Starting phenix.real_space_refine on Fri Mar 6 05:42:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pgp_13391/03_2026/7pgp_13391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pgp_13391/03_2026/7pgp_13391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pgp_13391/03_2026/7pgp_13391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pgp_13391/03_2026/7pgp_13391.map" model { file = "/net/cci-nas-00/data/ceres_data/7pgp_13391/03_2026/7pgp_13391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pgp_13391/03_2026/7pgp_13391.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians S 100 5.16 5 C 9030 2.51 5 N 2396 2.21 5 O 2617 1.98 5 H 14363 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28506 Number of models: 1 Model: "" Number of chains: 2 Chain: "F" Number of atoms: 10405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 10405 Classifications: {'peptide': 650} Link IDs: {'PTRANS': 27, 'TRANS': 622} Chain breaks: 1 Chain: "N" Number of atoms: 18101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1138, 18101 Classifications: {'peptide': 1138} Link IDs: {'PTRANS': 38, 'TRANS': 1099} Chain breaks: 6 Time building chain proxies: 4.79, per 1000 atoms: 0.17 Number of scatterers: 28506 At special positions: 0 Unit cell: (115.64, 127.351, 175.656, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 O 2617 8.00 N 2396 7.00 C 9030 6.00 H 14363 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 630.5 milliseconds 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3444 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 0 sheets defined 78.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'F' and resid 1956 through 1961 removed outlier: 4.211A pdb=" N LYS F1961 " --> pdb=" O VAL F1957 " (cutoff:3.500A) Processing helix chain 'F' and resid 1967 through 1985 removed outlier: 3.549A pdb=" N THR F1972 " --> pdb=" O ARG F1968 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F1973 " --> pdb=" O GLN F1969 " (cutoff:3.500A) Processing helix chain 'F' and resid 1988 through 2001 removed outlier: 4.042A pdb=" N ALA F1994 " --> pdb=" O PRO F1990 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP F1997 " --> pdb=" O GLN F1993 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY F1998 " --> pdb=" O ALA F1994 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER F1999 " --> pdb=" O LYS F1995 " (cutoff:3.500A) Processing helix chain 'F' and resid 2002 through 2005 removed outlier: 6.506A pdb=" N ASP F2005 " --> pdb=" O GLN F2002 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2002 through 2005' Processing helix chain 'F' and resid 2006 through 2022 removed outlier: 3.595A pdb=" N THR F2020 " --> pdb=" O LYS F2016 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY F2021 " --> pdb=" O THR F2017 " (cutoff:3.500A) Processing helix chain 'F' and resid 2025 through 2042 removed outlier: 3.607A pdb=" N ASP F2033 " --> pdb=" O GLU F2029 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL F2036 " --> pdb=" O ALA F2032 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA F2037 " --> pdb=" O ASP F2033 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY F2041 " --> pdb=" O ALA F2037 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN F2042 " --> pdb=" O LEU F2038 " (cutoff:3.500A) Processing helix chain 'F' and resid 2042 through 2058 removed outlier: 4.234A pdb=" N SER F2048 " --> pdb=" O LYS F2044 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS F2049 " --> pdb=" O LEU F2045 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY F2052 " --> pdb=" O SER F2048 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG F2053 " --> pdb=" O LYS F2049 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS F2056 " --> pdb=" O GLY F2052 " (cutoff:3.500A) Processing helix chain 'F' and resid 2059 through 2061 No H-bonds generated for 'chain 'F' and resid 2059 through 2061' Processing helix chain 'F' and resid 2068 through 2073 removed outlier: 6.137A pdb=" N LEU F2073 " --> pdb=" O GLU F2070 " (cutoff:3.500A) Processing helix chain 'F' and resid 2074 through 2090 removed outlier: 3.514A pdb=" N MET F2085 " --> pdb=" O LEU F2081 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE F2090 " --> pdb=" O LEU F2086 " (cutoff:3.500A) Processing helix chain 'F' and resid 2091 through 2093 No H-bonds generated for 'chain 'F' and resid 2091 through 2093' Processing helix chain 'F' and resid 2095 through 2109 Proline residue: F2101 - end of helix removed outlier: 3.926A pdb=" N VAL F2106 " --> pdb=" O TYR F2102 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE F2109 " --> pdb=" O HIS F2105 " (cutoff:3.500A) Processing helix chain 'F' and resid 2115 through 2135 Processing helix chain 'F' and resid 2142 through 2156 removed outlier: 3.788A pdb=" N GLN F2147 " --> pdb=" O GLU F2143 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL F2148 " --> pdb=" O GLU F2144 " (cutoff:3.500A) Processing helix chain 'F' and resid 2158 through 2166 removed outlier: 3.638A pdb=" N LEU F2163 " --> pdb=" O PRO F2159 " (cutoff:3.500A) Processing helix chain 'F' and resid 2172 through 2178 removed outlier: 3.957A pdb=" N ILE F2176 " --> pdb=" O SER F2172 " (cutoff:3.500A) Processing helix chain 'F' and resid 2198 through 2220 removed outlier: 3.618A pdb=" N GLU F2203 " --> pdb=" O LEU F2199 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP F2219 " --> pdb=" O ALA F2215 " (cutoff:3.500A) Processing helix chain 'F' and resid 2224 through 2238 removed outlier: 3.736A pdb=" N PHE F2236 " --> pdb=" O LEU F2232 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE F2238 " --> pdb=" O GLN F2234 " (cutoff:3.500A) Processing helix chain 'F' and resid 2244 through 2251 Processing helix chain 'F' and resid 2251 through 2256 Processing helix chain 'F' and resid 2260 through 2281 removed outlier: 3.717A pdb=" N GLN F2266 " --> pdb=" O GLY F2262 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER F2272 " --> pdb=" O ILE F2268 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS F2273 " --> pdb=" O ARG F2269 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU F2276 " --> pdb=" O SER F2272 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU F2279 " --> pdb=" O LEU F2275 " (cutoff:3.500A) Processing helix chain 'F' and resid 2288 through 2302 removed outlier: 3.977A pdb=" N GLU F2292 " --> pdb=" O GLN F2288 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR F2294 " --> pdb=" O LEU F2290 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS F2300 " --> pdb=" O ILE F2296 " (cutoff:3.500A) Processing helix chain 'F' and resid 2303 through 2305 No H-bonds generated for 'chain 'F' and resid 2303 through 2305' Processing helix chain 'F' and resid 2310 through 2315 Processing helix chain 'F' and resid 2316 through 2324 removed outlier: 3.657A pdb=" N GLN F2324 " --> pdb=" O VAL F2320 " (cutoff:3.500A) Processing helix chain 'F' and resid 2327 through 2348 removed outlier: 3.785A pdb=" N ALA F2336 " --> pdb=" O SER F2332 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN F2340 " --> pdb=" O ALA F2336 " (cutoff:3.500A) Processing helix chain 'F' and resid 2355 through 2364 Processing helix chain 'F' and resid 2367 through 2379 removed outlier: 3.543A pdb=" N CYS F2371 " --> pdb=" O LEU F2367 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN F2373 " --> pdb=" O TRP F2369 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET F2374 " --> pdb=" O HIS F2370 " (cutoff:3.500A) Processing helix chain 'F' and resid 2385 through 2393 removed outlier: 4.105A pdb=" N VAL F2391 " --> pdb=" O ASN F2387 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS F2393 " --> pdb=" O ALA F2389 " (cutoff:3.500A) Processing helix chain 'F' and resid 2395 through 2400 Processing helix chain 'F' and resid 2402 through 2425 removed outlier: 3.713A pdb=" N VAL F2406 " --> pdb=" O SER F2402 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA F2407 " --> pdb=" O PRO F2403 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG F2408 " --> pdb=" O ALA F2404 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU F2419 " --> pdb=" O THR F2415 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS F2422 " --> pdb=" O THR F2418 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS F2423 " --> pdb=" O LEU F2419 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG F2424 " --> pdb=" O VAL F2420 " (cutoff:3.500A) Processing helix chain 'F' and resid 2433 through 2435 No H-bonds generated for 'chain 'F' and resid 2433 through 2435' Processing helix chain 'F' and resid 2436 through 2442 Processing helix chain 'F' and resid 2446 through 2453 Processing helix chain 'F' and resid 2612 through 2630 removed outlier: 3.792A pdb=" N LEU F2619 " --> pdb=" O ILE F2615 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU F2620 " --> pdb=" O GLN F2616 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU F2623 " --> pdb=" O LEU F2619 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL F2627 " --> pdb=" O LEU F2623 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR F2629 " --> pdb=" O THR F2625 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR F2630 " --> pdb=" O LEU F2626 " (cutoff:3.500A) Processing helix chain 'F' and resid 2632 through 2650 removed outlier: 3.576A pdb=" N ILE F2638 " --> pdb=" O PHE F2634 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR F2642 " --> pdb=" O ILE F2638 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU F2645 " --> pdb=" O GLU F2641 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F2648 " --> pdb=" O ALA F2644 " (cutoff:3.500A) Processing helix chain 'F' and resid 2653 through 2656 Processing helix chain 'F' and resid 2657 through 2672 removed outlier: 4.305A pdb=" N SER F2663 " --> pdb=" O ASN F2659 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS F2664 " --> pdb=" O LEU F2660 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER F2670 " --> pdb=" O ASN F2666 " (cutoff:3.500A) Processing helix chain 'F' and resid 2674 through 2691 Proline residue: F2680 - end of helix Processing helix chain 'F' and resid 2699 through 2707 removed outlier: 4.273A pdb=" N LEU F2703 " --> pdb=" O THR F2700 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN F2704 " --> pdb=" O SER F2701 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER F2705 " --> pdb=" O TYR F2702 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY F2707 " --> pdb=" O GLN F2704 " (cutoff:3.500A) Processing helix chain 'F' and resid 2727 through 2743 removed outlier: 4.002A pdb=" N ILE F2731 " --> pdb=" O TYR F2727 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS F2733 " --> pdb=" O GLU F2729 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 19 removed outlier: 3.851A pdb=" N ALA N 12 " --> pdb=" O GLU N 8 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL N 13 " --> pdb=" O TRP N 9 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE N 17 " --> pdb=" O VAL N 13 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP N 18 " --> pdb=" O VAL N 14 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 47 removed outlier: 3.540A pdb=" N ASN N 39 " --> pdb=" O SER N 35 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS N 40 " --> pdb=" O THR N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 67 removed outlier: 3.523A pdb=" N THR N 60 " --> pdb=" O SER N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 97 removed outlier: 3.520A pdb=" N ILE N 85 " --> pdb=" O LEU N 81 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE N 86 " --> pdb=" O SER N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 112 removed outlier: 3.818A pdb=" N LYS N 111 " --> pdb=" O THR N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 122 removed outlier: 4.258A pdb=" N PHE N 120 " --> pdb=" O GLU N 116 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU N 121 " --> pdb=" O ILE N 117 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS N 122 " --> pdb=" O CYS N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 129 through 147 removed outlier: 3.846A pdb=" N GLU N 133 " --> pdb=" O GLN N 129 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY N 140 " --> pdb=" O ASN N 136 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL N 141 " --> pdb=" O SER N 137 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS N 147 " --> pdb=" O PHE N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 167 removed outlier: 3.627A pdb=" N VAL N 153 " --> pdb=" O ASN N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 173 through 182 removed outlier: 4.170A pdb=" N ASP N 176 " --> pdb=" O ASP N 173 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU N 179 " --> pdb=" O ASP N 176 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU N 180 " --> pdb=" O ILE N 177 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN N 181 " --> pdb=" O GLU N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 202 removed outlier: 3.580A pdb=" N ARG N 192 " --> pdb=" O ALA N 188 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LYS N 202 " --> pdb=" O ALA N 198 " (cutoff:3.500A) Processing helix chain 'N' and resid 205 through 227 removed outlier: 3.611A pdb=" N PHE N 220 " --> pdb=" O LEU N 216 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TRP N 221 " --> pdb=" O GLU N 217 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN N 222 " --> pdb=" O LYS N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 237 removed outlier: 3.693A pdb=" N PHE N 231 " --> pdb=" O TYR N 227 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR N 232 " --> pdb=" O PRO N 228 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR N 235 " --> pdb=" O PHE N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 239 through 257 Processing helix chain 'N' and resid 259 through 277 Proline residue: N 268 - end of helix removed outlier: 3.513A pdb=" N ILE N 271 " --> pdb=" O TRP N 267 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE N 272 " --> pdb=" O PRO N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 286 removed outlier: 4.256A pdb=" N ILE N 281 " --> pdb=" O CYS N 277 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN N 282 " --> pdb=" O PRO N 278 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 308 removed outlier: 3.568A pdb=" N LYS N 297 " --> pdb=" O ASN N 293 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG N 304 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA N 306 " --> pdb=" O SER N 302 " (cutoff:3.500A) Processing helix chain 'N' and resid 313 through 332 removed outlier: 3.720A pdb=" N THR N 332 " --> pdb=" O CYS N 328 " (cutoff:3.500A) Processing helix chain 'N' and resid 340 through 358 removed outlier: 3.793A pdb=" N LEU N 344 " --> pdb=" O SER N 340 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER N 348 " --> pdb=" O LEU N 344 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET N 349 " --> pdb=" O LEU N 345 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL N 351 " --> pdb=" O GLN N 347 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP N 352 " --> pdb=" O SER N 348 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN N 355 " --> pdb=" O VAL N 351 " (cutoff:3.500A) Processing helix chain 'N' and resid 372 through 387 Processing helix chain 'N' and resid 393 through 399 Processing helix chain 'N' and resid 403 through 420 removed outlier: 3.532A pdb=" N ILE N 417 " --> pdb=" O SER N 413 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE N 418 " --> pdb=" O LEU N 414 " (cutoff:3.500A) Processing helix chain 'N' and resid 428 through 434 removed outlier: 4.265A pdb=" N CYS N 434 " --> pdb=" O ALA N 431 " (cutoff:3.500A) Processing helix chain 'N' and resid 435 through 455 removed outlier: 3.572A pdb=" N ASN N 441 " --> pdb=" O VAL N 437 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS N 454 " --> pdb=" O ALA N 450 " (cutoff:3.500A) Processing helix chain 'N' and resid 483 through 503 removed outlier: 3.514A pdb=" N LYS N 490 " --> pdb=" O THR N 486 " (cutoff:3.500A) Processing helix chain 'N' and resid 504 through 509 removed outlier: 3.524A pdb=" N LEU N 508 " --> pdb=" O PRO N 504 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS N 509 " --> pdb=" O LYS N 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 504 through 509' Processing helix chain 'N' and resid 521 through 531 Processing helix chain 'N' and resid 538 through 552 removed outlier: 3.555A pdb=" N GLU N 547 " --> pdb=" O GLN N 543 " (cutoff:3.500A) Processing helix chain 'N' and resid 554 through 559 removed outlier: 4.234A pdb=" N ASP N 559 " --> pdb=" O LEU N 555 " (cutoff:3.500A) Processing helix chain 'N' and resid 560 through 562 No H-bonds generated for 'chain 'N' and resid 560 through 562' Processing helix chain 'N' and resid 568 through 588 removed outlier: 3.817A pdb=" N GLN N 576 " --> pdb=" O GLU N 572 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER N 587 " --> pdb=" O LYS N 583 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS N 588 " --> pdb=" O LYS N 584 " (cutoff:3.500A) Processing helix chain 'N' and resid 592 through 618 removed outlier: 3.890A pdb=" N LYS N 598 " --> pdb=" O THR N 594 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU N 602 " --> pdb=" O LYS N 598 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU N 604 " --> pdb=" O LEU N 600 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS N 609 " --> pdb=" O ILE N 605 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE N 610 " --> pdb=" O CYS N 606 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU N 611 " --> pdb=" O ARG N 607 " (cutoff:3.500A) Processing helix chain 'N' and resid 677 through 692 removed outlier: 3.547A pdb=" N ARG N 681 " --> pdb=" O PRO N 677 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS N 686 " --> pdb=" O GLN N 682 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU N 687 " --> pdb=" O ALA N 683 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU N 688 " --> pdb=" O GLN N 684 " (cutoff:3.500A) Processing helix chain 'N' and resid 699 through 709 Processing helix chain 'N' and resid 710 through 721 removed outlier: 3.743A pdb=" N GLU N 716 " --> pdb=" O HIS N 712 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA N 717 " --> pdb=" O LEU N 713 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP N 718 " --> pdb=" O CYS N 714 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE N 719 " --> pdb=" O GLU N 715 " (cutoff:3.500A) Processing helix chain 'N' and resid 723 through 728 removed outlier: 3.735A pdb=" N SER N 727 " --> pdb=" O VAL N 723 " (cutoff:3.500A) Processing helix chain 'N' and resid 734 through 746 removed outlier: 3.546A pdb=" N PHE N 738 " --> pdb=" O ASN N 734 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET N 739 " --> pdb=" O TYR N 735 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU N 740 " --> pdb=" O ASN N 736 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE N 741 " --> pdb=" O THR N 737 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA N 742 " --> pdb=" O PHE N 738 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER N 743 " --> pdb=" O MET N 739 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL N 744 " --> pdb=" O GLU N 740 " (cutoff:3.500A) Processing helix chain 'N' and resid 751 through 763 removed outlier: 3.697A pdb=" N ARG N 758 " --> pdb=" O ALA N 754 " (cutoff:3.500A) Processing helix chain 'N' and resid 764 through 766 No H-bonds generated for 'chain 'N' and resid 764 through 766' Processing helix chain 'N' and resid 770 through 794 removed outlier: 3.839A pdb=" N GLU N 778 " --> pdb=" O THR N 774 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS N 789 " --> pdb=" O GLU N 785 " (cutoff:3.500A) Processing helix chain 'N' and resid 832 through 847 removed outlier: 3.611A pdb=" N GLU N 836 " --> pdb=" O ASP N 832 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP N 837 " --> pdb=" O SER N 833 " (cutoff:3.500A) Processing helix chain 'N' and resid 848 through 852 Processing helix chain 'N' and resid 889 through 900 Processing helix chain 'N' and resid 909 through 924 removed outlier: 3.514A pdb=" N ASP N 919 " --> pdb=" O THR N 915 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY N 922 " --> pdb=" O LYS N 918 " (cutoff:3.500A) Processing helix chain 'N' and resid 929 through 943 removed outlier: 3.769A pdb=" N ASN N 935 " --> pdb=" O PRO N 931 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE N 941 " --> pdb=" O LEU N 937 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS N 943 " --> pdb=" O ASN N 939 " (cutoff:3.500A) Processing helix chain 'N' and resid 954 through 974 removed outlier: 3.731A pdb=" N ALA N 966 " --> pdb=" O GLU N 962 " (cutoff:3.500A) Processing helix chain 'N' and resid 978 through 984 removed outlier: 4.159A pdb=" N HIS N 982 " --> pdb=" O GLY N 978 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY N 984 " --> pdb=" O SER N 980 " (cutoff:3.500A) Processing helix chain 'N' and resid 988 through 1001 removed outlier: 3.511A pdb=" N ASN N 994 " --> pdb=" O THR N 990 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG N 997 " --> pdb=" O LEU N 993 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR N 998 " --> pdb=" O ASN N 994 " (cutoff:3.500A) Processing helix chain 'N' and resid 1005 through 1022 removed outlier: 3.811A pdb=" N GLN N1010 " --> pdb=" O VAL N1006 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE N1011 " --> pdb=" O HIS N1007 " (cutoff:3.500A) Processing helix chain 'N' and resid 1033 through 1047 removed outlier: 4.083A pdb=" N LYS N1040 " --> pdb=" O LYS N1036 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP N1047 " --> pdb=" O GLU N1043 " (cutoff:3.500A) Processing helix chain 'N' and resid 1052 through 1057 removed outlier: 3.829A pdb=" N ALA N1056 " --> pdb=" O THR N1052 " (cutoff:3.500A) Processing helix chain 'N' and resid 1059 through 1062 Processing helix chain 'N' and resid 1063 through 1081 removed outlier: 3.782A pdb=" N ASP N1067 " --> pdb=" O CYS N1063 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU N1074 " --> pdb=" O GLN N1070 " (cutoff:3.500A) Processing helix chain 'N' and resid 1094 through 1117 removed outlier: 3.680A pdb=" N LEU N1109 " --> pdb=" O LYS N1105 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS N1117 " --> pdb=" O LEU N1113 " (cutoff:3.500A) Processing helix chain 'N' and resid 1135 through 1156 removed outlier: 3.539A pdb=" N MET N1149 " --> pdb=" O THR N1145 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA N1155 " --> pdb=" O ASN N1151 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN N1156 " --> pdb=" O LEU N1152 " (cutoff:3.500A) Processing helix chain 'N' and resid 1156 through 1161 Processing helix chain 'N' and resid 1162 through 1168 removed outlier: 3.686A pdb=" N ILE N1165 " --> pdb=" O MET N1162 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLY N1166 " --> pdb=" O HIS N1163 " (cutoff:3.500A) Processing helix chain 'N' and resid 1172 through 1191 removed outlier: 3.906A pdb=" N THR N1178 " --> pdb=" O GLN N1174 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY N1190 " --> pdb=" O ILE N1186 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR N1191 " --> pdb=" O LEU N1187 " (cutoff:3.500A) Processing helix chain 'N' and resid 1846 through 1849 Processing helix chain 'N' and resid 1850 through 1862 removed outlier: 3.765A pdb=" N ASN N1856 " --> pdb=" O GLY N1852 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE N1857 " --> pdb=" O THR N1853 " (cutoff:3.500A) Processing helix chain 'N' and resid 1866 through 1885 removed outlier: 3.903A pdb=" N SER N1871 " --> pdb=" O PRO N1867 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA N1872 " --> pdb=" O SER N1868 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS N1882 " --> pdb=" O CYS N1878 " (cutoff:3.500A) Processing helix chain 'N' and resid 1905 through 1919 Processing helix chain 'N' and resid 1922 through 1937 removed outlier: 3.701A pdb=" N GLU N1929 " --> pdb=" O GLU N1925 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER N1935 " --> pdb=" O ILE N1931 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS N1936 " --> pdb=" O SER N1932 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER N1937 " --> pdb=" O GLY N1933 " (cutoff:3.500A) Processing helix chain 'N' and resid 1938 through 1950 removed outlier: 3.784A pdb=" N LEU N1944 " --> pdb=" O GLU N1940 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU N1947 " --> pdb=" O HIS N1943 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR N1950 " --> pdb=" O LEU N1946 " (cutoff:3.500A) Processing helix chain 'N' and resid 1951 through 1953 No H-bonds generated for 'chain 'N' and resid 1951 through 1953' 794 hydrogen bonds defined for protein. 2322 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: 6.24 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14314 1.03 - 1.23: 76 1.23 - 1.42: 5793 1.42 - 1.61: 8440 1.61 - 1.81: 151 Bond restraints: 28774 Sorted by residual: bond pdb=" CG GLN F2245 " pdb=" CD GLN F2245 " ideal model delta sigma weight residual 1.516 1.492 0.024 2.50e-02 1.60e+03 8.91e-01 bond pdb=" CB THR N 780 " pdb=" CG2 THR N 780 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.87e-01 bond pdb=" CB ASN F2341 " pdb=" CG ASN F2341 " ideal model delta sigma weight residual 1.516 1.492 0.024 2.50e-02 1.60e+03 8.84e-01 bond pdb=" CB GLN F2245 " pdb=" CG GLN F2245 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.11e-01 bond pdb=" CB THR F2294 " pdb=" CG2 THR F2294 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.85e-01 ... (remaining 28769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 48222 1.01 - 2.01: 3764 2.01 - 3.02: 125 3.02 - 4.03: 50 4.03 - 5.03: 14 Bond angle restraints: 52175 Sorted by residual: angle pdb=" N GLY F2707 " pdb=" CA GLY F2707 " pdb=" C GLY F2707 " ideal model delta sigma weight residual 113.18 117.99 -4.81 2.37e+00 1.78e-01 4.12e+00 angle pdb=" N TYR F2727 " pdb=" CA TYR F2727 " pdb=" C TYR F2727 " ideal model delta sigma weight residual 112.93 111.02 1.91 1.12e+00 7.97e-01 2.92e+00 angle pdb=" C LEU F2094 " pdb=" N ASP F2095 " pdb=" CA ASP F2095 " ideal model delta sigma weight residual 122.07 119.19 2.88 1.70e+00 3.46e-01 2.86e+00 angle pdb=" N LEU F2094 " pdb=" CA LEU F2094 " pdb=" C LEU F2094 " ideal model delta sigma weight residual 108.20 105.33 2.87 1.71e+00 3.42e-01 2.81e+00 angle pdb=" N ASP F2427 " pdb=" CA ASP F2427 " pdb=" CB ASP F2427 " ideal model delta sigma weight residual 113.65 111.30 2.35 1.47e+00 4.63e-01 2.56e+00 ... (remaining 52170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 12573 17.50 - 35.00: 675 35.00 - 52.50: 164 52.50 - 70.00: 54 70.00 - 87.50: 8 Dihedral angle restraints: 13474 sinusoidal: 7385 harmonic: 6089 Sorted by residual: dihedral pdb=" CA ASP F2726 " pdb=" C ASP F2726 " pdb=" N TYR F2727 " pdb=" CA TYR F2727 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA SER F2093 " pdb=" C SER F2093 " pdb=" N LEU F2094 " pdb=" CA LEU F2094 " ideal model delta harmonic sigma weight residual 180.00 158.19 21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA PHE F2706 " pdb=" C PHE F2706 " pdb=" N GLY F2707 " pdb=" CA GLY F2707 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 13471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1384 0.029 - 0.059: 660 0.059 - 0.088: 203 0.088 - 0.118: 45 0.118 - 0.147: 13 Chirality restraints: 2305 Sorted by residual: chirality pdb=" CA ILE F2724 " pdb=" N ILE F2724 " pdb=" C ILE F2724 " pdb=" CB ILE F2724 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA PRO N 927 " pdb=" N PRO N 927 " pdb=" C PRO N 927 " pdb=" CB PRO N 927 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA PRO F2655 " pdb=" N PRO F2655 " pdb=" C PRO F2655 " pdb=" CB PRO F2655 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 2302 not shown) Planarity restraints: 4177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE F2654 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO F2655 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO F2655 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO F2655 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F2066 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO F2067 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO F2067 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO F2067 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER N 926 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO N 927 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO N 927 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO N 927 " -0.024 5.00e-02 4.00e+02 ... (remaining 4174 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 785 2.17 - 2.78: 56257 2.78 - 3.38: 74848 3.38 - 3.99: 93277 3.99 - 4.60: 152023 Nonbonded interactions: 377190 Sorted by model distance: nonbonded pdb=" O ILE N1857 " pdb="HD22 ASN N1861 " model vdw 1.559 2.450 nonbonded pdb=" O THR F1980 " pdb="HD22 ASN F1984 " model vdw 1.563 2.450 nonbonded pdb=" OD1 ASN F2381 " pdb=" H SER F2384 " model vdw 1.581 2.450 nonbonded pdb=" OE1 GLU N 907 " pdb=" H GLU N 907 " model vdw 1.594 2.450 nonbonded pdb=" O ILE N 44 " pdb=" HG SER N 47 " model vdw 1.605 2.450 ... (remaining 377185 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.150 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.180 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 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 : 0.005 0.044 14411 Z= 0.218 Angle : 0.485 5.033 19533 Z= 0.258 Chirality : 0.037 0.147 2305 Planarity : 0.004 0.044 2463 Dihedral : 11.533 82.514 5326 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.81 % Allowed : 5.68 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.55 (0.19), residues: 1770 helix: -0.69 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -1.48 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F2247 TYR 0.012 0.001 TYR F2331 PHE 0.012 0.001 PHE F2706 TRP 0.008 0.001 TRP N 696 HIS 0.004 0.001 HIS N 393 Details of bonding type rmsd covalent geometry : bond 0.00510 (14411) covalent geometry : angle 0.48487 (19533) hydrogen bonds : bond 0.31292 ( 794) hydrogen bonds : angle 8.20322 ( 2322) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 216 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2085 MET cc_start: 0.8798 (mtp) cc_final: 0.8552 (mtp) REVERT: F 2151 LEU cc_start: 0.8334 (mp) cc_final: 0.7924 (mm) REVERT: F 2155 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7417 (mt-10) REVERT: N 8 GLU cc_start: 0.7395 (tt0) cc_final: 0.6933 (tp30) REVERT: N 119 HIS cc_start: 0.8357 (OUTLIER) cc_final: 0.8127 (t-90) REVERT: N 133 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6602 (mp0) REVERT: N 171 ASN cc_start: 0.8310 (t0) cc_final: 0.8076 (m-40) REVERT: N 206 LYS cc_start: 0.8454 (tttt) cc_final: 0.8116 (tppt) REVERT: N 297 LYS cc_start: 0.7662 (tmtp) cc_final: 0.7215 (tmtt) REVERT: N 372 ASP cc_start: 0.7772 (t0) cc_final: 0.7366 (t70) REVERT: N 389 HIS cc_start: 0.7653 (m-70) cc_final: 0.7365 (m-70) REVERT: N 442 MET cc_start: 0.8597 (ttp) cc_final: 0.8213 (ttp) REVERT: N 718 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7752 (m-30) REVERT: N 932 MET cc_start: 0.8694 (ttm) cc_final: 0.8367 (ttm) REVERT: N 1171 LYS cc_start: 0.8614 (tttt) cc_final: 0.8377 (tttm) REVERT: N 1910 SER cc_start: 0.8896 (t) cc_final: 0.8395 (m) outliers start: 13 outliers final: 7 residues processed: 228 average time/residue: 0.3114 time to fit residues: 99.6059 Evaluate side-chains 156 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 2113 THR Chi-restraints excluded: chain F residue 2294 THR Chi-restraints excluded: chain F residue 2432 ASN Chi-restraints excluded: chain N residue 119 HIS Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 564 ASP Chi-restraints excluded: chain N residue 718 ASP Chi-restraints excluded: chain N residue 892 SER Chi-restraints excluded: chain N residue 1150 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F2385 ASN F2676 ASN N 149 ASN N 905 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.140528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103694 restraints weight = 55247.582| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.89 r_work: 0.2944 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14411 Z= 0.206 Angle : 0.601 5.595 19533 Z= 0.335 Chirality : 0.038 0.152 2305 Planarity : 0.004 0.048 2463 Dihedral : 5.158 59.802 1902 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.62 % Allowed : 8.30 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.31 (0.20), residues: 1770 helix: 0.33 (0.15), residues: 1237 sheet: None (None), residues: 0 loop : -1.30 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F2258 TYR 0.013 0.001 TYR F1989 PHE 0.015 0.001 PHE N1037 TRP 0.011 0.001 TRP N 221 HIS 0.007 0.001 HIS N 393 Details of bonding type rmsd covalent geometry : bond 0.00461 (14411) covalent geometry : angle 0.60076 (19533) hydrogen bonds : bond 0.09898 ( 794) hydrogen bonds : angle 5.03477 ( 2322) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2151 LEU cc_start: 0.8760 (mp) cc_final: 0.8535 (mm) REVERT: F 2155 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8111 (mt-10) REVERT: F 2258 ARG cc_start: 0.8464 (mtm110) cc_final: 0.7942 (mtm-85) REVERT: N 119 HIS cc_start: 0.8406 (OUTLIER) cc_final: 0.8140 (t-90) REVERT: N 171 ASN cc_start: 0.8722 (t0) cc_final: 0.8446 (m-40) REVERT: N 274 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7560 (mt) REVERT: N 297 LYS cc_start: 0.7627 (tmtp) cc_final: 0.7298 (tmtt) REVERT: N 372 ASP cc_start: 0.7554 (t0) cc_final: 0.6855 (t70) REVERT: N 442 MET cc_start: 0.8999 (ttp) cc_final: 0.8740 (ttp) REVERT: N 688 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8213 (mt-10) REVERT: N 1023 MET cc_start: 0.9428 (mmm) cc_final: 0.9094 (mmt) REVERT: N 1096 MET cc_start: 0.8022 (mmp) cc_final: 0.7628 (mmt) REVERT: N 1171 LYS cc_start: 0.9073 (tttt) cc_final: 0.8847 (tttm) REVERT: N 1910 SER cc_start: 0.9306 (t) cc_final: 0.9065 (p) outliers start: 10 outliers final: 6 residues processed: 168 average time/residue: 0.2883 time to fit residues: 69.5266 Evaluate side-chains 152 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 2113 THR Chi-restraints excluded: chain F residue 2294 THR Chi-restraints excluded: chain F residue 2432 ASN Chi-restraints excluded: chain N residue 119 HIS Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 591 LEU Chi-restraints excluded: chain N residue 892 SER Chi-restraints excluded: chain N residue 1150 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 175 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 114 optimal weight: 0.0070 chunk 107 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F2673 GLN N 905 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.144582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.108340 restraints weight = 54446.916| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.67 r_work: 0.3038 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14411 Z= 0.124 Angle : 0.501 5.312 19533 Z= 0.268 Chirality : 0.035 0.153 2305 Planarity : 0.004 0.051 2463 Dihedral : 4.795 59.364 1896 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.31 % Allowed : 8.43 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.47 (0.20), residues: 1770 helix: 1.03 (0.15), residues: 1232 sheet: None (None), residues: 0 loop : -1.31 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F2258 TYR 0.014 0.001 TYR N1948 PHE 0.019 0.001 PHE N 343 TRP 0.008 0.001 TRP N 221 HIS 0.008 0.001 HIS N 393 Details of bonding type rmsd covalent geometry : bond 0.00269 (14411) covalent geometry : angle 0.50056 (19533) hydrogen bonds : bond 0.05699 ( 794) hydrogen bonds : angle 4.22206 ( 2322) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2713 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8338 (ttm-80) REVERT: N 76 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7205 (mm-30) REVERT: N 119 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.8146 (t-90) REVERT: N 149 ASN cc_start: 0.8246 (m110) cc_final: 0.7799 (t0) REVERT: N 200 LYS cc_start: 0.8618 (mttt) cc_final: 0.8340 (mttt) REVERT: N 201 PHE cc_start: 0.8689 (t80) cc_final: 0.8212 (t80) REVERT: N 274 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7333 (mt) REVERT: N 297 LYS cc_start: 0.7194 (tmtp) cc_final: 0.6965 (tmtt) REVERT: N 442 MET cc_start: 0.9000 (ttp) cc_final: 0.8717 (ttp) REVERT: N 688 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8078 (mt-10) REVERT: N 1171 LYS cc_start: 0.8922 (tttt) cc_final: 0.8677 (ttpp) outliers start: 21 outliers final: 9 residues processed: 177 average time/residue: 0.2836 time to fit residues: 72.9417 Evaluate side-chains 159 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 2057 ILE Chi-restraints excluded: chain F residue 2294 THR Chi-restraints excluded: chain F residue 2432 ASN Chi-restraints excluded: chain F residue 2713 ARG Chi-restraints excluded: chain N residue 119 HIS Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 394 PHE Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 591 LEU Chi-restraints excluded: chain N residue 1150 SER Chi-restraints excluded: chain N residue 1862 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 144 optimal weight: 0.3980 chunk 99 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F2241 ASN N 905 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.143426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107142 restraints weight = 54827.731| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.87 r_work: 0.3016 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14411 Z= 0.131 Angle : 0.487 5.050 19533 Z= 0.260 Chirality : 0.035 0.152 2305 Planarity : 0.004 0.052 2463 Dihedral : 4.530 58.211 1894 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.55 % Rotamer: Outliers : 0.81 % Allowed : 9.61 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.79 (0.20), residues: 1770 helix: 1.27 (0.15), residues: 1236 sheet: None (None), residues: 0 loop : -1.21 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F2258 TYR 0.010 0.001 TYR N1948 PHE 0.012 0.001 PHE N1907 TRP 0.008 0.001 TRP N 221 HIS 0.007 0.001 HIS N 393 Details of bonding type rmsd covalent geometry : bond 0.00301 (14411) covalent geometry : angle 0.48731 (19533) hydrogen bonds : bond 0.05329 ( 794) hydrogen bonds : angle 4.08273 ( 2322) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2258 ARG cc_start: 0.8276 (mtm110) cc_final: 0.7784 (mtm-85) REVERT: F 2367 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8701 (pp) REVERT: F 2399 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8662 (mmt-90) REVERT: N 119 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.8132 (t-90) REVERT: N 297 LYS cc_start: 0.7185 (tmtp) cc_final: 0.6957 (tmtt) REVERT: N 442 MET cc_start: 0.9002 (ttp) cc_final: 0.8737 (ttp) REVERT: N 1111 MET cc_start: 0.8438 (mmm) cc_final: 0.8225 (mmm) REVERT: N 1171 LYS cc_start: 0.8923 (tttt) cc_final: 0.8677 (tttm) outliers start: 13 outliers final: 8 residues processed: 161 average time/residue: 0.2919 time to fit residues: 67.8594 Evaluate side-chains 152 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 2113 THR Chi-restraints excluded: chain F residue 2203 GLU Chi-restraints excluded: chain F residue 2367 LEU Chi-restraints excluded: chain F residue 2399 ARG Chi-restraints excluded: chain F residue 2432 ASN Chi-restraints excluded: chain N residue 119 HIS Chi-restraints excluded: chain N residue 394 PHE Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 591 LEU Chi-restraints excluded: chain N residue 1150 SER Chi-restraints excluded: chain N residue 1862 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 156 optimal weight: 0.1980 chunk 174 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 158 optimal weight: 0.4980 chunk 1 optimal weight: 0.0270 chunk 152 optimal weight: 1.9990 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 905 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.145771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106330 restraints weight = 54325.931| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.22 r_work: 0.3080 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14411 Z= 0.102 Angle : 0.453 4.484 19533 Z= 0.241 Chirality : 0.034 0.152 2305 Planarity : 0.003 0.052 2463 Dihedral : 4.255 56.016 1893 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.12 % Rotamer: Outliers : 1.25 % Allowed : 9.43 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.24 (0.21), residues: 1770 helix: 1.62 (0.15), residues: 1237 sheet: None (None), residues: 0 loop : -1.08 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F2258 TYR 0.012 0.001 TYR N1948 PHE 0.011 0.001 PHE N 343 TRP 0.006 0.001 TRP N 696 HIS 0.010 0.001 HIS N 393 Details of bonding type rmsd covalent geometry : bond 0.00222 (14411) covalent geometry : angle 0.45335 (19533) hydrogen bonds : bond 0.04446 ( 794) hydrogen bonds : angle 3.82321 ( 2322) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2367 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8711 (pp) REVERT: F 2399 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8655 (mmt-90) REVERT: F 2713 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8334 (ttm-80) REVERT: N 109 LEU cc_start: 0.6898 (mp) cc_final: 0.6697 (mp) REVERT: N 119 HIS cc_start: 0.8474 (OUTLIER) cc_final: 0.8226 (t-90) REVERT: N 297 LYS cc_start: 0.7148 (tmtp) cc_final: 0.6921 (tmtt) REVERT: N 442 MET cc_start: 0.8988 (ttp) cc_final: 0.8732 (ttp) REVERT: N 1066 ARG cc_start: 0.8464 (tpp-160) cc_final: 0.8177 (mmt-90) REVERT: N 1111 MET cc_start: 0.8351 (mmm) cc_final: 0.8118 (mmm) REVERT: N 1171 LYS cc_start: 0.8902 (tttt) cc_final: 0.8660 (tttm) outliers start: 20 outliers final: 13 residues processed: 167 average time/residue: 0.2936 time to fit residues: 70.2341 Evaluate side-chains 154 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 2113 THR Chi-restraints excluded: chain F residue 2151 LEU Chi-restraints excluded: chain F residue 2203 GLU Chi-restraints excluded: chain F residue 2279 LEU Chi-restraints excluded: chain F residue 2367 LEU Chi-restraints excluded: chain F residue 2399 ARG Chi-restraints excluded: chain F residue 2432 ASN Chi-restraints excluded: chain F residue 2713 ARG Chi-restraints excluded: chain N residue 102 MET Chi-restraints excluded: chain N residue 119 HIS Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 394 PHE Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 591 LEU Chi-restraints excluded: chain N residue 748 MET Chi-restraints excluded: chain N residue 1150 SER Chi-restraints excluded: chain N residue 1862 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 72 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 173 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 905 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.144725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108512 restraints weight = 54474.305| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.74 r_work: 0.3037 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14411 Z= 0.123 Angle : 0.464 4.547 19533 Z= 0.247 Chirality : 0.035 0.148 2305 Planarity : 0.004 0.055 2463 Dihedral : 4.234 55.334 1893 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 1.19 % Allowed : 9.86 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.33 (0.21), residues: 1770 helix: 1.69 (0.15), residues: 1237 sheet: None (None), residues: 0 loop : -1.05 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F2258 TYR 0.010 0.001 TYR N1948 PHE 0.011 0.001 PHE N1907 TRP 0.006 0.001 TRP N 221 HIS 0.007 0.001 HIS N 393 Details of bonding type rmsd covalent geometry : bond 0.00287 (14411) covalent geometry : angle 0.46446 (19533) hydrogen bonds : bond 0.04666 ( 794) hydrogen bonds : angle 3.82687 ( 2322) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2367 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8731 (pp) REVERT: F 2399 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8683 (mmt-90) REVERT: F 2713 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8373 (ttm-80) REVERT: N 109 LEU cc_start: 0.6915 (mp) cc_final: 0.6694 (mp) REVERT: N 119 HIS cc_start: 0.8512 (OUTLIER) cc_final: 0.8224 (t-90) REVERT: N 297 LYS cc_start: 0.7220 (tmtp) cc_final: 0.6945 (tmtt) REVERT: N 442 MET cc_start: 0.9002 (ttp) cc_final: 0.8762 (ttp) REVERT: N 1066 ARG cc_start: 0.8488 (tpp-160) cc_final: 0.8206 (mmt-90) REVERT: N 1111 MET cc_start: 0.8409 (mmm) cc_final: 0.8187 (mmm) REVERT: N 1171 LYS cc_start: 0.8902 (tttt) cc_final: 0.8654 (tttm) outliers start: 19 outliers final: 14 residues processed: 153 average time/residue: 0.3211 time to fit residues: 69.1571 Evaluate side-chains 158 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 2113 THR Chi-restraints excluded: chain F residue 2203 GLU Chi-restraints excluded: chain F residue 2243 SER Chi-restraints excluded: chain F residue 2279 LEU Chi-restraints excluded: chain F residue 2367 LEU Chi-restraints excluded: chain F residue 2399 ARG Chi-restraints excluded: chain F residue 2432 ASN Chi-restraints excluded: chain F residue 2713 ARG Chi-restraints excluded: chain N residue 102 MET Chi-restraints excluded: chain N residue 119 HIS Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 394 PHE Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 591 LEU Chi-restraints excluded: chain N residue 748 MET Chi-restraints excluded: chain N residue 1150 SER Chi-restraints excluded: chain N residue 1862 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 21 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 905 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.145396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109266 restraints weight = 53917.754| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.61 r_work: 0.3061 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14411 Z= 0.106 Angle : 0.448 4.584 19533 Z= 0.237 Chirality : 0.034 0.149 2305 Planarity : 0.003 0.053 2463 Dihedral : 4.127 54.556 1893 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 1.06 % Allowed : 9.93 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.53 (0.21), residues: 1770 helix: 1.85 (0.15), residues: 1237 sheet: None (None), residues: 0 loop : -1.00 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F2258 TYR 0.011 0.001 TYR N1948 PHE 0.010 0.001 PHE N1907 TRP 0.006 0.001 TRP N 696 HIS 0.009 0.001 HIS N 393 Details of bonding type rmsd covalent geometry : bond 0.00237 (14411) covalent geometry : angle 0.44841 (19533) hydrogen bonds : bond 0.04299 ( 794) hydrogen bonds : angle 3.72367 ( 2322) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2367 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8709 (pp) REVERT: F 2399 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8682 (mmt-90) REVERT: F 2713 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8361 (ttm-80) REVERT: N 119 HIS cc_start: 0.8376 (OUTLIER) cc_final: 0.8063 (t-90) REVERT: N 297 LYS cc_start: 0.7227 (tmtp) cc_final: 0.6924 (tmtt) REVERT: N 442 MET cc_start: 0.8993 (ttp) cc_final: 0.8751 (ttp) REVERT: N 1066 ARG cc_start: 0.8455 (tpp-160) cc_final: 0.8180 (mmt-90) REVERT: N 1111 MET cc_start: 0.8390 (mmm) cc_final: 0.8174 (mmm) REVERT: N 1171 LYS cc_start: 0.8881 (tttt) cc_final: 0.8638 (tttm) outliers start: 17 outliers final: 12 residues processed: 153 average time/residue: 0.3112 time to fit residues: 67.2532 Evaluate side-chains 153 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 2113 THR Chi-restraints excluded: chain F residue 2203 GLU Chi-restraints excluded: chain F residue 2243 SER Chi-restraints excluded: chain F residue 2279 LEU Chi-restraints excluded: chain F residue 2367 LEU Chi-restraints excluded: chain F residue 2399 ARG Chi-restraints excluded: chain F residue 2432 ASN Chi-restraints excluded: chain F residue 2713 ARG Chi-restraints excluded: chain N residue 102 MET Chi-restraints excluded: chain N residue 119 HIS Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 394 PHE Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 591 LEU Chi-restraints excluded: chain N residue 1150 SER Chi-restraints excluded: chain N residue 1862 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 170 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 905 ASN N 963 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.141770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.104842 restraints weight = 55261.985| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.88 r_work: 0.2972 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14411 Z= 0.210 Angle : 0.533 5.604 19533 Z= 0.284 Chirality : 0.038 0.146 2305 Planarity : 0.004 0.060 2463 Dihedral : 4.419 56.869 1893 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.27 % Rotamer: Outliers : 1.25 % Allowed : 10.17 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.07 (0.20), residues: 1770 helix: 1.48 (0.15), residues: 1236 sheet: None (None), residues: 0 loop : -1.10 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F2258 TYR 0.012 0.002 TYR F2742 PHE 0.021 0.002 PHE N1037 TRP 0.009 0.002 TRP F1997 HIS 0.006 0.001 HIS F2099 Details of bonding type rmsd covalent geometry : bond 0.00509 (14411) covalent geometry : angle 0.53279 (19533) hydrogen bonds : bond 0.05769 ( 794) hydrogen bonds : angle 4.03267 ( 2322) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2399 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8719 (mmt-90) REVERT: F 2713 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8410 (mtm-85) REVERT: N 76 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7173 (mm-30) REVERT: N 109 LEU cc_start: 0.6934 (mp) cc_final: 0.6585 (mp) REVERT: N 119 HIS cc_start: 0.8517 (OUTLIER) cc_final: 0.8199 (t-90) REVERT: N 297 LYS cc_start: 0.7288 (tmtp) cc_final: 0.6980 (tmtt) REVERT: N 442 MET cc_start: 0.9059 (ttp) cc_final: 0.8817 (ttp) REVERT: N 595 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8244 (mp0) REVERT: N 1066 ARG cc_start: 0.8571 (tpp-160) cc_final: 0.8291 (mmt-90) REVERT: N 1171 LYS cc_start: 0.8984 (tttt) cc_final: 0.8728 (tttm) outliers start: 20 outliers final: 14 residues processed: 160 average time/residue: 0.3169 time to fit residues: 71.8009 Evaluate side-chains 157 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 2113 THR Chi-restraints excluded: chain F residue 2203 GLU Chi-restraints excluded: chain F residue 2243 SER Chi-restraints excluded: chain F residue 2279 LEU Chi-restraints excluded: chain F residue 2367 LEU Chi-restraints excluded: chain F residue 2399 ARG Chi-restraints excluded: chain F residue 2432 ASN Chi-restraints excluded: chain F residue 2713 ARG Chi-restraints excluded: chain N residue 102 MET Chi-restraints excluded: chain N residue 119 HIS Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 394 PHE Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 591 LEU Chi-restraints excluded: chain N residue 595 GLU Chi-restraints excluded: chain N residue 1150 SER Chi-restraints excluded: chain N residue 1862 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 144 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 35 optimal weight: 0.0770 chunk 151 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 172 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 95 optimal weight: 4.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 905 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.145274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.109696 restraints weight = 54171.342| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.71 r_work: 0.3050 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14411 Z= 0.099 Angle : 0.453 4.763 19533 Z= 0.239 Chirality : 0.034 0.149 2305 Planarity : 0.004 0.060 2463 Dihedral : 4.137 55.641 1893 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.77 % Favored : 97.18 % Rotamer: Outliers : 1.12 % Allowed : 10.36 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.52 (0.21), residues: 1770 helix: 1.84 (0.15), residues: 1242 sheet: None (None), residues: 0 loop : -1.03 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F2258 TYR 0.012 0.001 TYR N1948 PHE 0.015 0.001 PHE N 154 TRP 0.007 0.001 TRP N 696 HIS 0.007 0.001 HIS N 393 Details of bonding type rmsd covalent geometry : bond 0.00214 (14411) covalent geometry : angle 0.45331 (19533) hydrogen bonds : bond 0.04274 ( 794) hydrogen bonds : angle 3.71516 ( 2322) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 2367 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8719 (pp) REVERT: F 2399 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8781 (mmt-90) REVERT: F 2713 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8366 (ttm-80) REVERT: N 109 LEU cc_start: 0.6875 (mp) cc_final: 0.6500 (mp) REVERT: N 442 MET cc_start: 0.8988 (ttp) cc_final: 0.8729 (ttp) REVERT: N 1066 ARG cc_start: 0.8489 (tpp-160) cc_final: 0.8224 (mmt-90) REVERT: N 1111 MET cc_start: 0.8390 (mmm) cc_final: 0.8184 (mmm) REVERT: N 1171 LYS cc_start: 0.8891 (tttt) cc_final: 0.8649 (tttm) outliers start: 18 outliers final: 13 residues processed: 153 average time/residue: 0.3060 time to fit residues: 66.7297 Evaluate side-chains 150 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 2113 THR Chi-restraints excluded: chain F residue 2203 GLU Chi-restraints excluded: chain F residue 2243 SER Chi-restraints excluded: chain F residue 2279 LEU Chi-restraints excluded: chain F residue 2367 LEU Chi-restraints excluded: chain F residue 2399 ARG Chi-restraints excluded: chain F residue 2432 ASN Chi-restraints excluded: chain F residue 2713 ARG Chi-restraints excluded: chain N residue 102 MET Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 394 PHE Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 591 LEU Chi-restraints excluded: chain N residue 892 SER Chi-restraints excluded: chain N residue 1150 SER Chi-restraints excluded: chain N residue 1862 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 0.0040 chunk 87 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 905 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.145089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108056 restraints weight = 53983.990| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.80 r_work: 0.3017 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14411 Z= 0.110 Angle : 0.456 4.901 19533 Z= 0.240 Chirality : 0.034 0.149 2305 Planarity : 0.004 0.065 2463 Dihedral : 4.010 54.716 1891 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.11 % Favored : 96.84 % Rotamer: Outliers : 1.12 % Allowed : 10.36 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.61 (0.21), residues: 1770 helix: 1.90 (0.15), residues: 1247 sheet: None (None), residues: 0 loop : -1.00 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F2258 TYR 0.010 0.001 TYR N1948 PHE 0.017 0.001 PHE N 154 TRP 0.006 0.001 TRP N 837 HIS 0.007 0.001 HIS N 393 Details of bonding type rmsd covalent geometry : bond 0.00253 (14411) covalent geometry : angle 0.45617 (19533) hydrogen bonds : bond 0.04297 ( 794) hydrogen bonds : angle 3.70079 ( 2322) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 2367 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8704 (pp) REVERT: F 2399 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8784 (mmt-90) REVERT: F 2713 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8342 (mtm-85) REVERT: N 109 LEU cc_start: 0.6871 (mp) cc_final: 0.6497 (mp) REVERT: N 442 MET cc_start: 0.9000 (ttp) cc_final: 0.8756 (ttp) REVERT: N 1066 ARG cc_start: 0.8508 (tpp-160) cc_final: 0.8249 (mmt-90) REVERT: N 1111 MET cc_start: 0.8469 (mmm) cc_final: 0.8265 (mmm) REVERT: N 1171 LYS cc_start: 0.8854 (tttt) cc_final: 0.8614 (tttm) outliers start: 18 outliers final: 13 residues processed: 151 average time/residue: 0.2979 time to fit residues: 64.6068 Evaluate side-chains 153 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 2113 THR Chi-restraints excluded: chain F residue 2203 GLU Chi-restraints excluded: chain F residue 2243 SER Chi-restraints excluded: chain F residue 2279 LEU Chi-restraints excluded: chain F residue 2367 LEU Chi-restraints excluded: chain F residue 2399 ARG Chi-restraints excluded: chain F residue 2713 ARG Chi-restraints excluded: chain N residue 102 MET Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 394 PHE Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 591 LEU Chi-restraints excluded: chain N residue 892 SER Chi-restraints excluded: chain N residue 1150 SER Chi-restraints excluded: chain N residue 1862 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 121 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 905 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.143561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.106777 restraints weight = 54426.772| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.86 r_work: 0.2982 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14411 Z= 0.157 Angle : 0.488 5.143 19533 Z= 0.259 Chirality : 0.036 0.147 2305 Planarity : 0.004 0.066 2463 Dihedral : 4.074 55.869 1889 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 1.25 % Allowed : 10.42 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.42 (0.21), residues: 1770 helix: 1.74 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : -1.02 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F2258 TYR 0.009 0.001 TYR F2742 PHE 0.015 0.001 PHE N 343 TRP 0.007 0.001 TRP F1997 HIS 0.008 0.001 HIS N 393 Details of bonding type rmsd covalent geometry : bond 0.00378 (14411) covalent geometry : angle 0.48764 (19533) hydrogen bonds : bond 0.04937 ( 794) hydrogen bonds : angle 3.82463 ( 2322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7627.43 seconds wall clock time: 129 minutes 30.37 seconds (7770.37 seconds total)