE A2488 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A2496 " --> pdb=" O ILE A2492 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A2497 " --> pdb=" O MET A2493 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2511 removed outlier: 4.403A pdb=" N ILE A2510 " --> pdb=" O LEU A2506 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE A2511 " --> pdb=" O CYS A2507 " (cutoff:3.500A) Processing helix chain 'A' and resid 2511 through 2520 removed outlier: 3.967A pdb=" N GLU A2515 " --> pdb=" O PHE A2511 " (cutoff:3.500A) Processing helix chain 'A' and resid 2521 through 2525 Processing helix chain 'A' and resid 2527 through 2544 removed outlier: 3.749A pdb=" N TYR A2533 " --> pdb=" O LEU A2529 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A2534 " --> pdb=" O ILE A2530 " (cutoff:3.500A) Proline residue: A2536 - end of helix Processing helix chain 'B' and resid 202 through 242 removed outlier: 3.915A pdb=" N UNK B 237 " --> pdb=" O UNK B 233 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N UNK B 238 " --> pdb=" O UNK B 234 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N UNK B 239 " --> pdb=" O UNK B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 250 through 296 removed outlier: 4.486A pdb=" N UNK B 256 " --> pdb=" O UNK B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 471 Processing helix chain 'B' and resid 563 through 576 removed outlier: 4.789A pdb=" N UNK B 569 " --> pdb=" O UNK B 565 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N UNK B 571 " --> pdb=" O UNK B 567 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N UNK B 572 " --> pdb=" O UNK B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 896 removed outlier: 3.601A pdb=" N UNK B 882 " --> pdb=" O UNK B 878 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N UNK B 884 " --> pdb=" O UNK B 880 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N UNK B 885 " --> pdb=" O UNK B 881 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N UNK B 886 " --> pdb=" O UNK B 882 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N UNK B 887 " --> pdb=" O UNK B 883 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N UNK B 890 " --> pdb=" O UNK B 886 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N UNK B 893 " --> pdb=" O UNK B 889 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N UNK B 894 " --> pdb=" O UNK B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1019 Processing helix chain 'B' and resid 1121 through 1130 removed outlier: 3.693A pdb=" N UNK B1126 " --> pdb=" O UNK B1122 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1147 removed outlier: 3.971A pdb=" N UNK B1134 " --> pdb=" O UNK B1130 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N UNK B1139 " --> pdb=" O UNK B1135 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N UNK B1140 " --> pdb=" O UNK B1136 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N UNK B1142 " --> pdb=" O UNK B1138 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N UNK B1143 " --> pdb=" O UNK B1139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N UNK B1144 " --> pdb=" O UNK B1140 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N UNK B1147 " --> pdb=" O UNK B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1249 through 1263 Processing helix chain 'B' and resid 1365 through 1386 removed outlier: 3.923A pdb=" N UNK B1373 " --> pdb=" O UNK B1369 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N UNK B1374 " --> pdb=" O UNK B1370 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N UNK B1378 " --> pdb=" O UNK B1374 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N UNK B1379 " --> pdb=" O UNK B1375 " (cutoff:3.500A) Processing helix chain 'B' and resid 1488 through 1505 removed outlier: 3.694A pdb=" N UNK B1493 " --> pdb=" O UNK B1489 " (cutoff:3.500A) Processing helix chain 'B' and resid 1508 through 1512 Processing helix chain 'B' and resid 1740 through 1759 Processing helix chain 'B' and resid 1759 through 1780 removed outlier: 3.505A pdb=" N UNK B1778 " --> pdb=" O UNK B1774 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N UNK B1779 " --> pdb=" O UNK B1775 " (cutoff:3.500A) Processing helix chain 'B' and resid 1785 through 1804 removed outlier: 3.951A pdb=" N UNK B1792 " --> pdb=" O UNK B1788 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N UNK B1796 " --> pdb=" O UNK B1792 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N UNK B1800 " --> pdb=" O UNK B1796 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N UNK B1801 " --> pdb=" O UNK B1797 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N UNK B1802 " --> pdb=" O UNK B1798 " (cutoff:3.500A) Processing helix chain 'B' and resid 1962 through 1969 removed outlier: 3.521A pdb=" N LYS B1969 " --> pdb=" O ILE B1965 " (cutoff:3.500A) Processing helix chain 'B' and resid 1969 through 1974 removed outlier: 3.846A pdb=" N ALA B1973 " --> pdb=" O LYS B1969 " (cutoff:3.500A) Processing helix chain 'B' and resid 1975 through 1989 removed outlier: 3.557A pdb=" N ILE B1989 " --> pdb=" O ILE B1985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1994 through 2021 Proline residue: B2017 - end of helix removed outlier: 4.286A pdb=" N LEU B2021 " --> pdb=" O PRO B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2025 through 2050 removed outlier: 3.757A pdb=" N VAL B2043 " --> pdb=" O LEU B2039 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY B2045 " --> pdb=" O LYS B2041 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA B2048 " --> pdb=" O LEU B2044 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2078 removed outlier: 3.642A pdb=" N PHE B2063 " --> pdb=" O ILE B2059 " (cutoff:3.500A) Proline residue: B2066 - end of helix removed outlier: 5.836A pdb=" N THR B2069 " --> pdb=" O LEU B2065 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL B2078 " --> pdb=" O SER B2074 " (cutoff:3.500A) Processing helix chain 'B' and resid 2082 through 2105 removed outlier: 3.959A pdb=" N LYS B2086 " --> pdb=" O TRP B2082 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR B2089 " --> pdb=" O VAL B2085 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE B2090 " --> pdb=" O LYS B2086 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B2091 " --> pdb=" O CYS B2087 " (cutoff:3.500A) Proline residue: B2102 - end of helix Processing helix chain 'B' and resid 2106 through 2111 Processing helix chain 'B' and resid 2111 through 2123 removed outlier: 3.580A pdb=" N ASN B2115 " --> pdb=" O THR B2111 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS B2116 " --> pdb=" O LYS B2112 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B2119 " --> pdb=" O ASN B2115 " (cutoff:3.500A) Processing helix chain 'B' and resid 2123 through 2149 Proline residue: B2129 - end of helix removed outlier: 3.934A pdb=" N LEU B2134 " --> pdb=" O PHE B2130 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ARG B2135 " --> pdb=" O LEU B2131 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ALA B2136 " --> pdb=" O VAL B2132 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL B2137 " --> pdb=" O GLU B2133 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET B2138 " --> pdb=" O LEU B2134 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP B2144 " --> pdb=" O TRP B2140 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B2149 " --> pdb=" O THR B2145 " (cutoff:3.500A) Processing helix chain 'B' and resid 2149 through 2175 removed outlier: 3.991A pdb=" N VAL B2155 " --> pdb=" O ASN B2151 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE B2158 " --> pdb=" O CYS B2154 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR B2159 " --> pdb=" O VAL B2155 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B2175 " --> pdb=" O THR B2171 " (cutoff:3.500A) Processing helix chain 'B' and resid 2175 through 2180 Processing helix chain 'B' and resid 2186 through 2205 removed outlier: 3.505A pdb=" N GLY B2190 " --> pdb=" O ILE B2186 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B2193 " --> pdb=" O TYR B2189 " (cutoff:3.500A) Processing helix chain 'B' and resid 2207 through 2212 removed outlier: 3.556A pdb=" N LEU B2212 " --> pdb=" O PHE B2209 " (cutoff:3.500A) Processing helix chain 'B' and resid 2252 through 2264 Processing helix chain 'B' and resid 2266 through 2274 Processing helix chain 'B' and resid 2275 through 2276 No H-bonds generated for 'chain 'B' and resid 2275 through 2276' Processing helix chain 'B' and resid 2277 through 2279 No H-bonds generated for 'chain 'B' and resid 2277 through 2279' Processing helix chain 'B' and resid 2297 through 2311 removed outlier: 3.513A pdb=" N MET B2304 " --> pdb=" O SER B2300 " (cutoff:3.500A) Processing helix chain 'B' and resid 2326 through 2330 Processing helix chain 'B' and resid 2348 through 2358 removed outlier: 3.898A pdb=" N LEU B2358 " --> pdb=" O LEU B2354 " (cutoff:3.500A) Processing helix chain 'B' and resid 2393 through 2398 Processing helix chain 'B' and resid 2461 through 2484 removed outlier: 3.706A pdb=" N GLY B2483 " --> pdb=" O LYS B2479 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE B2484 " --> pdb=" O PHE B2480 " (cutoff:3.500A) Processing helix chain 'B' and resid 2486 through 2497 removed outlier: 3.590A pdb=" N ILE B2492 " --> pdb=" O ILE B2488 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU B2496 " --> pdb=" O ILE B2492 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B2497 " --> pdb=" O MET B2493 " (cutoff:3.500A) Processing helix chain 'B' and resid 2500 through 2511 removed outlier: 4.402A pdb=" N ILE B2510 " --> pdb=" O LEU B2506 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE B2511 " --> pdb=" O CYS B2507 " (cutoff:3.500A) Processing helix chain 'B' and resid 2511 through 2520 removed outlier: 3.967A pdb=" N GLU B2515 " --> pdb=" O PHE B2511 " (cutoff:3.500A) Processing helix chain 'B' and resid 2521 through 2525 Processing helix chain 'B' and resid 2527 through 2544 removed outlier: 3.749A pdb=" N TYR B2533 " --> pdb=" O LEU B2529 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B2534 " --> pdb=" O ILE B2530 " (cutoff:3.500A) Proline residue: B2536 - end of helix Processing helix chain 'C' and resid 202 through 244 removed outlier: 4.035A pdb=" N UNK C 243 " --> pdb=" O UNK C 239 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N UNK C 244 " --> pdb=" O UNK C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'C' and resid 248 through 253 Processing helix chain 'C' and resid 253 through 296 Processing helix chain 'C' and resid 448 through 471 Processing helix chain 'C' and resid 563 through 576 removed outlier: 4.790A pdb=" N UNK C 569 " --> pdb=" O UNK C 565 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N UNK C 571 " --> pdb=" O UNK C 567 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N UNK C 572 " --> pdb=" O UNK C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 896 removed outlier: 3.622A pdb=" N UNK C 890 " --> pdb=" O UNK C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1019 Processing helix chain 'C' and resid 1121 through 1141 removed outlier: 3.694A pdb=" N UNK C1126 " --> pdb=" O UNK C1122 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N UNK C1137 " --> pdb=" O UNK C1133 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N UNK C1138 " --> pdb=" O UNK C1134 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N UNK C1139 " --> pdb=" O UNK C1135 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N UNK C1140 " --> pdb=" O UNK C1136 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 4.131A pdb=" N UNK C1146 " --> pdb=" O UNK C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1249 through 1263 Processing helix chain 'C' and resid 1365 through 1386 removed outlier: 3.922A pdb=" N UNK C1373 " --> pdb=" O UNK C1369 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N UNK C1374 " --> pdb=" O UNK C1370 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N UNK C1378 " --> pdb=" O UNK C1374 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N UNK C1379 " --> pdb=" O UNK C1375 " (cutoff:3.500A) Processing helix chain 'C' and resid 1488 through 1505 removed outlier: 3.693A pdb=" N UNK C1493 " --> pdb=" O UNK C1489 " (cutoff:3.500A) Processing helix chain 'C' and resid 1508 through 1512 Processing helix chain 'C' and resid 1740 through 1759 Processing helix chain 'C' and resid 1759 through 1780 removed outlier: 3.504A pdb=" N UNK C1778 " --> pdb=" O UNK C1774 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N UNK C1779 " --> pdb=" O UNK C1775 " (cutoff:3.500A) Processing helix chain 'C' and resid 1782 through 1804 removed outlier: 3.659A pdb=" N UNK C1786 " --> pdb=" O UNK C1782 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N UNK C1788 " --> pdb=" O UNK C1784 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N UNK C1789 " --> pdb=" O UNK C1785 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N UNK C1801 " --> pdb=" O UNK C1797 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N UNK C1802 " --> pdb=" O UNK C1798 " (cutoff:3.500A) Processing helix chain 'C' and resid 1962 through 1969 removed outlier: 3.521A pdb=" N LYS C1969 " --> pdb=" O ILE C1965 " (cutoff:3.500A) Processing helix chain 'C' and resid 1969 through 1974 removed outlier: 3.846A pdb=" N ALA C1973 " --> pdb=" O LYS C1969 " (cutoff:3.500A) Processing helix chain 'C' and resid 1975 through 1991 Processing helix chain 'C' and resid 1995 through 2021 Proline residue: C2017 - end of helix removed outlier: 4.286A pdb=" N LEU C2021 " --> pdb=" O PRO C2017 " (cutoff:3.500A) Processing helix chain 'C' and resid 2025 through 2048 removed outlier: 3.515A pdb=" N VAL C2043 " --> pdb=" O LEU C2039 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C2045 " --> pdb=" O LYS C2041 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS C2046 " --> pdb=" O THR C2042 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA C2048 " --> pdb=" O LEU C2044 " (cutoff:3.500A) Processing helix chain 'C' and resid 2058 through 2078 Proline residue: C2066 - end of helix removed outlier: 5.836A pdb=" N THR C2069 " --> pdb=" O LEU C2065 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL C2078 " --> pdb=" O SER C2074 " (cutoff:3.500A) Processing helix chain 'C' and resid 2082 through 2105 removed outlier: 3.958A pdb=" N LYS C2086 " --> pdb=" O TRP C2082 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR C2089 " --> pdb=" O VAL C2085 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE C2090 " --> pdb=" O LYS C2086 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C2091 " --> pdb=" O CYS C2087 " (cutoff:3.500A) Proline residue: C2102 - end of helix Processing helix chain 'C' and resid 2106 through 2111 Processing helix chain 'C' and resid 2111 through 2123 removed outlier: 3.579A pdb=" N ASN C2115 " --> pdb=" O THR C2111 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS C2116 " --> pdb=" O LYS C2112 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C2119 " --> pdb=" O ASN C2115 " (cutoff:3.500A) Processing helix chain 'C' and resid 2123 through 2149 Proline residue: C2129 - end of helix removed outlier: 3.934A pdb=" N LEU C2134 " --> pdb=" O PHE C2130 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG C2135 " --> pdb=" O LEU C2131 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA C2136 " --> pdb=" O VAL C2132 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL C2137 " --> pdb=" O GLU C2133 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET C2138 " --> pdb=" O LEU C2134 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP C2144 " --> pdb=" O TRP C2140 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C2149 " --> pdb=" O THR C2145 " (cutoff:3.500A) Processing helix chain 'C' and resid 2149 through 2175 removed outlier: 3.990A pdb=" N VAL C2155 " --> pdb=" O ASN C2151 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE C2158 " --> pdb=" O CYS C2154 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C2159 " --> pdb=" O VAL C2155 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C2175 " --> pdb=" O THR C2171 " (cutoff:3.500A) Processing helix chain 'C' and resid 2175 through 2180 Processing helix chain 'C' and resid 2186 through 2212 removed outlier: 3.505A pdb=" N GLY C2190 " --> pdb=" O ILE C2186 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY C2193 " --> pdb=" O TYR C2189 " (cutoff:3.500A) Proline residue: C2206 - end of helix Processing helix chain 'C' and resid 2252 through 2264 Processing helix chain 'C' and resid 2266 through 2274 Processing helix chain 'C' and resid 2275 through 2276 No H-bonds generated for 'chain 'C' and resid 2275 through 2276' Processing helix chain 'C' and resid 2277 through 2279 No H-bonds generated for 'chain 'C' and resid 2277 through 2279' Processing helix chain 'C' and resid 2297 through 2311 Processing helix chain 'C' and resid 2326 through 2330 Processing helix chain 'C' and resid 2348 through 2358 removed outlier: 3.899A pdb=" N LEU C2358 " --> pdb=" O LEU C2354 " (cutoff:3.500A) Processing helix chain 'C' and resid 2393 through 2398 Processing helix chain 'C' and resid 2461 through 2484 removed outlier: 3.705A pdb=" N GLY C2483 " --> pdb=" O LYS C2479 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE C2484 " --> pdb=" O PHE C2480 " (cutoff:3.500A) Processing helix chain 'C' and resid 2486 through 2497 removed outlier: 3.590A pdb=" N ILE C2492 " --> pdb=" O ILE C2488 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C2496 " --> pdb=" O ILE C2492 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU C2497 " --> pdb=" O MET C2493 " (cutoff:3.500A) Processing helix chain 'C' and resid 2500 through 2511 removed outlier: 4.402A pdb=" N ILE C2510 " --> pdb=" O LEU C2506 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE C2511 " --> pdb=" O CYS C2507 " (cutoff:3.500A) Processing helix chain 'C' and resid 2511 through 2520 removed outlier: 3.967A pdb=" N GLU C2515 " --> pdb=" O PHE C2511 " (cutoff:3.500A) Processing helix chain 'C' and resid 2521 through 2525 Processing helix chain 'C' and resid 2527 through 2544 removed outlier: 3.750A pdb=" N TYR C2533 " --> pdb=" O LEU C2529 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C2534 " --> pdb=" O ILE C2530 " (cutoff:3.500A) Proline residue: C2536 - end of helix Processing sheet with id=A, first strand: chain 'A' and resid 2239 through 2243 removed outlier: 3.547A pdb=" N ASP A2225 " --> pdb=" O GLN A2324 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 2248 through 2250 Processing sheet with id=C, first strand: chain 'A' and resid 2366 through 2372 removed outlier: 3.751A pdb=" N HIS A2370 " --> pdb=" O LEU A2399 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU A2399 " --> pdb=" O HIS A2370 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 2239 through 2243 removed outlier: 3.547A pdb=" N ASP B2225 " --> pdb=" O GLN B2324 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'B' and resid 2248 through 2250 Processing sheet with id=F, first strand: chain 'B' and resid 2366 through 2372 removed outlier: 3.751A pdb=" N HIS B2370 " --> pdb=" O LEU B2399 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU B2399 " --> pdb=" O HIS B2370 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'C' and resid 2239 through 2243 removed outlier: 3.547A pdb=" N ASP C2225 " --> pdb=" O GLN C2324 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'C' and resid 2248 through 2250 Processing sheet with id=I, first strand: chain 'C' and resid 2366 through 2372 removed outlier: 3.751A pdb=" N HIS C2370 " --> pdb=" O LEU C2399 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU C2399 " --> pdb=" O HIS C2370 " (cutoff:3.500A) 1481 hydrogen bonds defined for protein. 4332 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: 3.07 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5873 1.34 - 1.46: 2949 1.46 - 1.58: 6991 1.58 - 1.70: 3 1.70 - 1.82: 30 Bond restraints: 15846 Sorted by residual: bond pdb=" C SER C2454 " pdb=" N PRO C2455 " ideal model delta sigma weight residual 1.329 1.408 -0.078 1.18e-02 7.18e+03 4.42e+01 bond pdb=" C SER A2297 " pdb=" N PRO A2298 " ideal model delta sigma weight residual 1.329 1.406 -0.077 1.18e-02 7.18e+03 4.26e+01 bond pdb=" C GLN B2222 " pdb=" N PRO B2223 " ideal model delta sigma weight residual 1.331 1.408 -0.076 1.20e-02 6.94e+03 4.06e+01 bond pdb=" C GLN C2222 " pdb=" N PRO C2223 " ideal model delta sigma weight residual 1.331 1.407 -0.076 1.20e-02 6.94e+03 4.04e+01 bond pdb=" C GLN A2222 " pdb=" N PRO A2223 " ideal model delta sigma weight residual 1.331 1.407 -0.076 1.20e-02 6.94e+03 4.03e+01 ... (remaining 15841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 21366 3.37 - 6.74: 246 6.74 - 10.10: 46 10.10 - 13.47: 234 13.47 - 16.84: 8 Bond angle restraints: 21900 Sorted by residual: angle pdb=" O TYR C2038 " pdb=" C TYR C2038 " pdb=" N LEU C2039 " ideal model delta sigma weight residual 122.07 109.71 12.36 1.03e+00 9.43e-01 1.44e+02 angle pdb=" O TYR A2038 " pdb=" C TYR A2038 " pdb=" N LEU A2039 " ideal model delta sigma weight residual 122.07 109.73 12.34 1.03e+00 9.43e-01 1.43e+02 angle pdb=" O LYS A2041 " pdb=" C LYS A2041 " pdb=" N THR A2042 " ideal model delta sigma weight residual 122.07 109.73 12.34 1.03e+00 9.43e-01 1.43e+02 angle pdb=" O THR A2042 " pdb=" C THR A2042 " pdb=" N VAL A2043 " ideal model delta sigma weight residual 122.07 109.75 12.32 1.03e+00 9.43e-01 1.43e+02 angle pdb=" O LEU A2039 " pdb=" C LEU A2039 " pdb=" N ARG A2040 " ideal model delta sigma weight residual 122.07 109.75 12.32 1.03e+00 9.43e-01 1.43e+02 ... (remaining 21895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 9218 17.68 - 35.36: 180 35.36 - 53.03: 66 53.03 - 70.71: 8 70.71 - 88.39: 14 Dihedral angle restraints: 9486 sinusoidal: 1410 harmonic: 8076 Sorted by residual: dihedral pdb=" C VAL B2410 " pdb=" N VAL B2410 " pdb=" CA VAL B2410 " pdb=" CB VAL B2410 " ideal model delta harmonic sigma weight residual -122.00 -155.86 33.86 0 2.50e+00 1.60e-01 1.83e+02 dihedral pdb=" N VAL B2410 " pdb=" C VAL B2410 " pdb=" CA VAL B2410 " pdb=" CB VAL B2410 " ideal model delta harmonic sigma weight residual 123.40 151.27 -27.87 0 2.50e+00 1.60e-01 1.24e+02 dihedral pdb=" N VAL A2410 " pdb=" C VAL A2410 " pdb=" CA VAL A2410 " pdb=" CB VAL A2410 " ideal model delta harmonic sigma weight residual 123.40 148.32 -24.92 0 2.50e+00 1.60e-01 9.93e+01 ... (remaining 9483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.217: 2820 0.217 - 0.434: 28 0.434 - 0.651: 0 0.651 - 0.869: 0 0.869 - 1.086: 2 Chirality restraints: 2850 Sorted by residual: chirality pdb=" CA VAL B2410 " pdb=" N VAL B2410 " pdb=" C VAL B2410 " pdb=" CB VAL B2410 " both_signs ideal model delta sigma weight residual False 2.44 1.36 1.09 2.00e-01 2.50e+01 2.95e+01 chirality pdb=" CA VAL A2410 " pdb=" N VAL A2410 " pdb=" C VAL A2410 " pdb=" CB VAL A2410 " both_signs ideal model delta sigma weight residual False 2.44 1.44 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CA PRO C2456 " pdb=" N PRO C2456 " pdb=" C PRO C2456 " pdb=" CB PRO C2456 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 2847 not shown) Planarity restraints: 3051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA UNK C1127 " -0.068 2.00e-02 2.50e+03 1.26e-01 1.58e+02 pdb=" C UNK C1127 " 0.217 2.00e-02 2.50e+03 pdb=" O UNK C1127 " -0.080 2.00e-02 2.50e+03 pdb=" N UNK C1128 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK B1127 " 0.067 2.00e-02 2.50e+03 1.26e-01 1.58e+02 pdb=" C UNK B1127 " -0.217 2.00e-02 2.50e+03 pdb=" O UNK B1127 " 0.080 2.00e-02 2.50e+03 pdb=" N UNK B1128 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK B1498 " 0.068 2.00e-02 2.50e+03 1.26e-01 1.58e+02 pdb=" C UNK B1498 " -0.217 2.00e-02 2.50e+03 pdb=" O UNK B1498 " 0.080 2.00e-02 2.50e+03 pdb=" N UNK B1499 " 0.070 2.00e-02 2.50e+03 ... (remaining 3048 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.80: 38 1.80 - 2.57: 868 2.57 - 3.35: 24179 3.35 - 4.12: 36895 4.12 - 4.90: 61865 Nonbonded interactions: 123845 Sorted by model distance: nonbonded pdb=" CB UNK A 208 " pdb=" CB UNK A 281 " model vdw 1.020 3.840 nonbonded pdb=" NE2 GLN C2409 " pdb=" CG2 VAL C2410 " model vdw 1.045 3.540 nonbonded pdb=" CB LEU A2512 " pdb=" C SER B2491 " model vdw 1.083 3.670 nonbonded pdb=" O VAL B2217 " pdb=" CB SER B2454 " model vdw 1.124 3.440 nonbonded pdb=" CB UNK B 219 " pdb=" CB UNK B 270 " model vdw 1.150 3.840 ... (remaining 123840 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.330 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4036 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 15849 Z= 0.494 Angle : 1.810 16.839 21906 Z= 1.208 Chirality : 0.071 1.086 2850 Planarity : 0.034 0.126 3051 Dihedral : 10.639 88.391 4143 Min Nonbonded Distance : 1.020 Molprobity Statistics. All-atom Clashscore : 57.64 Ramachandran Plot: Outliers : 4.75 % Allowed : 4.99 % Favored : 90.26 % Rotamer: Outliers : 4.17 % Allowed : 3.83 % Favored : 92.00 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.21), residues: 1704 helix: 2.84 (0.17), residues: 828 sheet: -0.18 (0.30), residues: 237 loop : -1.39 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2301 TYR 0.023 0.004 TYR C2276 PHE 0.019 0.002 PHE A2372 TRP 0.012 0.002 TRP C2429 HIS 0.004 0.001 HIS A2370 Details of bonding type rmsd/Z covalent geometry : bond 0.00744 / 0.49 (15846) covalent geometry : angle 1.80908 / 1.21 (21900) SS BOND : bond 0.01810 / 0.91 ( 3) SS BOND : angle 2.97756 / 1.45 ( 6) hydrogen bonds : bond 0.30113 / 16.48 ( 1481) hydrogen bonds : angle 8.78772 / 5.63 ( 4332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2241 MET cc_start: 0.7912 (tpp) cc_final: 0.7505 (tpt) REVERT: A 2295 ARG cc_start: 0.3620 (OUTLIER) cc_final: 0.2264 (tpt90) outliers start: 7 outliers final: 3 residues processed: 57 average time/residue: 0.0683 time to fit residues: 5.2322 Evaluate side-chains 31 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 GLN A2310 ASN A2356 GLN ** A2391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2409 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.046902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.038441 restraints weight = 99242.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.038662 restraints weight = 91825.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.038820 restraints weight = 84095.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.038820 restraints weight = 79302.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.038820 restraints weight = 79301.850| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5765 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 15849 Z= 0.376 Angle : 1.143 15.237 21906 Z= 0.579 Chirality : 0.047 0.338 2850 Planarity : 0.008 0.085 3051 Dihedral : 7.108 108.353 2775 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 1.58 % Allowed : 5.28 % Favored : 93.13 % Rotamer: Outliers : 0.50 % Allowed : 3.50 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.20), residues: 1704 helix: 0.63 (0.16), residues: 906 sheet: -0.24 (0.32), residues: 237 loop : -1.64 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG B2318 TYR 0.017 0.002 TYR C2375 PHE 0.028 0.003 PHE C2251 TRP 0.029 0.004 TRP C2430 HIS 0.004 0.002 HIS B2370 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.38 (15846) covalent geometry : angle 1.14321 / 0.58 (21900) SS BOND : bond 0.00506 / 0.25 ( 3) SS BOND : angle 1.90844 / 0.95 ( 6) hydrogen bonds : bond 0.07432 / 4.07 ( 1481) hydrogen bonds : angle 7.07244 / 4.70 ( 4332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2317 LEU cc_start: 0.9297 (tp) cc_final: 0.8808 (pp) outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 0.0456 time to fit residues: 2.1385 Evaluate side-chains 21 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 30.0000 overall best weight: 30.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C2221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2262 GLN ** C2337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2340 HIS ** C2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.042801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.035160 restraints weight = 109400.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.035370 restraints weight = 100325.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.035494 restraints weight = 88759.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.035685 restraints weight = 81907.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.035738 restraints weight = 76030.633| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 1.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 15849 Z= 0.437 Angle : 1.352 19.622 21906 Z= 0.674 Chirality : 0.053 0.365 2850 Planarity : 0.010 0.109 3051 Dihedral : 8.366 109.056 2775 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 37.22 Ramachandran Plot: Outliers : 0.70 % Allowed : 10.04 % Favored : 89.26 % Rotamer: Outliers : 1.50 % Allowed : 7.00 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.19), residues: 1704 helix: -0.68 (0.15), residues: 930 sheet: -1.54 (0.30), residues: 228 loop : -2.23 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG B2352 TYR 0.030 0.004 TYR C2266 PHE 0.025 0.004 PHE B2263 TRP 0.032 0.005 TRP C2430 HIS 0.004 0.002 HIS C2340 Details of bonding type rmsd/Z covalent geometry : bond 0.00851 / 0.44 (15846) covalent geometry : angle 1.35179 / 0.67 (21900) SS BOND : bond 0.00163 / 0.08 ( 3) SS BOND : angle 2.62747 / 1.31 ( 6) hydrogen bonds : bond 0.07977 / 4.36 ( 1481) hydrogen bonds : angle 8.42794 / 5.64 ( 4332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.164 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 21 average time/residue: 0.0445 time to fit residues: 1.5608 Evaluate side-chains 17 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 30.0000 overall best weight: 30.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C2221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2356 GLN ** C2391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.037786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.031869 restraints weight = 118866.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.031869 restraints weight = 114815.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.031869 restraints weight = 114815.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.031869 restraints weight = 114815.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.031869 restraints weight = 114815.015| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 1.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 15849 Z= 0.420 Angle : 1.255 16.515 21906 Z= 0.628 Chirality : 0.051 0.439 2850 Planarity : 0.009 0.103 3051 Dihedral : 8.457 110.399 2775 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 34.12 Ramachandran Plot: Outliers : 0.70 % Allowed : 11.09 % Favored : 88.20 % Rotamer: Outliers : 1.50 % Allowed : 8.00 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.19), residues: 1704 helix: -0.71 (0.16), residues: 909 sheet: -2.04 (0.31), residues: 228 loop : -2.87 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B2352 TYR 0.023 0.003 TYR C2256 PHE 0.035 0.004 PHE B2449 TRP 0.042 0.005 TRP C2430 HIS 0.007 0.003 HIS A2370 Details of bonding type rmsd/Z covalent geometry : bond 0.00830 / 0.42 (15846) covalent geometry : angle 1.25507 / 0.63 (21900) SS BOND : bond 0.00356 / 0.18 ( 3) SS BOND : angle 1.66572 / 0.84 ( 6) hydrogen bonds : bond 0.06769 / 3.71 ( 1481) hydrogen bonds : angle 8.16642 / 5.48 ( 4332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: C 2283 THR cc_start: 0.0803 (OUTLIER) cc_final: 0.0545 (m) outliers start: 3 outliers final: 1 residues processed: 20 average time/residue: 0.0261 time to fit residues: 1.0237 Evaluate side-chains 19 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 30.0000 overall best weight: 30.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C2221 ASN ** C2275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2310 ASN ** C2391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.035906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.031258 restraints weight = 133165.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.031242 restraints weight = 135521.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.031240 restraints weight = 134207.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.031241 restraints weight = 133864.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.031241 restraints weight = 133161.191| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 moved from start: 1.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 15849 Z= 0.420 Angle : 1.261 13.825 21906 Z= 0.630 Chirality : 0.053 0.421 2850 Planarity : 0.008 0.099 3051 Dihedral : 8.737 113.493 2775 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 35.79 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.38 % Favored : 85.92 % Rotamer: Outliers : 1.50 % Allowed : 6.00 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.37 % Twisted Proline : 3.33 % Twisted General : 0.56 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.19), residues: 1704 helix: -0.90 (0.16), residues: 888 sheet: -2.39 (0.29), residues: 249 loop : -3.14 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C2402 TYR 0.019 0.004 TYR B2256 PHE 0.033 0.003 PHE B2272 TRP 0.049 0.005 TRP A2430 HIS 0.001 0.001 HIS A2370 Details of bonding type rmsd/Z covalent geometry : bond 0.00834 / 0.42 (15846) covalent geometry : angle 1.26104 / 0.63 (21900) SS BOND : bond 0.00199 / 0.10 ( 3) SS BOND : angle 0.94438 / 0.46 ( 6) hydrogen bonds : bond 0.07153 / 3.93 ( 1481) hydrogen bonds : angle 8.47135 / 5.68 ( 4332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.160 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 20 average time/residue: 0.0331 time to fit residues: 1.2087 Evaluate side-chains 19 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 30.0000 overall best weight: 30.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C2221 ASN ** C2262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.035492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.030962 restraints weight = 131221.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.030962 restraints weight = 129102.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.030962 restraints weight = 129064.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.030962 restraints weight = 129032.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.030962 restraints weight = 129031.214| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5890 moved from start: 1.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 15849 Z= 0.415 Angle : 1.239 16.260 21906 Z= 0.623 Chirality : 0.052 0.333 2850 Planarity : 0.008 0.122 3051 Dihedral : 8.695 111.698 2775 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 37.64 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.03 % Favored : 86.27 % Rotamer: Outliers : 1.00 % Allowed : 7.50 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.37 % Twisted Proline : 3.33 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.19), residues: 1704 helix: -1.08 (0.16), residues: 915 sheet: -2.37 (0.31), residues: 243 loop : -3.69 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG B2295 TYR 0.026 0.004 TYR C2256 PHE 0.035 0.004 PHE C2449 TRP 0.048 0.005 TRP A2430 HIS 0.009 0.005 HIS A2370 Details of bonding type rmsd/Z covalent geometry : bond 0.00807 / 0.41 (15846) covalent geometry : angle 1.23933 / 0.62 (21900) SS BOND : bond 0.00384 / 0.19 ( 3) SS BOND : angle 0.61557 / 0.31 ( 6) hydrogen bonds : bond 0.06937 / 3.80 ( 1481) hydrogen bonds : angle 8.51296 / 5.70 ( 4332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.146 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.0276 time to fit residues: 0.9941 Evaluate side-chains 17 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 30.0000 overall best weight: 30.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C2221 ASN ** C2262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2391 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.035374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.030772 restraints weight = 146310.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.030784 restraints weight = 138708.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.030785 restraints weight = 135480.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.030785 restraints weight = 135446.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.030785 restraints weight = 135446.369| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6032 moved from start: 1.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 15849 Z= 0.414 Angle : 1.236 14.892 21906 Z= 0.622 Chirality : 0.052 0.449 2850 Planarity : 0.008 0.117 3051 Dihedral : 8.810 114.048 2775 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 37.93 Ramachandran Plot: Outliers : 0.70 % Allowed : 14.08 % Favored : 85.21 % Rotamer: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.37 % Twisted Proline : 3.33 % Twisted General : 0.74 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.19), residues: 1704 helix: -1.10 (0.16), residues: 897 sheet: -2.51 (0.31), residues: 243 loop : -3.42 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG C2402 TYR 0.023 0.003 TYR B2256 PHE 0.024 0.003 PHE C2263 TRP 0.054 0.005 TRP C2430 HIS 0.006 0.003 HIS A2370 Details of bonding type rmsd/Z covalent geometry : bond 0.00798 / 0.41 (15846) covalent geometry : angle 1.23641 / 0.62 (21900) SS BOND : bond 0.00407 / 0.20 ( 3) SS BOND : angle 0.84447 / 0.43 ( 6) hydrogen bonds : bond 0.06974 / 3.84 ( 1481) hydrogen bonds : angle 8.62680 / 5.77 ( 4332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.139 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0238 time to fit residues: 0.7415 Evaluate side-chains 15 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 30.0000 overall best weight: 30.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2221 ASN ** A2262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2391 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.034802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.030509 restraints weight = 121220.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.030509 restraints weight = 118438.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.030511 restraints weight = 115464.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.030511 restraints weight = 115295.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.030511 restraints weight = 115295.993| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5944 moved from start: 1.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 15849 Z= 0.410 Angle : 1.247 13.541 21906 Z= 0.626 Chirality : 0.053 0.426 2850 Planarity : 0.008 0.108 3051 Dihedral : 8.828 111.479 2775 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 39.93 Ramachandran Plot: Outliers : 0.70 % Allowed : 14.26 % Favored : 85.04 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.37 % Twisted Proline : 3.33 % Twisted General : 0.93 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.26 (0.19), residues: 1704 helix: -1.17 (0.16), residues: 891 sheet: -2.63 (0.31), residues: 243 loop : -3.37 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B2402 TYR 0.024 0.003 TYR C2309 PHE 0.044 0.003 PHE A2449 TRP 0.051 0.004 TRP B2430 HIS 0.006 0.002 HIS A2370 Details of bonding type rmsd/Z covalent geometry : bond 0.00799 / 0.41 (15846) covalent geometry : angle 1.24705 / 0.63 (21900) SS BOND : bond 0.00043 / 0.02 ( 3) SS BOND : angle 1.93181 / 0.98 ( 6) hydrogen bonds : bond 0.06926 / 3.82 ( 1481) hydrogen bonds : angle 8.65108 / 5.79 ( 4332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.171 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0310 time to fit residues: 0.9750 Evaluate side-chains 15 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 30.0000 overall best weight: 30.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C2221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2391 GLN C2409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.034896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.031034 restraints weight = 162402.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.031181 restraints weight = 146562.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.031188 restraints weight = 129228.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.031188 restraints weight = 129633.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.031188 restraints weight = 129633.718| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 1.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 15849 Z= 0.412 Angle : 1.247 13.207 21906 Z= 0.633 Chirality : 0.054 0.383 2850 Planarity : 0.008 0.112 3051 Dihedral : 8.913 115.944 2775 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 43.00 Ramachandran Plot: Outliers : 0.70 % Allowed : 15.32 % Favored : 83.98 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.37 % Twisted Proline : 3.33 % Twisted General : 1.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.19), residues: 1704 helix: -1.10 (0.16), residues: 870 sheet: -2.92 (0.27), residues: 243 loop : -3.24 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C2402 TYR 0.033 0.004 TYR C2256 PHE 0.044 0.004 PHE B2449 TRP 0.046 0.005 TRP B2430 HIS 0.006 0.003 HIS A2370 Details of bonding type rmsd/Z covalent geometry : bond 0.00802 / 0.41 (15846) covalent geometry : angle 1.24720 / 0.63 (21900) SS BOND : bond 0.00010 / 0.01 ( 3) SS BOND : angle 1.80976 / 0.91 ( 6) hydrogen bonds : bond 0.07018 / 3.87 ( 1481) hydrogen bonds : angle 8.76166 / 5.85 ( 4332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.162 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0322 time to fit residues: 1.0180 Evaluate side-chains 15 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 30.0000 overall best weight: 30.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2221 ASN ** A2262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2391 GLN A2409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.034759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.030415 restraints weight = 130955.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.030417 restraints weight = 127890.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.030417 restraints weight = 127464.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.030417 restraints weight = 127464.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.030417 restraints weight = 127464.089| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5937 moved from start: 1.6900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 15849 Z= 0.411 Angle : 1.247 14.259 21906 Z= 0.629 Chirality : 0.054 0.458 2850 Planarity : 0.008 0.104 3051 Dihedral : 8.919 110.745 2775 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 43.00 Ramachandran Plot: Outliers : 0.70 % Allowed : 15.49 % Favored : 83.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.37 % Twisted Proline : 3.33 % Twisted General : 0.93 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.19), residues: 1704 helix: -1.06 (0.17), residues: 858 sheet: -2.99 (0.27), residues: 249 loop : -3.36 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C2402 TYR 0.017 0.003 TYR B2256 PHE 0.042 0.003 PHE C2449 TRP 0.038 0.004 TRP A2430 HIS 0.005 0.002 HIS A2370 Details of bonding type rmsd/Z covalent geometry : bond 0.00800 / 0.41 (15846) covalent geometry : angle 1.24682 / 0.63 (21900) SS BOND : bond 0.00062 / 0.03 ( 3) SS BOND : angle 1.46900 / 0.74 ( 6) hydrogen bonds : bond 0.06968 / 3.84 ( 1481) hydrogen bonds : angle 8.72929 / 5.83 ( 4332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.159 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0334 time to fit residues: 1.0929 Evaluate side-chains 16 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 30.0000 overall best weight: 30.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C2221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2391 GLN C2409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.034738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.030888 restraints weight = 159223.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.030888 restraints weight = 142747.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.030888 restraints weight = 142747.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.030888 restraints weight = 142747.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.030888 restraints weight = 142747.601| |-----------------------------------------------------------------------------| r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5954 moved from start: 1.7275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 15849 Z= 0.406 Angle : 1.227 14.334 21906 Z= 0.622 Chirality : 0.053 0.432 2850 Planarity : 0.008 0.111 3051 Dihedral : 8.802 114.978 2775 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 43.49 Ramachandran Plot: Outliers : 0.70 % Allowed : 15.67 % Favored : 83.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.37 % Twisted Proline : 3.33 % Twisted General : 0.93 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.19), residues: 1704 helix: -1.12 (0.16), residues: 879 sheet: -2.99 (0.28), residues: 249 loop : -3.42 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B2402 TYR 0.022 0.003 TYR C2256 PHE 0.042 0.003 PHE B2449 TRP 0.037 0.004 TRP A2430 HIS 0.005 0.002 HIS A2370 Details of bonding type rmsd/Z covalent geometry : bond 0.00790 / 0.41 (15846) covalent geometry : angle 1.22724 / 0.62 (21900) SS BOND : bond 0.00172 / 0.09 ( 3) SS BOND : angle 1.32681 / 0.65 ( 6) hydrogen bonds : bond 0.06967 / 3.85 ( 1481) hydrogen bonds : angle 8.71628 / 5.85 ( 4332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1601.87 seconds wall clock time: 28 minutes 29.64 seconds (1709.64 seconds total)