Starting phenix.real_space_refine on Wed Mar 20 19:48:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pgp_13391/03_2024/7pgp_13391.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pgp_13391/03_2024/7pgp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pgp_13391/03_2024/7pgp_13391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pgp_13391/03_2024/7pgp_13391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pgp_13391/03_2024/7pgp_13391.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pgp_13391/03_2024/7pgp_13391.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 Residue "F TYR 2182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 12.66, per 1000 atoms: 0.44 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.35 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 1.91 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: 9.81 Time building geometry restraints manager: 21.32 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: 98.63 - 105.71: 258 105.71 - 112.79: 34608 112.79 - 119.87: 7262 119.87 - 126.95: 9872 126.95 - 134.03: 175 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 1.850 nonbonded pdb=" O THR F1980 " pdb="HD22 ASN F1984 " model vdw 1.563 1.850 nonbonded pdb=" OD1 ASN F2381 " pdb=" H SER F2384 " model vdw 1.581 1.850 nonbonded pdb=" OE1 GLU N 907 " pdb=" H GLU N 907 " model vdw 1.594 1.850 nonbonded pdb=" O ILE N 44 " pdb=" HG SER N 47 " model vdw 1.605 1.850 ... (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 ========== 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.400 Extract box with map and model: 4.260 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 81.500 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.070 ------------------------------------------------------------------------------- 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= 0.333 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (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 TRP 0.008 0.001 TRP N 696 HIS 0.004 0.001 HIS N 393 PHE 0.012 0.001 PHE F2706 TYR 0.012 0.001 TYR F2331 ARG 0.004 0.000 ARG F2247 *********************** 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 fitting. rotamer outliers: 13 poor density : 216 time to evaluate : 2.171 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: 0.8077 (m-40) REVERT: N 206 LYS cc_start: 0.8454 (tttt) cc_final: 0.8117 (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: 0.7755 (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: 0.6755 time to fit residues: 215.9705 Evaluate side-chains 158 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 149 time to evaluate : 2.085 ------------------------------------------------------------------------------- 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 150 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14411 Z= 0.233 Angle : 0.598 5.355 19533 Z= 0.327 Chirality : 0.037 0.153 2305 Planarity : 0.004 0.049 2463 Dihedral : 5.059 58.361 1902 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.16 % Rotamer: Outliers : 0.81 % Allowed : 7.99 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1770 helix: 0.45 (0.15), residues: 1235 sheet: None (None), residues: 0 loop : -1.31 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 221 HIS 0.007 0.001 HIS N 393 PHE 0.015 0.001 PHE N 343 TYR 0.015 0.001 TYR F1989 ARG 0.004 0.000 ARG F2349 *********************** 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 182 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2151 LEU cc_start: 0.8439 (mp) cc_final: 0.8133 (mm) REVERT: F 2258 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7556 (mtm-85) REVERT: F 2280 LYS cc_start: 0.8266 (tptt) cc_final: 0.7442 (mtmm) REVERT: N 171 ASN cc_start: 0.8324 (t0) cc_final: 0.8077 (m-40) REVERT: N 274 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6956 (mt) REVERT: N 297 LYS cc_start: 0.7311 (tmtp) cc_final: 0.6988 (tmtt) REVERT: N 372 ASP cc_start: 0.6930 (t0) cc_final: 0.6373 (t70) REVERT: N 442 MET cc_start: 0.8741 (ttp) cc_final: 0.8395 (ttp) REVERT: N 688 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7106 (mt-10) REVERT: N 707 MET cc_start: 0.8777 (mtp) cc_final: 0.8545 (mtm) REVERT: N 1023 MET cc_start: 0.9103 (mmm) cc_final: 0.8787 (mmm) REVERT: N 1180 MET cc_start: 0.8324 (mtm) cc_final: 0.7948 (mtm) REVERT: N 1910 SER cc_start: 0.8522 (t) cc_final: 0.8234 (p) outliers start: 13 outliers final: 9 residues processed: 180 average time/residue: 0.6279 time to fit residues: 166.9222 Evaluate side-chains 154 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 2.014 ------------------------------------------------------------------------------- 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 F residue 2435 SER Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 564 ASP 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 89 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F2673 GLN N 905 ASN N1054 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14411 Z= 0.239 Angle : 0.516 4.689 19533 Z= 0.278 Chirality : 0.036 0.151 2305 Planarity : 0.004 0.053 2463 Dihedral : 4.815 58.490 1898 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.31 % Allowed : 9.30 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1770 helix: 0.93 (0.15), residues: 1232 sheet: None (None), residues: 0 loop : -1.34 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 221 HIS 0.007 0.001 HIS N 393 PHE 0.015 0.001 PHE N1037 TYR 0.010 0.001 TYR F1989 ARG 0.004 0.000 ARG N 487 *********************** 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 177 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 156 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2399 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8443 (mmt-90) REVERT: F 2713 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7740 (ttm-80) REVERT: N 171 ASN cc_start: 0.8256 (t0) cc_final: 0.8049 (m-40) REVERT: N 297 LYS cc_start: 0.7192 (tmtp) cc_final: 0.6944 (tmtt) REVERT: N 442 MET cc_start: 0.8786 (ttp) cc_final: 0.8444 (ttp) REVERT: N 707 MET cc_start: 0.8753 (mtp) cc_final: 0.8533 (mtm) REVERT: N 1023 MET cc_start: 0.9120 (mmm) cc_final: 0.8850 (mmm) REVERT: N 1910 SER cc_start: 0.8550 (t) cc_final: 0.8263 (p) outliers start: 21 outliers final: 16 residues processed: 172 average time/residue: 0.6009 time to fit residues: 151.0644 Evaluate side-chains 166 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1981 MET Chi-restraints excluded: chain F residue 2077 ASP Chi-restraints excluded: chain F residue 2113 THR Chi-restraints excluded: chain F residue 2119 ARG Chi-restraints excluded: chain F residue 2203 GLU Chi-restraints excluded: chain F residue 2279 LEU Chi-restraints excluded: chain F residue 2294 THR Chi-restraints excluded: chain F residue 2399 ARG Chi-restraints excluded: chain F residue 2432 ASN Chi-restraints excluded: chain F residue 2435 SER Chi-restraints excluded: chain F residue 2713 ARG Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 591 LEU Chi-restraints excluded: chain N residue 718 ASP 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 159 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 172 optimal weight: 0.0870 chunk 154 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 905 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2992 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= 0.172 Angle : 0.485 6.472 19533 Z= 0.257 Chirality : 0.035 0.152 2305 Planarity : 0.004 0.053 2463 Dihedral : 4.496 58.203 1895 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.28 % Favored : 96.67 % Rotamer: Outliers : 1.44 % Allowed : 9.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 1770 helix: 1.27 (0.15), residues: 1234 sheet: None (None), residues: 0 loop : -1.26 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 221 HIS 0.007 0.001 HIS N 393 PHE 0.012 0.001 PHE N 343 TYR 0.011 0.001 TYR N1948 ARG 0.006 0.000 ARG F2258 *********************** 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 178 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 155 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2258 ARG cc_start: 0.7692 (mtm110) cc_final: 0.7328 (mtm-85) REVERT: F 2367 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8628 (pp) REVERT: F 2713 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7750 (ttm-80) REVERT: N 109 LEU cc_start: 0.7417 (mp) cc_final: 0.7011 (mp) REVERT: N 171 ASN cc_start: 0.8334 (t0) cc_final: 0.8076 (m-40) REVERT: N 442 MET cc_start: 0.8775 (ttp) cc_final: 0.8460 (ttp) REVERT: N 707 MET cc_start: 0.8728 (mtp) cc_final: 0.8523 (mtm) REVERT: N 1023 MET cc_start: 0.9133 (mmm) cc_final: 0.8898 (mmm) REVERT: N 1111 MET cc_start: 0.7991 (mmm) cc_final: 0.7758 (mmm) REVERT: N 1910 SER cc_start: 0.8524 (t) cc_final: 0.8262 (p) outliers start: 23 outliers final: 15 residues processed: 170 average time/residue: 0.6111 time to fit residues: 152.4252 Evaluate side-chains 163 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 2113 THR Chi-restraints excluded: chain F residue 2119 ARG 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 2294 THR Chi-restraints excluded: chain F residue 2367 LEU Chi-restraints excluded: chain F residue 2432 ASN Chi-restraints excluded: chain F residue 2435 SER Chi-restraints excluded: chain F residue 2713 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 128 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F2241 ASN F2673 GLN ** N 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 ASN N 905 ASN N 963 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14411 Z= 0.269 Angle : 0.508 5.377 19533 Z= 0.272 Chirality : 0.037 0.150 2305 Planarity : 0.004 0.055 2463 Dihedral : 4.565 56.843 1893 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.07 % Favored : 95.88 % Rotamer: Outliers : 1.69 % Allowed : 10.24 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.20), residues: 1770 helix: 1.23 (0.15), residues: 1239 sheet: None (None), residues: 0 loop : -1.30 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 221 HIS 0.011 0.001 HIS N 393 PHE 0.016 0.001 PHE N1037 TYR 0.010 0.001 TYR F2084 ARG 0.003 0.000 ARG F2258 *********************** 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 174 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 147 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2367 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8680 (pp) REVERT: F 2399 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8591 (mmt-90) REVERT: F 2713 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7753 (mtm-85) REVERT: N 81 LEU cc_start: 0.8675 (tp) cc_final: 0.8444 (mt) REVERT: N 109 LEU cc_start: 0.7351 (mp) cc_final: 0.7037 (mp) REVERT: N 171 ASN cc_start: 0.8358 (t0) cc_final: 0.8088 (m-40) REVERT: N 442 MET cc_start: 0.8787 (ttp) cc_final: 0.8477 (ttp) REVERT: N 707 MET cc_start: 0.8747 (mtp) cc_final: 0.8519 (mtm) REVERT: N 718 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7633 (m-30) REVERT: N 1023 MET cc_start: 0.9120 (mmm) cc_final: 0.8867 (mmm) REVERT: N 1111 MET cc_start: 0.8000 (mmm) cc_final: 0.7756 (mmm) REVERT: N 1910 SER cc_start: 0.8538 (t) cc_final: 0.8258 (p) outliers start: 27 outliers final: 22 residues processed: 168 average time/residue: 0.6232 time to fit residues: 153.2369 Evaluate side-chains 170 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 2061 THR Chi-restraints excluded: chain F residue 2077 ASP Chi-restraints excluded: chain F residue 2113 THR Chi-restraints excluded: chain F residue 2119 ARG 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 2294 THR 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 2435 SER Chi-restraints excluded: chain F residue 2713 ARG Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 275 ILE Chi-restraints excluded: chain N residue 372 ASP Chi-restraints excluded: chain N residue 394 PHE Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 564 ASP Chi-restraints excluded: chain N residue 591 LEU Chi-restraints excluded: chain N residue 718 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F2673 GLN ** N 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 905 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14411 Z= 0.191 Angle : 0.472 4.672 19533 Z= 0.251 Chirality : 0.035 0.151 2305 Planarity : 0.004 0.058 2463 Dihedral : 4.420 57.140 1893 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.55 % Rotamer: Outliers : 1.75 % Allowed : 10.05 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.21), residues: 1770 helix: 1.44 (0.15), residues: 1239 sheet: None (None), residues: 0 loop : -1.21 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 837 HIS 0.008 0.001 HIS N 393 PHE 0.012 0.001 PHE N1037 TYR 0.010 0.001 TYR N1948 ARG 0.006 0.000 ARG F2258 *********************** 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 177 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2367 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8688 (pp) REVERT: F 2399 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8585 (mmt-90) REVERT: F 2713 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7764 (ttm-80) REVERT: N 81 LEU cc_start: 0.8644 (tp) cc_final: 0.8439 (mt) REVERT: N 442 MET cc_start: 0.8781 (ttp) cc_final: 0.8475 (ttp) REVERT: N 1023 MET cc_start: 0.9126 (mmm) cc_final: 0.8892 (mmm) REVERT: N 1066 ARG cc_start: 0.8166 (tpp-160) cc_final: 0.7865 (mmt-90) REVERT: N 1111 MET cc_start: 0.7989 (mmm) cc_final: 0.7752 (mmm) REVERT: N 1910 SER cc_start: 0.8515 (t) cc_final: 0.8260 (p) outliers start: 28 outliers final: 22 residues processed: 170 average time/residue: 0.6314 time to fit residues: 156.4252 Evaluate side-chains 170 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 2061 THR Chi-restraints excluded: chain F residue 2077 ASP Chi-restraints excluded: chain F residue 2113 THR Chi-restraints excluded: chain F residue 2119 ARG 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 2294 THR 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 2435 SER Chi-restraints excluded: chain F residue 2713 ARG Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 149 ASN Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 372 ASP Chi-restraints excluded: chain N residue 394 PHE Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 591 LEU Chi-restraints excluded: chain N residue 718 ASP 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 19 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 905 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14411 Z= 0.252 Angle : 0.495 4.963 19533 Z= 0.263 Chirality : 0.036 0.149 2305 Planarity : 0.004 0.056 2463 Dihedral : 4.464 56.269 1893 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.01 % Favored : 95.93 % Rotamer: Outliers : 2.00 % Allowed : 10.30 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.20), residues: 1770 helix: 1.44 (0.15), residues: 1234 sheet: None (None), residues: 0 loop : -1.15 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 837 HIS 0.007 0.001 HIS N 393 PHE 0.014 0.001 PHE N1037 TYR 0.009 0.001 TYR F2084 ARG 0.007 0.000 ARG F2258 *********************** 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 175 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2367 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8712 (pp) REVERT: F 2399 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8612 (mmt-90) REVERT: F 2713 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7748 (mtm-85) REVERT: N 442 MET cc_start: 0.8788 (ttp) cc_final: 0.8483 (ttp) REVERT: N 595 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: N 1023 MET cc_start: 0.9132 (mmm) cc_final: 0.8892 (mmm) REVERT: N 1066 ARG cc_start: 0.8184 (tpp-160) cc_final: 0.7884 (mmt-90) REVERT: N 1111 MET cc_start: 0.7989 (mmm) cc_final: 0.7758 (mmm) REVERT: N 1910 SER cc_start: 0.8524 (t) cc_final: 0.8255 (p) outliers start: 32 outliers final: 23 residues processed: 168 average time/residue: 0.6277 time to fit residues: 152.8417 Evaluate side-chains 168 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 2061 THR Chi-restraints excluded: chain F residue 2077 ASP Chi-restraints excluded: chain F residue 2119 ARG 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 2294 THR 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 2435 SER Chi-restraints excluded: chain F residue 2713 ARG Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain N residue 372 ASP Chi-restraints excluded: chain N residue 394 PHE Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 564 ASP Chi-restraints excluded: chain N residue 591 LEU Chi-restraints excluded: chain N residue 595 GLU Chi-restraints excluded: chain N residue 718 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 134 optimal weight: 0.5980 chunk 156 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 905 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14411 Z= 0.190 Angle : 0.469 4.751 19533 Z= 0.248 Chirality : 0.035 0.152 2305 Planarity : 0.004 0.058 2463 Dihedral : 4.285 56.266 1892 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 1.69 % Allowed : 10.36 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.21), residues: 1770 helix: 1.65 (0.15), residues: 1234 sheet: None (None), residues: 0 loop : -1.08 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 837 HIS 0.009 0.001 HIS N 393 PHE 0.015 0.001 PHE N 343 TYR 0.010 0.001 TYR N1948 ARG 0.009 0.000 ARG F2258 *********************** 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 175 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 2367 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8694 (pp) REVERT: F 2399 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8612 (mmt-90) REVERT: F 2713 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7752 (mtm-85) REVERT: N 442 MET cc_start: 0.8779 (ttp) cc_final: 0.8478 (ttp) REVERT: N 707 MET cc_start: 0.8778 (mtp) cc_final: 0.8507 (mtm) REVERT: N 1023 MET cc_start: 0.9131 (mmm) cc_final: 0.8905 (mmm) REVERT: N 1066 ARG cc_start: 0.8170 (tpp-160) cc_final: 0.7876 (mmt-90) REVERT: N 1111 MET cc_start: 0.7980 (mmm) cc_final: 0.7748 (mmm) REVERT: N 1910 SER cc_start: 0.8501 (t) cc_final: 0.8255 (p) outliers start: 27 outliers final: 21 residues processed: 171 average time/residue: 0.6437 time to fit residues: 159.5864 Evaluate side-chains 167 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 2058 ILE Chi-restraints excluded: chain F residue 2061 THR Chi-restraints excluded: chain F residue 2077 ASP Chi-restraints excluded: chain F residue 2119 ARG Chi-restraints excluded: chain F residue 2243 SER Chi-restraints excluded: chain F residue 2279 LEU Chi-restraints excluded: chain F residue 2294 THR 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 2435 SER Chi-restraints excluded: chain F residue 2713 ARG Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain N residue 372 ASP Chi-restraints excluded: chain N residue 394 PHE Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 591 LEU Chi-restraints excluded: chain N residue 718 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 151 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 905 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14411 Z= 0.257 Angle : 0.495 4.667 19533 Z= 0.263 Chirality : 0.036 0.149 2305 Planarity : 0.004 0.061 2463 Dihedral : 4.350 55.805 1892 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.24 % Favored : 95.71 % Rotamer: Outliers : 1.75 % Allowed : 10.67 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.21), residues: 1770 helix: 1.58 (0.15), residues: 1232 sheet: None (None), residues: 0 loop : -1.10 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 837 HIS 0.008 0.001 HIS N 393 PHE 0.016 0.001 PHE N 154 TYR 0.009 0.001 TYR F2742 ARG 0.011 0.000 ARG F2258 *********************** 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 173 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2367 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8721 (pp) REVERT: F 2399 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8640 (mmt-90) REVERT: F 2713 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7748 (mtm-85) REVERT: N 442 MET cc_start: 0.8825 (ttp) cc_final: 0.8520 (ttp) REVERT: N 707 MET cc_start: 0.8788 (mtp) cc_final: 0.8519 (mtm) REVERT: N 718 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7660 (m-30) REVERT: N 1023 MET cc_start: 0.9130 (mmm) cc_final: 0.8887 (mmm) REVERT: N 1066 ARG cc_start: 0.8199 (tpp-160) cc_final: 0.7900 (mmt-90) REVERT: N 1111 MET cc_start: 0.7984 (mmm) cc_final: 0.7759 (mmm) REVERT: N 1910 SER cc_start: 0.8512 (t) cc_final: 0.8248 (p) outliers start: 28 outliers final: 23 residues processed: 167 average time/residue: 0.6484 time to fit residues: 156.9478 Evaluate side-chains 167 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 2058 ILE Chi-restraints excluded: chain F residue 2061 THR Chi-restraints excluded: chain F residue 2077 ASP Chi-restraints excluded: chain F residue 2119 ARG 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 2294 THR 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 2435 SER Chi-restraints excluded: chain F residue 2713 ARG Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 149 ASN Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain N residue 372 ASP Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 564 ASP Chi-restraints excluded: chain N residue 591 LEU Chi-restraints excluded: chain N residue 718 ASP 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 103 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 905 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14411 Z= 0.297 Angle : 0.515 4.695 19533 Z= 0.274 Chirality : 0.037 0.148 2305 Planarity : 0.004 0.066 2463 Dihedral : 4.426 56.432 1892 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.90 % Favored : 96.05 % Rotamer: Outliers : 1.75 % Allowed : 10.80 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1770 helix: 1.46 (0.15), residues: 1233 sheet: None (None), residues: 0 loop : -1.08 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 837 HIS 0.008 0.001 HIS N 393 PHE 0.017 0.002 PHE N 154 TYR 0.010 0.001 TYR F2240 ARG 0.011 0.000 ARG F2258 ********************** 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 173 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 2.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2367 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8726 (pp) REVERT: F 2399 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8559 (mmt-90) REVERT: F 2713 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7749 (mtm-85) REVERT: N 442 MET cc_start: 0.8829 (ttp) cc_final: 0.8522 (ttp) REVERT: N 707 MET cc_start: 0.8789 (mtp) cc_final: 0.8520 (mtm) REVERT: N 718 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7765 (m-30) REVERT: N 1023 MET cc_start: 0.9119 (mmm) cc_final: 0.8860 (mmm) REVERT: N 1910 SER cc_start: 0.8514 (t) cc_final: 0.8246 (p) outliers start: 28 outliers final: 23 residues processed: 169 average time/residue: 0.7011 time to fit residues: 172.5925 Evaluate side-chains 167 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 2058 ILE Chi-restraints excluded: chain F residue 2061 THR Chi-restraints excluded: chain F residue 2077 ASP Chi-restraints excluded: chain F residue 2119 ARG 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 2294 THR 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 2435 SER Chi-restraints excluded: chain F residue 2713 ARG Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 149 ASN Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 372 ASP Chi-restraints excluded: chain N residue 394 PHE Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 564 ASP Chi-restraints excluded: chain N residue 591 LEU Chi-restraints excluded: chain N residue 718 ASP 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 43 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.143476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.106622 restraints weight = 54713.883| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.87 r_work: 0.3020 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14411 Z= 0.183 Angle : 0.476 4.728 19533 Z= 0.252 Chirality : 0.035 0.151 2305 Planarity : 0.004 0.065 2463 Dihedral : 4.286 56.714 1892 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.50 % Favored : 96.44 % Rotamer: Outliers : 1.75 % Allowed : 10.99 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.21), residues: 1770 helix: 1.69 (0.15), residues: 1232 sheet: None (None), residues: 0 loop : -0.99 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 696 HIS 0.008 0.001 HIS N 393 PHE 0.016 0.001 PHE N 154 TYR 0.010 0.001 TYR N1948 ARG 0.010 0.000 ARG F2258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5778.62 seconds wall clock time: 102 minutes 54.85 seconds (6174.85 seconds total)