Starting phenix.real_space_refine (version: dev) on Tue Feb 21 21:41:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jac_6343/02_2023/3jac_6343.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jac_6343/02_2023/3jac_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jac_6343/02_2023/3jac_6343.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jac_6343/02_2023/3jac_6343.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jac_6343/02_2023/3jac_6343.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jac_6343/02_2023/3jac_6343.pdb" } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A GLU 2279": "OE1" <-> "OE2" Residue "A ARG 2295": "NH1" <-> "NH2" Residue "A ARG 2318": "NH1" <-> "NH2" Residue "A ARG 2352": "NH1" <-> "NH2" Residue "A ARG 2361": "NH1" <-> "NH2" Residue "A ARG 2377": "NH1" <-> "NH2" Residue "A GLU 2395": "OE1" <-> "OE2" Residue "A ARG 2402": "NH1" <-> "NH2" Residue "A ARG 2406": "NH1" <-> "NH2" Residue "B GLU 2279": "OE1" <-> "OE2" Residue "B ARG 2295": "NH1" <-> "NH2" Residue "B ARG 2318": "NH1" <-> "NH2" Residue "B ARG 2352": "NH1" <-> "NH2" Residue "B ARG 2361": "NH1" <-> "NH2" Residue "B ARG 2377": "NH1" <-> "NH2" Residue "B GLU 2395": "OE1" <-> "OE2" Residue "B ARG 2402": "NH1" <-> "NH2" Residue "B ARG 2406": "NH1" <-> "NH2" Residue "B GLU 2408": "OE1" <-> "OE2" Residue "C GLU 2279": "OE1" <-> "OE2" Residue "C ARG 2295": "NH1" <-> "NH2" Residue "C ARG 2318": "NH1" <-> "NH2" Residue "C ARG 2352": "NH1" <-> "NH2" Residue "C ARG 2361": "NH1" <-> "NH2" Residue "C ARG 2377": "NH1" <-> "NH2" Residue "C GLU 2395": "OE1" <-> "OE2" Residue "C ARG 2402": "NH1" <-> "NH2" Residue "C ARG 2406": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/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: {'GLN:plan1': 11, 'HIS:plan': 6, 'ASN:plan1': 6, 'TYR:plan': 15, 'UNK:plan-1': 346, 'TRP:plan': 8, 'ASP:plan': 13, 'PHE:plan': 31, 'GLU:plan': 15, 'ARG:plan': 16} 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: {'GLN:plan1': 11, 'HIS:plan': 6, 'ASN:plan1': 6, 'TYR:plan': 15, 'UNK:plan-1': 346, 'TRP:plan': 8, 'ASP:plan': 13, 'PHE:plan': 31, 'GLU:plan': 15, 'ARG:plan': 16} 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: {'GLN:plan1': 11, 'HIS:plan': 6, 'ASN:plan1': 6, 'TYR:plan': 15, 'UNK:plan-1': 346, 'TRP:plan': 8, 'ASP:plan': 13, 'PHE:plan': 31, 'GLU:plan': 15, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 980 Time building chain proxies: 9.18, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 6.91 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.28 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: 6.30 Time building geometry restraints manager: 7.40 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: 97.79 - 106.50: 292 106.50 - 115.21: 9758 115.21 - 123.92: 11536 123.92 - 132.63: 292 132.63 - 141.34: 22 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 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. 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. 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.510 Check model and map are aligned: 0.230 Process input model: 42.030 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.130 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.630 ------------------------------------------------------------------------------- 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 15846 Z= 0.482 Angle : 1.808 16.839 21900 Z= 1.207 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 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (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 *********************** 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 fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 57 average time/residue: 0.1747 time to fit residues: 13.0299 Evaluate side-chains 31 residues out of total 507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.444 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0694 time to fit residues: 0.9262 ------------------------------------------------------------------------------- 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5257 moved from start: 0.9918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.140 15846 Z= 0.885 Angle : 1.933 26.922 21900 Z= 0.950 Chirality : 0.065 0.394 2850 Planarity : 0.013 0.190 3051 Dihedral : 10.253 100.801 2775 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 66.53 Ramachandran Plot: Outliers : 2.11 % Allowed : 9.15 % Favored : 88.73 % Rotamer Outliers : 3.50 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.74 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.17), residues: 1704 helix: -1.97 (0.14), residues: 906 sheet: -1.37 (0.30), residues: 219 loop : -2.78 (0.25), residues: 579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 20 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 27 average time/residue: 0.1126 time to fit residues: 4.9455 Evaluate side-chains 21 residues out of total 507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 18 time to evaluate : 0.461 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0565 time to fit residues: 0.8972 ------------------------------------------------------------------------------- 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5552 moved from start: 1.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.114 15846 Z= 0.811 Angle : 1.727 25.730 21900 Z= 0.861 Chirality : 0.066 0.419 2850 Planarity : 0.011 0.137 3051 Dihedral : 10.878 109.285 2775 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 75.01 Ramachandran Plot: Outliers : 2.64 % Allowed : 17.61 % Favored : 79.75 % Rotamer Outliers : 5.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 6.67 % Twisted General : 1.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (0.17), residues: 1704 helix: -2.82 (0.13), residues: 945 sheet: -2.73 (0.31), residues: 243 loop : -4.06 (0.26), residues: 516 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 16 time to evaluate : 0.487 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 26 average time/residue: 0.0867 time to fit residues: 4.0293 Evaluate side-chains 18 residues out of total 507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0445 time to fit residues: 0.8000 ------------------------------------------------------------------------------- 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2356 GLN ** C2385 ASN ** 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5651 moved from start: 1.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.099 15846 Z= 0.765 Angle : 1.648 27.617 21900 Z= 0.821 Chirality : 0.062 0.360 2850 Planarity : 0.010 0.114 3051 Dihedral : 11.048 107.585 2775 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 74.04 Ramachandran Plot: Outliers : 1.58 % Allowed : 20.95 % Favored : 77.46 % Rotamer Outliers : 3.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 6.67 % Twisted General : 2.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.01 (0.18), residues: 1704 helix: -2.81 (0.14), residues: 855 sheet: -3.22 (0.31), residues: 234 loop : -3.87 (0.24), residues: 615 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 17 time to evaluate : 0.486 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 24 average time/residue: 0.0871 time to fit residues: 3.9712 Evaluate side-chains 19 residues out of total 507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.547 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0439 time to fit residues: 0.7847 ------------------------------------------------------------------------------- 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5704 moved from start: 1.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.100 15846 Z= 0.752 Angle : 1.612 26.980 21900 Z= 0.806 Chirality : 0.062 0.334 2850 Planarity : 0.011 0.162 3051 Dihedral : 11.118 109.256 2775 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 74.01 Ramachandran Plot: Outliers : 1.76 % Allowed : 23.42 % Favored : 74.82 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 6.67 % Twisted General : 2.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.50 (0.17), residues: 1704 helix: -3.02 (0.14), residues: 867 sheet: -3.40 (0.33), residues: 210 loop : -4.47 (0.22), residues: 627 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 19 average time/residue: 0.1131 time to fit residues: 3.6685 Evaluate side-chains 17 residues out of total 507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.532 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0545 time to fit residues: 0.7463 ------------------------------------------------------------------------------- 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2222 GLN ** C2254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5753 moved from start: 1.6986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.091 15846 Z= 0.760 Angle : 1.622 25.849 21900 Z= 0.813 Chirality : 0.063 0.421 2850 Planarity : 0.011 0.192 3051 Dihedral : 11.359 108.260 2775 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 76.12 Ramachandran Plot: Outliers : 1.76 % Allowed : 22.71 % Favored : 75.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 6.67 % Twisted General : 2.96 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.44 (0.17), residues: 1704 helix: -3.02 (0.14), residues: 903 sheet: -3.48 (0.35), residues: 183 loop : -4.36 (0.23), residues: 618 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 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 fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1114 time to fit residues: 3.1404 Evaluate side-chains 16 residues out of total 507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.458 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5947 ------------------------------------------------------------------------------- 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5777 moved from start: 1.7575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.089 15846 Z= 0.746 Angle : 1.613 26.701 21900 Z= 0.806 Chirality : 0.063 0.328 2850 Planarity : 0.011 0.188 3051 Dihedral : 11.348 109.878 2775 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 77.99 Ramachandran Plot: Outliers : 1.76 % Allowed : 23.24 % Favored : 75.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 6.67 % Twisted General : 2.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.38 (0.17), residues: 1704 helix: -2.93 (0.14), residues: 882 sheet: -3.47 (0.32), residues: 201 loop : -4.36 (0.23), residues: 621 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 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 fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1075 time to fit residues: 3.1586 Evaluate side-chains 16 residues out of total 507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.496 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6197 ------------------------------------------------------------------------------- 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: 40.0000 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 moved from start: 1.8181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.095 15846 Z= 0.749 Angle : 1.622 26.582 21900 Z= 0.807 Chirality : 0.064 0.481 2850 Planarity : 0.012 0.190 3051 Dihedral : 11.361 110.001 2775 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 77.68 Ramachandran Plot: Outliers : 1.58 % Allowed : 24.82 % Favored : 73.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 6.67 % Twisted General : 2.78 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.44 (0.17), residues: 1704 helix: -3.01 (0.14), residues: 906 sheet: -3.64 (0.33), residues: 183 loop : -4.32 (0.23), residues: 615 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 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 fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.531 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1093 time to fit residues: 3.2073 Evaluate side-chains 16 residues out of total 507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6258 ------------------------------------------------------------------------------- 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: 40.0000 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 1.8535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.083 15846 Z= 0.746 Angle : 1.621 26.571 21900 Z= 0.807 Chirality : 0.063 0.368 2850 Planarity : 0.012 0.182 3051 Dihedral : 11.258 110.300 2775 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 76.07 Ramachandran Plot: Outliers : 1.58 % Allowed : 25.70 % Favored : 72.71 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 6.67 % Twisted General : 2.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.37 (0.17), residues: 1704 helix: -2.98 (0.14), residues: 888 sheet: -3.71 (0.31), residues: 204 loop : -4.17 (0.24), residues: 612 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 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 fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1128 time to fit residues: 3.1339 Evaluate side-chains 16 residues out of total 507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.462 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5580 ------------------------------------------------------------------------------- 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: 40.0000 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5832 moved from start: 1.9316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.092 15846 Z= 0.755 Angle : 1.636 26.656 21900 Z= 0.813 Chirality : 0.064 0.347 2850 Planarity : 0.012 0.194 3051 Dihedral : 11.372 110.633 2775 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 79.25 Ramachandran Plot: Outliers : 1.76 % Allowed : 25.35 % Favored : 72.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 13.33 % Twisted General : 2.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.38 (0.17), residues: 1704 helix: -3.00 (0.14), residues: 897 sheet: -3.81 (0.28), residues: 219 loop : -4.08 (0.25), residues: 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 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 fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.474 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1211 time to fit residues: 3.4047 Evaluate side-chains 16 residues out of total 507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.507 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6158 ------------------------------------------------------------------------------- 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.034136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.030129 restraints weight = 186851.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.030217 restraints weight = 165034.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.030356 restraints weight = 152932.247| |-----------------------------------------------------------------------------| r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 1.9597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.094 15846 Z= 0.750 Angle : 1.634 26.957 21900 Z= 0.812 Chirality : 0.063 0.339 2850 Planarity : 0.012 0.191 3051 Dihedral : 11.268 110.951 2775 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 77.57 Ramachandran Plot: Outliers : 1.76 % Allowed : 26.76 % Favored : 71.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 10.00 % Twisted General : 1.85 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.39 (0.17), residues: 1704 helix: -3.02 (0.14), residues: 897 sheet: -3.76 (0.31), residues: 204 loop : -4.12 (0.24), residues: 603 =============================================================================== Job complete usr+sys time: 2621.50 seconds wall clock time: 48 minutes 24.69 seconds (2904.69 seconds total)