Starting phenix.real_space_refine on Tue Jul 23 03:39:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rf9_19116/07_2024/8rf9_19116.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rf9_19116/07_2024/8rf9_19116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rf9_19116/07_2024/8rf9_19116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rf9_19116/07_2024/8rf9_19116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rf9_19116/07_2024/8rf9_19116.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rf9_19116/07_2024/8rf9_19116.cif" } resolution = 3.28 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= 0.001 sd= 0.109 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 13032 2.51 5 N 3694 2.21 5 O 3851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 723": "OE1" <-> "OE2" Residue "A GLU 755": "OE1" <-> "OE2" Residue "A TYR 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 778": "OD1" <-> "OD2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1029": "OE1" <-> "OE2" Residue "A GLU 1228": "OE1" <-> "OE2" Residue "A GLU 1291": "OE1" <-> "OE2" Residue "A TYR 1398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1651": "OE1" <-> "OE2" Residue "A GLU 1748": "OE1" <-> "OE2" Residue "A PHE 1803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1812": "OE1" <-> "OE2" Residue "A PHE 1898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2175": "OE1" <-> "OE2" Residue "A ASP 2236": "OD1" <-> "OD2" Residue "A PHE 2309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2667": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 20646 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 20646 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2642, 20624 Classifications: {'peptide': 2642} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 81} Link IDs: {'PTRANS': 110, 'TRANS': 2531} Chain breaks: 5 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 164 Conformer: "B" Number of residues, atoms: 2642, 20624 Classifications: {'peptide': 2642} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 81} Link IDs: {'PTRANS': 110, 'TRANS': 2531} Chain breaks: 5 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 164 bond proxies already assigned to first conformer: 21068 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 194 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG A 194 " occ=0.40 residue: pdb=" N AARG A1355 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A1355 " occ=0.50 Time building chain proxies: 21.27, per 1000 atoms: 1.03 Number of scatterers: 20646 At special positions: 0 Unit cell: (99.9336, 120.433, 194.742, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 3851 8.00 N 3694 7.00 C 13032 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 7.77 Conformation dependent library (CDL) restraints added in 7.0 seconds 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4926 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 20 sheets defined 47.5% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'A' and resid 34 through 46 Processing helix chain 'A' and resid 57 through 79 removed outlier: 3.533A pdb=" N ARG A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N THR A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 96 removed outlier: 3.611A pdb=" N TRP A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 112 through 119 removed outlier: 3.686A pdb=" N GLN A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 4.363A pdb=" N GLY A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 142 removed outlier: 3.573A pdb=" N ALA A 134 " --> pdb=" O PRO A 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 168 through 212 Proline residue: A 174 - end of helix removed outlier: 3.513A pdb=" N ARG A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN A 200 " --> pdb=" O ARG A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 225 removed outlier: 3.543A pdb=" N ALA A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 4.064A pdb=" N ASP A 230 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A 231 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.968A pdb=" N GLN A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 removed outlier: 3.580A pdb=" N TRP A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLU A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 268 through 276 removed outlier: 3.526A pdb=" N GLU A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 298 removed outlier: 3.507A pdb=" N VAL A 289 " --> pdb=" O MET A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 308 Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.624A pdb=" N LYS A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 removed outlier: 4.575A pdb=" N GLU A 321 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 323 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 341 removed outlier: 3.707A pdb=" N ARG A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 359 Processing helix chain 'A' and resid 373 through 378 removed outlier: 3.581A pdb=" N LEU A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 390 Processing helix chain 'A' and resid 394 through 407 Processing helix chain 'A' and resid 408 through 431 Proline residue: A 414 - end of helix Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 439 through 467 removed outlier: 4.167A pdb=" N LEU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Proline residue: A 450 - end of helix Processing helix chain 'A' and resid 499 through 515 removed outlier: 3.755A pdb=" N ASN A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 557 Processing helix chain 'A' and resid 587 through 599 removed outlier: 3.797A pdb=" N LEU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 643 removed outlier: 3.538A pdb=" N LEU A 637 " --> pdb=" O ALA A 633 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A 639 " --> pdb=" O THR A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 686 removed outlier: 3.603A pdb=" N VAL A 684 " --> pdb=" O VAL A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 707 Processing helix chain 'A' and resid 719 through 730 removed outlier: 4.030A pdb=" N ARG A 729 " --> pdb=" O ALA A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 746 removed outlier: 4.184A pdb=" N LEU A 741 " --> pdb=" O SER A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 782 removed outlier: 3.502A pdb=" N SER A 769 " --> pdb=" O GLU A 765 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP A 774 " --> pdb=" O ARG A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 787 removed outlier: 3.725A pdb=" N ILE A 786 " --> pdb=" O LEU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 821 Proline residue: A 810 - end of helix Processing helix chain 'A' and resid 828 through 850 removed outlier: 3.596A pdb=" N LEU A 840 " --> pdb=" O LEU A 836 " (cutoff:3.500A) Proline residue: A 844 - end of helix removed outlier: 4.857A pdb=" N SER A 847 " --> pdb=" O ALA A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 907 removed outlier: 4.015A pdb=" N GLU A 871 " --> pdb=" O THR A 867 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ALA A 887 " --> pdb=" O ILE A 883 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP A 888 " --> pdb=" O VAL A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 927 through 935 Processing helix chain 'A' and resid 937 through 951 removed outlier: 4.229A pdb=" N LEU A 951 " --> pdb=" O LEU A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 969 removed outlier: 3.665A pdb=" N GLY A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Proline residue: A 962 - end of helix Processing helix chain 'A' and resid 969 through 978 removed outlier: 3.941A pdb=" N VAL A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1005 removed outlier: 3.593A pdb=" N GLU A 996 " --> pdb=" O HIS A 992 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A1000 " --> pdb=" O GLU A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1012 removed outlier: 3.589A pdb=" N VAL A1012 " --> pdb=" O TYR A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1055 removed outlier: 3.697A pdb=" N ILE A1049 " --> pdb=" O LEU A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1076 removed outlier: 3.518A pdb=" N THR A1062 " --> pdb=" O SER A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1125 removed outlier: 4.284A pdb=" N ALA A1125 " --> pdb=" O ASP A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1149 removed outlier: 3.579A pdb=" N ALA A1141 " --> pdb=" O ILE A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1182 Processing helix chain 'A' and resid 1187 through 1211 removed outlier: 4.009A pdb=" N ILE A1191 " --> pdb=" O SER A1187 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A1210 " --> pdb=" O ASN A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1238 removed outlier: 3.555A pdb=" N ALA A1217 " --> pdb=" O SER A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1264 removed outlier: 3.740A pdb=" N LEU A1261 " --> pdb=" O ARG A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1271 Processing helix chain 'A' and resid 1300 through 1312 Processing helix chain 'A' and resid 1316 through 1322 removed outlier: 4.068A pdb=" N TYR A1320 " --> pdb=" O THR A1316 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A1322 " --> pdb=" O HIS A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1351 Processing helix chain 'A' and resid 1358 through 1379 removed outlier: 3.672A pdb=" N GLN A1362 " --> pdb=" O GLY A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1409 Processing helix chain 'A' and resid 1413 through 1417 removed outlier: 4.033A pdb=" N GLN A1416 " --> pdb=" O GLY A1413 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN A1417 " --> pdb=" O LEU A1414 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1413 through 1417' Processing helix chain 'A' and resid 1421 through 1429 removed outlier: 3.706A pdb=" N SER A1425 " --> pdb=" O ALA A1421 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1446 Processing helix chain 'A' and resid 1479 through 1494 Processing helix chain 'A' and resid 1496 through 1503 removed outlier: 3.604A pdb=" N PHE A1502 " --> pdb=" O LEU A1498 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1512 Processing helix chain 'A' and resid 1513 through 1515 No H-bonds generated for 'chain 'A' and resid 1513 through 1515' Processing helix chain 'A' and resid 1696 through 1701 Processing helix chain 'A' and resid 1810 through 1822 removed outlier: 3.908A pdb=" N LYS A1816 " --> pdb=" O GLU A1812 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG A1820 " --> pdb=" O LYS A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1830 through 1845 removed outlier: 3.699A pdb=" N TRP A1835 " --> pdb=" O LEU A1831 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET A1842 " --> pdb=" O THR A1838 " (cutoff:3.500A) Processing helix chain 'A' and resid 1848 through 1864 removed outlier: 3.625A pdb=" N ALA A1854 " --> pdb=" O GLN A1850 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A1861 " --> pdb=" O HIS A1857 " (cutoff:3.500A) Processing helix chain 'A' and resid 1909 through 1924 Processing helix chain 'A' and resid 1937 through 1957 removed outlier: 4.599A pdb=" N GLN A1942 " --> pdb=" O ALA A1938 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ASP A1943 " --> pdb=" O SER A1939 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS A1950 " --> pdb=" O HIS A1946 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE A1951 " --> pdb=" O ALA A1947 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A1954 " --> pdb=" O HIS A1950 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLN A1955 " --> pdb=" O ILE A1951 " (cutoff:3.500A) Processing helix chain 'A' and resid 1977 through 1988 removed outlier: 3.547A pdb=" N ALA A1986 " --> pdb=" O SER A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2010 removed outlier: 4.046A pdb=" N VAL A2007 " --> pdb=" O ILE A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2139 Processing helix chain 'A' and resid 2212 through 2216 removed outlier: 3.891A pdb=" N ILE A2216 " --> pdb=" O ALA A2213 " (cutoff:3.500A) Processing helix chain 'A' and resid 2256 through 2261 Processing helix chain 'A' and resid 2316 through 2330 removed outlier: 3.731A pdb=" N ALA A2320 " --> pdb=" O ASN A2316 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A2321 " --> pdb=" O ALA A2317 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN A2329 " --> pdb=" O LYS A2325 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A2330 " --> pdb=" O ASP A2326 " (cutoff:3.500A) Processing helix chain 'A' and resid 2332 through 2348 removed outlier: 3.673A pdb=" N THR A2347 " --> pdb=" O TRP A2343 " (cutoff:3.500A) Processing helix chain 'A' and resid 2359 through 2364 Processing helix chain 'A' and resid 2365 through 2374 removed outlier: 3.527A pdb=" N TYR A2369 " --> pdb=" O ASN A2365 " (cutoff:3.500A) Processing helix chain 'A' and resid 2391 through 2398 removed outlier: 3.547A pdb=" N LEU A2395 " --> pdb=" O PHE A2391 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A2396 " --> pdb=" O ARG A2392 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP A2397 " --> pdb=" O ASP A2393 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A2398 " --> pdb=" O GLN A2394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2391 through 2398' Processing helix chain 'A' and resid 2399 through 2401 No H-bonds generated for 'chain 'A' and resid 2399 through 2401' Processing helix chain 'A' and resid 2407 through 2417 Processing helix chain 'A' and resid 2418 through 2420 No H-bonds generated for 'chain 'A' and resid 2418 through 2420' Processing helix chain 'A' and resid 2444 through 2461 removed outlier: 4.030A pdb=" N LEU A2449 " --> pdb=" O ASP A2445 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA A2450 " --> pdb=" O VAL A2446 " (cutoff:3.500A) Processing helix chain 'A' and resid 2462 through 2467 Processing helix chain 'A' and resid 2497 through 2512 Processing helix chain 'A' and resid 2542 through 2563 removed outlier: 3.909A pdb=" N ASP A2554 " --> pdb=" O GLY A2550 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A2555 " --> pdb=" O ALA A2551 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A2556 " --> pdb=" O LEU A2552 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU A2557 " --> pdb=" O ARG A2553 " (cutoff:3.500A) Processing helix chain 'A' and resid 2564 through 2586 removed outlier: 3.584A pdb=" N GLY A2569 " --> pdb=" O THR A2565 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS A2570 " --> pdb=" O ASP A2566 " (cutoff:3.500A) Processing helix chain 'A' and resid 2614 through 2624 removed outlier: 3.759A pdb=" N GLN A2618 " --> pdb=" O ASP A2614 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A2621 " --> pdb=" O GLY A2617 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL A2622 " --> pdb=" O GLN A2618 " (cutoff:3.500A) Processing helix chain 'A' and resid 2628 through 2640 Processing helix chain 'A' and resid 2666 through 2671 removed outlier: 3.888A pdb=" N LYS A2669 " --> pdb=" O GLY A2666 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 565 through 569 removed outlier: 8.786A pdb=" N TYR A 566 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE A 522 " --> pdb=" O TYR A 566 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU A 568 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU A 524 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N THR A 487 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER A 523 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL A 489 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL A 525 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU A 488 " --> pdb=" O MET A 621 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG A 667 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASP A 753 " --> pdb=" O ARG A 667 " (cutoff:3.500A) removed outlier: 10.500A pdb=" N THR A 669 " --> pdb=" O ASP A 753 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N GLU A 755 " --> pdb=" O THR A 669 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1023 through 1025 removed outlier: 3.617A pdb=" N TYR A1477 " --> pdb=" O PHE A1024 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1035 through 1036 Processing sheet with id=AA4, first strand: chain 'A' and resid 1099 through 1101 removed outlier: 3.559A pdb=" N GLU A1288 " --> pdb=" O ARG A1283 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1278 through 1279 removed outlier: 4.460A pdb=" N LEU A1278 " --> pdb=" O TYR A1294 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1326 through 1328 Processing sheet with id=AA7, first strand: chain 'A' and resid 1387 through 1388 removed outlier: 3.995A pdb=" N THR A1401 " --> pdb=" O ALA A1387 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1419 through 1420 removed outlier: 4.404A pdb=" N ALA A1457 " --> pdb=" O VAL A1474 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1449 through 1450 removed outlier: 3.706A pdb=" N GLY A1453 " --> pdb=" O GLY A1450 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1549 through 1550 removed outlier: 3.507A pdb=" N PHE A1803 " --> pdb=" O ARG A1663 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1549 through 1550 removed outlier: 3.507A pdb=" N PHE A1803 " --> pdb=" O ARG A1663 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER A1800 " --> pdb=" O ASN A1738 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A1738 " --> pdb=" O SER A1800 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1561 through 1564 removed outlier: 6.823A pdb=" N SER A1580 " --> pdb=" O ILE A1587 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLN A1585 " --> pdb=" O ALA A1688 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ALA A1688 " --> pdb=" O GLN A1585 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A1587 " --> pdb=" O VAL A1686 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1613 through 1615 removed outlier: 3.865A pdb=" N LEU A1787 " --> pdb=" O SER A1681 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1901 through 1902 removed outlier: 6.128A pdb=" N LEU A1930 " --> pdb=" O PHE A1969 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL A1971 " --> pdb=" O LEU A1930 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE A1932 " --> pdb=" O VAL A1971 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2051 through 2053 removed outlier: 3.514A pdb=" N TYR A2060 " --> pdb=" O HIS A2150 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A2185 " --> pdb=" O ARG A2305 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A2226 " --> pdb=" O ASP A2221 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2076 through 2079 removed outlier: 3.582A pdb=" N GLY A2084 " --> pdb=" O TRP A2096 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2119 through 2122 Processing sheet with id=AB9, first strand: chain 'A' and resid 2389 through 2390 removed outlier: 6.652A pdb=" N GLN A2427 " --> pdb=" O THR A2440 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR A2440 " --> pdb=" O GLN A2427 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TRP A2429 " --> pdb=" O VAL A2438 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2470 through 2474 removed outlier: 6.477A pdb=" N ILE A2470 " --> pdb=" O ARG A2494 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG A2494 " --> pdb=" O ILE A2470 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE A2472 " --> pdb=" O SER A2492 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2540 through 2541 removed outlier: 3.571A pdb=" N GLY A2595 " --> pdb=" O LEU A2603 " (cutoff:3.500A) 978 hydrogen bonds defined for protein. 2803 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: 12.90 Time building geometry restraints manager: 8.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7011 1.34 - 1.46: 4824 1.46 - 1.58: 9156 1.58 - 1.70: 1 1.70 - 1.82: 124 Bond restraints: 21116 Sorted by residual: bond pdb=" N GLU A1228 " pdb=" CA GLU A1228 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.40e+00 bond pdb=" CB PRO A1960 " pdb=" CG PRO A1960 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.21e+00 bond pdb=" N ASN A1996 " pdb=" CA ASN A1996 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.33e-02 5.65e+03 3.90e+00 bond pdb=" N ASP A1866 " pdb=" CA ASP A1866 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.25e+00 bond pdb=" C ALA A 843 " pdb=" N PRO A 844 " ideal model delta sigma weight residual 1.336 1.352 -0.016 9.80e-03 1.04e+04 2.71e+00 ... (remaining 21111 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.58: 393 105.58 - 112.72: 11049 112.72 - 119.86: 7118 119.86 - 127.00: 9818 127.00 - 134.14: 305 Bond angle restraints: 28683 Sorted by residual: angle pdb=" N PRO A2030 " pdb=" CA PRO A2030 " pdb=" CB PRO A2030 " ideal model delta sigma weight residual 102.81 110.12 -7.31 6.70e-01 2.23e+00 1.19e+02 angle pdb=" N PRO A2033 " pdb=" CA PRO A2033 " pdb=" CB PRO A2033 " ideal model delta sigma weight residual 103.36 110.33 -6.97 8.30e-01 1.45e+00 7.06e+01 angle pdb=" N PRO A2028 " pdb=" CA PRO A2028 " pdb=" CB PRO A2028 " ideal model delta sigma weight residual 103.25 111.26 -8.01 1.05e+00 9.07e-01 5.82e+01 angle pdb=" N PRO A1525 " pdb=" CA PRO A1525 " pdb=" CB PRO A1525 " ideal model delta sigma weight residual 103.31 109.99 -6.68 8.90e-01 1.26e+00 5.63e+01 angle pdb=" N PRO A2037 " pdb=" CA PRO A2037 " pdb=" CB PRO A2037 " ideal model delta sigma weight residual 103.25 110.88 -7.63 1.05e+00 9.07e-01 5.29e+01 ... (remaining 28678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 11280 17.96 - 35.93: 1025 35.93 - 53.89: 181 53.89 - 71.85: 26 71.85 - 89.82: 18 Dihedral angle restraints: 12530 sinusoidal: 4887 harmonic: 7643 Sorted by residual: dihedral pdb=" CA VAL A 253 " pdb=" C VAL A 253 " pdb=" N ALA A 254 " pdb=" CA ALA A 254 " ideal model delta harmonic sigma weight residual 180.00 144.10 35.90 0 5.00e+00 4.00e-02 5.16e+01 dihedral pdb=" CA GLU A 106 " pdb=" C GLU A 106 " pdb=" N VAL A 107 " pdb=" CA VAL A 107 " ideal model delta harmonic sigma weight residual 180.00 152.27 27.73 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA THR A1772 " pdb=" C THR A1772 " pdb=" N LEU A1773 " pdb=" CA LEU A1773 " ideal model delta harmonic sigma weight residual 180.00 154.50 25.50 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 12527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2504 0.051 - 0.102: 542 0.102 - 0.153: 93 0.153 - 0.205: 10 0.205 - 0.256: 5 Chirality restraints: 3154 Sorted by residual: chirality pdb=" CA PRO A2037 " pdb=" N PRO A2037 " pdb=" C PRO A2037 " pdb=" CB PRO A2037 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA PRO A2028 " pdb=" N PRO A2028 " pdb=" C PRO A2028 " pdb=" CB PRO A2028 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA PRO A1888 " pdb=" N PRO A1888 " pdb=" C PRO A1888 " pdb=" CB PRO A1888 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 3151 not shown) Planarity restraints: 3756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 821 " 0.025 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP A 821 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 821 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 821 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 821 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 821 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 821 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 821 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 821 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 821 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A1865 " -0.018 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C PRO A1865 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO A1865 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP A1866 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 774 " -0.020 2.00e-02 2.50e+03 2.10e-02 1.11e+01 pdb=" CG TRP A 774 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 774 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 774 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 774 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 774 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 774 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 774 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 774 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 774 " 0.001 2.00e-02 2.50e+03 ... (remaining 3753 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 249 2.64 - 3.20: 19277 3.20 - 3.77: 31097 3.77 - 4.33: 42113 4.33 - 4.90: 70065 Nonbonded interactions: 162801 Sorted by model distance: nonbonded pdb=" O TYR A 702 " pdb=" OG1 THR A 706 " model vdw 2.070 2.440 nonbonded pdb=" OG1 THR A1749 " pdb=" OD1 ASP A1777 " model vdw 2.079 2.440 nonbonded pdb=" OG1 THR A 318 " pdb=" O VAL A 371 " model vdw 2.123 2.440 nonbonded pdb=" OG SER A1034 " pdb=" OG1 THR A1089 " model vdw 2.146 2.440 nonbonded pdb=" O ASN A1417 " pdb=" OG1 THR A1461 " model vdw 2.172 2.440 ... (remaining 162796 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.790 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 76.800 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.140 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.003 0.114 21116 Z= 0.223 Angle : 0.700 11.930 28683 Z= 0.399 Chirality : 0.044 0.256 3154 Planarity : 0.005 0.074 3756 Dihedral : 14.244 89.816 7604 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 1.14 % Allowed : 9.51 % Favored : 89.35 % Rotamer: Outliers : 0.14 % Allowed : 0.19 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.17), residues: 2636 helix: 0.83 (0.16), residues: 1129 sheet: 0.29 (0.30), residues: 311 loop : -2.44 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP A 821 HIS 0.017 0.001 HIS A 772 PHE 0.019 0.001 PHE A 447 TYR 0.029 0.001 TYR A2237 ARG 0.005 0.000 ARG A1120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 2.614 Fit side-chains REVERT: A 294 GLU cc_start: 0.8015 (tp30) cc_final: 0.7445 (tp30) REVERT: A 704 ASP cc_start: 0.7963 (m-30) cc_final: 0.7634 (m-30) REVERT: A 966 LEU cc_start: 0.7892 (mt) cc_final: 0.7677 (mt) REVERT: A 1396 MET cc_start: 0.7818 (mpp) cc_final: 0.7485 (mpp) REVERT: A 2637 ASP cc_start: 0.7816 (m-30) cc_final: 0.7605 (m-30) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2869 time to fit residues: 97.4324 Evaluate side-chains 165 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 5.9990 chunk 200 optimal weight: 0.0050 chunk 111 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 134 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 overall best weight: 2.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN A1162 HIS ** A1585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 21116 Z= 0.357 Angle : 0.720 10.449 28683 Z= 0.380 Chirality : 0.046 0.188 3154 Planarity : 0.005 0.087 3756 Dihedral : 5.431 35.336 2920 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 1.06 % Allowed : 10.19 % Favored : 88.75 % Rotamer: Outliers : 1.13 % Allowed : 6.37 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 2636 helix: 0.92 (0.16), residues: 1151 sheet: 0.18 (0.30), residues: 324 loop : -2.52 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1122 HIS 0.011 0.001 HIS A 772 PHE 0.028 0.002 PHE A2215 TYR 0.019 0.002 TYR A 139 ARG 0.004 0.001 ARG A1972 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 2.474 Fit side-chains REVERT: A 704 ASP cc_start: 0.8140 (m-30) cc_final: 0.7929 (m-30) REVERT: A 841 PHE cc_start: 0.7410 (t80) cc_final: 0.7192 (t80) REVERT: A 2470 ILE cc_start: 0.9025 (mm) cc_final: 0.8732 (mm) outliers start: 21 outliers final: 16 residues processed: 184 average time/residue: 0.2935 time to fit residues: 88.4880 Evaluate side-chains 164 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 821 TRP Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1635 ASP Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1692 ASP Chi-restraints excluded: chain A residue 2316 ASN Chi-restraints excluded: chain A residue 2565 THR Chi-restraints excluded: chain A residue 2599 ASP Chi-restraints excluded: chain A residue 2655 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 199 optimal weight: 20.0000 chunk 163 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 238 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1162 HIS ** A1585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 21116 Z= 0.253 Angle : 0.655 10.542 28683 Z= 0.345 Chirality : 0.044 0.183 3154 Planarity : 0.005 0.089 3756 Dihedral : 5.300 35.014 2920 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.99 % Allowed : 9.92 % Favored : 89.09 % Rotamer: Outliers : 1.37 % Allowed : 8.26 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.17), residues: 2636 helix: 1.02 (0.16), residues: 1152 sheet: 0.13 (0.30), residues: 307 loop : -2.53 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 255 HIS 0.011 0.001 HIS A 772 PHE 0.024 0.001 PHE A 838 TYR 0.015 0.001 TYR A2667 ARG 0.004 0.000 ARG A 770 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 163 time to evaluate : 2.357 Fit side-chains REVERT: A 294 GLU cc_start: 0.7855 (tp30) cc_final: 0.7446 (tp30) REVERT: A 823 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7780 (t80) REVERT: A 841 PHE cc_start: 0.7398 (t80) cc_final: 0.7179 (t80) REVERT: A 1167 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: A 1571 MET cc_start: 0.8401 (ttp) cc_final: 0.8172 (tmm) REVERT: A 2470 ILE cc_start: 0.9018 (mm) cc_final: 0.8751 (mm) outliers start: 26 outliers final: 17 residues processed: 177 average time/residue: 0.2887 time to fit residues: 85.2956 Evaluate side-chains 170 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 821 TRP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1635 ASP Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1692 ASP Chi-restraints excluded: chain A residue 1836 THR Chi-restraints excluded: chain A residue 2446 VAL Chi-restraints excluded: chain A residue 2599 ASP Chi-restraints excluded: chain A residue 2655 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 228 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 21116 Z= 0.412 Angle : 0.728 11.082 28683 Z= 0.386 Chirality : 0.047 0.186 3154 Planarity : 0.005 0.089 3756 Dihedral : 5.555 35.580 2920 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 1.06 % Allowed : 10.49 % Favored : 88.44 % Rotamer: Outliers : 1.70 % Allowed : 9.30 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.17), residues: 2636 helix: 0.94 (0.16), residues: 1147 sheet: -0.07 (0.29), residues: 322 loop : -2.66 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 255 HIS 0.009 0.002 HIS A2086 PHE 0.035 0.002 PHE A2215 TYR 0.019 0.002 TYR A 139 ARG 0.004 0.001 ARG A2257 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 150 time to evaluate : 2.360 Fit side-chains REVERT: A 446 MET cc_start: 0.8046 (ttm) cc_final: 0.7715 (ttp) REVERT: A 606 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.7346 (m-80) REVERT: A 841 PHE cc_start: 0.7394 (t80) cc_final: 0.7167 (t80) REVERT: A 1163 ARG cc_start: 0.8525 (mpt-90) cc_final: 0.8054 (mmt90) REVERT: A 1167 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8204 (pp20) outliers start: 33 outliers final: 23 residues processed: 171 average time/residue: 0.2900 time to fit residues: 82.3491 Evaluate side-chains 168 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 821 TRP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1635 ASP Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1692 ASP Chi-restraints excluded: chain A residue 2316 ASN Chi-restraints excluded: chain A residue 2433 LEU Chi-restraints excluded: chain A residue 2446 VAL Chi-restraints excluded: chain A residue 2599 ASP Chi-restraints excluded: chain A residue 2655 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 190 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 217 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1585 GLN ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 21116 Z= 0.235 Angle : 0.649 11.482 28683 Z= 0.342 Chirality : 0.043 0.224 3154 Planarity : 0.005 0.089 3756 Dihedral : 5.355 34.211 2920 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.95 % Allowed : 9.89 % Favored : 89.16 % Rotamer: Outliers : 1.61 % Allowed : 10.48 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.17), residues: 2636 helix: 1.14 (0.16), residues: 1148 sheet: -0.11 (0.29), residues: 321 loop : -2.60 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 936 HIS 0.008 0.001 HIS A 772 PHE 0.026 0.001 PHE A 838 TYR 0.015 0.001 TYR A 73 ARG 0.003 0.000 ARG A2660 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 152 time to evaluate : 2.346 Fit side-chains REVERT: A 133 MET cc_start: 0.9064 (tpp) cc_final: 0.8722 (tpp) REVERT: A 255 TRP cc_start: 0.7476 (OUTLIER) cc_final: 0.7106 (t-100) REVERT: A 285 MET cc_start: 0.8971 (tpp) cc_final: 0.8693 (tpp) REVERT: A 294 GLU cc_start: 0.7883 (tp30) cc_final: 0.7305 (tp30) REVERT: A 841 PHE cc_start: 0.7342 (t80) cc_final: 0.7120 (t80) REVERT: A 911 MET cc_start: 0.7050 (pmm) cc_final: 0.6712 (pmm) REVERT: A 1163 ARG cc_start: 0.8702 (mpt-90) cc_final: 0.8039 (mmm160) REVERT: A 1167 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8274 (pp20) REVERT: A 1343 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.7773 (t80) REVERT: A 2184 ILE cc_start: 0.8624 (mt) cc_final: 0.8421 (tp) REVERT: A 2470 ILE cc_start: 0.8978 (mm) cc_final: 0.8708 (mm) outliers start: 31 outliers final: 21 residues processed: 169 average time/residue: 0.2994 time to fit residues: 83.5708 Evaluate side-chains 170 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 821 TRP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1635 ASP Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1692 ASP Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 2307 MET Chi-restraints excluded: chain A residue 2446 VAL Chi-restraints excluded: chain A residue 2565 THR Chi-restraints excluded: chain A residue 2655 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 21116 Z= 0.328 Angle : 0.677 10.119 28683 Z= 0.358 Chirality : 0.045 0.206 3154 Planarity : 0.005 0.087 3756 Dihedral : 5.418 34.739 2920 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.72 % Favored : 88.40 % Rotamer: Outliers : 1.75 % Allowed : 10.86 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2636 helix: 1.10 (0.16), residues: 1146 sheet: -0.26 (0.29), residues: 325 loop : -2.62 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 821 HIS 0.009 0.001 HIS A2086 PHE 0.019 0.002 PHE A2215 TYR 0.015 0.002 TYR A 139 ARG 0.003 0.000 ARG A2660 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 149 time to evaluate : 2.362 Fit side-chains REVERT: A 133 MET cc_start: 0.9081 (tpp) cc_final: 0.8703 (tpp) REVERT: A 255 TRP cc_start: 0.7578 (OUTLIER) cc_final: 0.7165 (t-100) REVERT: A 460 ASN cc_start: 0.8612 (m-40) cc_final: 0.8109 (m-40) REVERT: A 841 PHE cc_start: 0.7441 (t80) cc_final: 0.7238 (t80) REVERT: A 911 MET cc_start: 0.7064 (pmm) cc_final: 0.6761 (pmm) REVERT: A 1163 ARG cc_start: 0.8645 (mpt-90) cc_final: 0.8064 (mmm160) REVERT: A 1167 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8257 (pp20) REVERT: A 1343 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.7916 (t80) REVERT: A 2184 ILE cc_start: 0.8640 (mt) cc_final: 0.8391 (tp) REVERT: A 2294 MET cc_start: 0.7967 (tmm) cc_final: 0.7724 (tmm) REVERT: A 2470 ILE cc_start: 0.8999 (mm) cc_final: 0.8724 (mm) outliers start: 34 outliers final: 25 residues processed: 171 average time/residue: 0.2933 time to fit residues: 83.1568 Evaluate side-chains 176 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 821 TRP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1635 ASP Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1686 VAL Chi-restraints excluded: chain A residue 1692 ASP Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 2178 VAL Chi-restraints excluded: chain A residue 2307 MET Chi-restraints excluded: chain A residue 2446 VAL Chi-restraints excluded: chain A residue 2565 THR Chi-restraints excluded: chain A residue 2599 ASP Chi-restraints excluded: chain A residue 2623 LEU Chi-restraints excluded: chain A residue 2655 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 144 optimal weight: 0.1980 chunk 215 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 254 optimal weight: 0.5980 chunk 159 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 21116 Z= 0.186 Angle : 0.623 12.062 28683 Z= 0.326 Chirality : 0.042 0.243 3154 Planarity : 0.004 0.087 3756 Dihedral : 5.196 34.840 2920 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.84 % Allowed : 9.32 % Favored : 89.85 % Rotamer: Outliers : 1.56 % Allowed : 11.47 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.17), residues: 2636 helix: 1.31 (0.16), residues: 1140 sheet: -0.15 (0.29), residues: 307 loop : -2.49 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 936 HIS 0.007 0.001 HIS A 772 PHE 0.027 0.001 PHE A 838 TYR 0.018 0.001 TYR A 73 ARG 0.006 0.000 ARG A1276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 2.399 Fit side-chains REVERT: A 133 MET cc_start: 0.9052 (tpp) cc_final: 0.8681 (tpp) REVERT: A 255 TRP cc_start: 0.7621 (OUTLIER) cc_final: 0.7050 (t-100) REVERT: A 285 MET cc_start: 0.8968 (tpp) cc_final: 0.8710 (tpp) REVERT: A 294 GLU cc_start: 0.7787 (tp30) cc_final: 0.7532 (tp30) REVERT: A 435 MET cc_start: 0.6295 (mpp) cc_final: 0.5585 (mpp) REVERT: A 446 MET cc_start: 0.7998 (ttm) cc_final: 0.7638 (ttp) REVERT: A 460 ASN cc_start: 0.8653 (m-40) cc_final: 0.8032 (m-40) REVERT: A 911 MET cc_start: 0.7062 (pmm) cc_final: 0.6767 (pmm) REVERT: A 1163 ARG cc_start: 0.8774 (mpt-90) cc_final: 0.8273 (mmt90) REVERT: A 1167 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8306 (pp20) REVERT: A 1343 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.7756 (t80) REVERT: A 2184 ILE cc_start: 0.8643 (mt) cc_final: 0.8414 (tp) REVERT: A 2294 MET cc_start: 0.7900 (tmm) cc_final: 0.7675 (tmm) REVERT: A 2470 ILE cc_start: 0.8948 (mm) cc_final: 0.8703 (mm) REVERT: A 2671 TYR cc_start: 0.8624 (m-80) cc_final: 0.8334 (m-80) outliers start: 30 outliers final: 20 residues processed: 173 average time/residue: 0.3034 time to fit residues: 86.0342 Evaluate side-chains 171 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 821 TRP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1692 ASP Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 2178 VAL Chi-restraints excluded: chain A residue 2446 VAL Chi-restraints excluded: chain A residue 2565 THR Chi-restraints excluded: chain A residue 2599 ASP Chi-restraints excluded: chain A residue 2623 LEU Chi-restraints excluded: chain A residue 2655 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 151 optimal weight: 0.0050 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 173 optimal weight: 0.0570 chunk 125 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 200 optimal weight: 20.0000 chunk 231 optimal weight: 0.2980 overall best weight: 1.0716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 21116 Z= 0.214 Angle : 0.630 11.153 28683 Z= 0.329 Chirality : 0.043 0.228 3154 Planarity : 0.004 0.085 3756 Dihedral : 5.101 34.659 2920 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.96 % Favored : 89.16 % Rotamer: Outliers : 1.37 % Allowed : 11.85 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.17), residues: 2636 helix: 1.32 (0.16), residues: 1143 sheet: -0.16 (0.29), residues: 316 loop : -2.47 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 821 HIS 0.007 0.001 HIS A2086 PHE 0.034 0.001 PHE A2215 TYR 0.016 0.001 TYR A 73 ARG 0.003 0.000 ARG A2660 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 2.382 Fit side-chains REVERT: A 133 MET cc_start: 0.9077 (tpp) cc_final: 0.8689 (tpp) REVERT: A 255 TRP cc_start: 0.7653 (OUTLIER) cc_final: 0.7118 (t-100) REVERT: A 294 GLU cc_start: 0.7813 (tp30) cc_final: 0.7553 (tp30) REVERT: A 435 MET cc_start: 0.6144 (mpp) cc_final: 0.5429 (mpp) REVERT: A 446 MET cc_start: 0.7972 (ttm) cc_final: 0.7739 (ttp) REVERT: A 460 ASN cc_start: 0.8689 (m-40) cc_final: 0.8103 (m-40) REVERT: A 582 MET cc_start: 0.7841 (mmm) cc_final: 0.7624 (mmm) REVERT: A 911 MET cc_start: 0.7092 (pmm) cc_final: 0.6816 (pmm) REVERT: A 1163 ARG cc_start: 0.8798 (mpt-90) cc_final: 0.8226 (mmm160) REVERT: A 1167 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8301 (pp20) REVERT: A 1343 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.7779 (t80) REVERT: A 2294 MET cc_start: 0.7908 (tmm) cc_final: 0.7688 (tmm) REVERT: A 2640 MET cc_start: 0.7934 (mmp) cc_final: 0.7731 (mmm) REVERT: A 2671 TYR cc_start: 0.8669 (m-80) cc_final: 0.8394 (m-80) outliers start: 26 outliers final: 20 residues processed: 166 average time/residue: 0.3012 time to fit residues: 82.8258 Evaluate side-chains 172 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 149 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 821 TRP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1692 ASP Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 2178 VAL Chi-restraints excluded: chain A residue 2307 MET Chi-restraints excluded: chain A residue 2446 VAL Chi-restraints excluded: chain A residue 2565 THR Chi-restraints excluded: chain A residue 2599 ASP Chi-restraints excluded: chain A residue 2623 LEU Chi-restraints excluded: chain A residue 2655 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.9990 chunk 222 optimal weight: 0.0010 chunk 237 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 224 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 21116 Z= 0.219 Angle : 0.627 12.006 28683 Z= 0.328 Chirality : 0.043 0.184 3154 Planarity : 0.004 0.084 3756 Dihedral : 5.065 34.385 2920 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.73 % Favored : 89.47 % Rotamer: Outliers : 1.42 % Allowed : 11.95 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.17), residues: 2636 helix: 1.37 (0.16), residues: 1143 sheet: -0.12 (0.30), residues: 313 loop : -2.45 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 821 HIS 0.007 0.001 HIS A2086 PHE 0.035 0.001 PHE A2215 TYR 0.018 0.001 TYR A1345 ARG 0.003 0.000 ARG A2660 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 2.442 Fit side-chains REVERT: A 133 MET cc_start: 0.8987 (tpp) cc_final: 0.8576 (tpp) REVERT: A 255 TRP cc_start: 0.7564 (OUTLIER) cc_final: 0.7012 (t-100) REVERT: A 285 MET cc_start: 0.8995 (tpp) cc_final: 0.8634 (tpp) REVERT: A 294 GLU cc_start: 0.7818 (tp30) cc_final: 0.7547 (tp30) REVERT: A 435 MET cc_start: 0.6236 (mpp) cc_final: 0.5524 (mpp) REVERT: A 446 MET cc_start: 0.7964 (ttm) cc_final: 0.7735 (ttp) REVERT: A 460 ASN cc_start: 0.8667 (m-40) cc_final: 0.8094 (m-40) REVERT: A 911 MET cc_start: 0.7033 (pmm) cc_final: 0.6742 (pmm) REVERT: A 1163 ARG cc_start: 0.8677 (mpt-90) cc_final: 0.8178 (mmm160) REVERT: A 1167 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8304 (pp20) REVERT: A 1244 MET cc_start: 0.6169 (mtm) cc_final: 0.5907 (mtm) REVERT: A 2294 MET cc_start: 0.7908 (tmm) cc_final: 0.7692 (tmm) REVERT: A 2640 MET cc_start: 0.7818 (mmp) cc_final: 0.7558 (mmm) REVERT: A 2671 TYR cc_start: 0.8674 (m-80) cc_final: 0.8414 (m-80) outliers start: 27 outliers final: 21 residues processed: 166 average time/residue: 0.3104 time to fit residues: 86.1845 Evaluate side-chains 169 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 146 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 821 TRP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1692 ASP Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 2178 VAL Chi-restraints excluded: chain A residue 2307 MET Chi-restraints excluded: chain A residue 2446 VAL Chi-restraints excluded: chain A residue 2565 THR Chi-restraints excluded: chain A residue 2599 ASP Chi-restraints excluded: chain A residue 2623 LEU Chi-restraints excluded: chain A residue 2655 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 263 optimal weight: 0.0470 chunk 242 optimal weight: 0.9990 chunk 209 optimal weight: 4.9990 chunk 21 optimal weight: 0.0670 chunk 161 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 166 optimal weight: 0.0270 overall best weight: 0.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 HIS ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 21116 Z= 0.165 Angle : 0.604 11.955 28683 Z= 0.314 Chirality : 0.041 0.183 3154 Planarity : 0.004 0.083 3756 Dihedral : 4.888 34.510 2920 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.35 % Favored : 89.85 % Rotamer: Outliers : 1.04 % Allowed : 12.42 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.17), residues: 2636 helix: 1.35 (0.16), residues: 1161 sheet: 0.02 (0.30), residues: 316 loop : -2.45 (0.17), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 936 HIS 0.007 0.001 HIS A 772 PHE 0.029 0.001 PHE A2215 TYR 0.019 0.001 TYR A 73 ARG 0.004 0.000 ARG A1120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 169 time to evaluate : 2.391 Fit side-chains REVERT: A 133 MET cc_start: 0.9042 (tpp) cc_final: 0.8669 (tpp) REVERT: A 255 TRP cc_start: 0.7430 (OUTLIER) cc_final: 0.6841 (t-100) REVERT: A 285 MET cc_start: 0.8891 (tpp) cc_final: 0.8602 (tpp) REVERT: A 294 GLU cc_start: 0.7683 (tp30) cc_final: 0.7412 (tp30) REVERT: A 460 ASN cc_start: 0.8641 (m-40) cc_final: 0.8086 (m-40) REVERT: A 823 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8168 (t80) REVERT: A 885 PHE cc_start: 0.8800 (m-80) cc_final: 0.8462 (m-80) REVERT: A 911 MET cc_start: 0.6968 (pmm) cc_final: 0.6691 (pmm) REVERT: A 1163 ARG cc_start: 0.8744 (mpt-90) cc_final: 0.8468 (mmt90) REVERT: A 1167 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8288 (pp20) REVERT: A 1396 MET cc_start: 0.7895 (mpp) cc_final: 0.7596 (mpp) REVERT: A 2184 ILE cc_start: 0.8699 (mt) cc_final: 0.8421 (tp) REVERT: A 2470 ILE cc_start: 0.8889 (mm) cc_final: 0.8554 (mm) outliers start: 19 outliers final: 13 residues processed: 179 average time/residue: 0.2952 time to fit residues: 87.0495 Evaluate side-chains 170 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 2178 VAL Chi-restraints excluded: chain A residue 2446 VAL Chi-restraints excluded: chain A residue 2565 THR Chi-restraints excluded: chain A residue 2655 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.0170 chunk 64 optimal weight: 0.0000 chunk 193 optimal weight: 10.0000 chunk 30 optimal weight: 0.0870 chunk 58 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 overall best weight: 0.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.111189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.083302 restraints weight = 103536.282| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 4.93 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 21116 Z= 0.165 Angle : 0.597 12.139 28683 Z= 0.311 Chirality : 0.042 0.222 3154 Planarity : 0.004 0.081 3756 Dihedral : 4.757 34.623 2920 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.90 % Favored : 90.30 % Rotamer: Outliers : 0.85 % Allowed : 13.27 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.17), residues: 2636 helix: 1.36 (0.16), residues: 1161 sheet: 0.12 (0.30), residues: 315 loop : -2.40 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 936 HIS 0.007 0.001 HIS A 772 PHE 0.035 0.001 PHE A2215 TYR 0.022 0.001 TYR A 73 ARG 0.006 0.000 ARG A1376 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3773.48 seconds wall clock time: 68 minutes 35.66 seconds (4115.66 seconds total)