Starting phenix.real_space_refine on Wed May 21 05:23:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rf9_19116/05_2025/8rf9_19116.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rf9_19116/05_2025/8rf9_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/cci-nas-00/data/ceres_data/8rf9_19116/05_2025/8rf9_19116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rf9_19116/05_2025/8rf9_19116.map" model { file = "/net/cci-nas-00/data/ceres_data/8rf9_19116/05_2025/8rf9_19116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rf9_19116/05_2025/8rf9_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. Time to flip 30 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 20.17, per 1000 atoms: 0.98 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.67 Conformation dependent library (CDL) restraints added in 4.7 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: 3.39 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: 11.62 Time building geometry restraints manager: 6.51 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: 0.00 - 2.39: 28206 2.39 - 4.77: 409 4.77 - 7.16: 51 7.16 - 9.54: 14 9.54 - 11.93: 3 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 3.040 nonbonded pdb=" OG1 THR A1749 " pdb=" OD1 ASP A1777 " model vdw 2.079 3.040 nonbonded pdb=" OG1 THR A 318 " pdb=" O VAL A 371 " model vdw 2.123 3.040 nonbonded pdb=" OG SER A1034 " pdb=" OG1 THR A1089 " model vdw 2.146 3.040 nonbonded pdb=" O ASN A1417 " pdb=" OG1 THR A1461 " model vdw 2.172 3.040 ... (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: 1.510 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: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 63.480 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.120 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.290 ------------------------------------------------------------------------------- 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= 0.159 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 Details of bonding type rmsd hydrogen bonds : bond 0.20209 ( 947) hydrogen bonds : angle 6.88549 ( 2803) covalent geometry : bond 0.00332 (21116) covalent geometry : angle 0.70010 (28683) *********************** 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 to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 2.325 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: 0.2971 time to fit residues: 100.5060 Evaluate side-chains 165 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 2.195 ------------------------------------------------------------------------------- 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: 20.0000 chunk 111 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 134 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 239 optimal weight: 0.0770 overall best weight: 2.1544 ------------------------------------------------------------------------------- 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 A1015 GLN A1162 HIS ** A1585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2225 ASN A2306 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.109254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.083139 restraints weight = 69611.629| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.97 r_work: 0.3116 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 21116 Z= 0.222 Angle : 0.723 11.065 28683 Z= 0.383 Chirality : 0.046 0.189 3154 Planarity : 0.006 0.090 3756 Dihedral : 5.370 34.914 2920 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 1.06 % Allowed : 9.77 % Favored : 89.16 % Rotamer: Outliers : 0.80 % Allowed : 6.75 % Favored : 92.45 % 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: -0.88 (0.17), residues: 2636 helix: 0.94 (0.16), residues: 1146 sheet: 0.12 (0.29), residues: 327 loop : -2.47 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A1122 HIS 0.013 0.001 HIS A 772 PHE 0.027 0.002 PHE A2215 TYR 0.022 0.002 TYR A2237 ARG 0.006 0.001 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.05208 ( 947) hydrogen bonds : angle 5.17460 ( 2803) covalent geometry : bond 0.00505 (21116) covalent geometry : angle 0.72330 (28683) *********************** 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 187 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 2.333 Fit side-chains revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8905 (tp30) cc_final: 0.8286 (tp30) REVERT: A 704 ASP cc_start: 0.8511 (m-30) cc_final: 0.8249 (m-30) REVERT: A 841 PHE cc_start: 0.6960 (t80) cc_final: 0.6729 (t80) REVERT: A 911 MET cc_start: 0.6865 (pmm) cc_final: 0.6562 (pmm) REVERT: A 1029 GLU cc_start: 0.8597 (pt0) cc_final: 0.8341 (pm20) REVERT: A 1700 SER cc_start: 0.8954 (m) cc_final: 0.8603 (t) REVERT: A 2162 ASP cc_start: 0.7632 (t0) cc_final: 0.7366 (t70) REVERT: A 2470 ILE cc_start: 0.8921 (mm) cc_final: 0.8644 (mm) REVERT: A 2637 ASP cc_start: 0.8558 (m-30) cc_final: 0.8293 (m-30) outliers start: 14 outliers final: 9 residues processed: 180 average time/residue: 0.3037 time to fit residues: 89.6437 Evaluate side-chains 162 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 2.393 ------------------------------------------------------------------------------- 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 1227 VAL 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 21 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 183 optimal weight: 0.2980 chunk 64 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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** A1162 HIS A1439 ASN ** A1585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.107051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.080784 restraints weight = 74848.612| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 4.16 r_work: 0.3070 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 21116 Z= 0.154 Angle : 0.657 10.753 28683 Z= 0.346 Chirality : 0.044 0.214 3154 Planarity : 0.005 0.094 3756 Dihedral : 5.279 35.566 2920 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 1.03 % Allowed : 9.58 % Favored : 89.39 % Rotamer: Outliers : 1.13 % Allowed : 8.17 % Favored : 90.70 % 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: 1.02 (0.16), residues: 1142 sheet: 0.07 (0.30), residues: 309 loop : -2.46 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 255 HIS 0.011 0.001 HIS A 772 PHE 0.030 0.001 PHE A2215 TYR 0.017 0.001 TYR A1345 ARG 0.005 0.000 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 947) hydrogen bonds : angle 4.80747 ( 2803) covalent geometry : bond 0.00347 (21116) covalent geometry : angle 0.65690 (28683) *********************** 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 187 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 2.298 Fit side-chains REVERT: A 294 GLU cc_start: 0.8812 (tp30) cc_final: 0.8146 (tp30) REVERT: A 435 MET cc_start: 0.6552 (mpp) cc_final: 0.6076 (mpp) REVERT: A 823 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7985 (t80) REVERT: A 841 PHE cc_start: 0.6872 (t80) cc_final: 0.6633 (t80) REVERT: A 911 MET cc_start: 0.7144 (pmm) cc_final: 0.6815 (pmm) REVERT: A 1029 GLU cc_start: 0.8596 (pt0) cc_final: 0.8320 (pm20) REVERT: A 1121 ASP cc_start: 0.7992 (t0) cc_final: 0.7783 (t0) REVERT: A 1166 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: A 1167 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.7966 (tm-30) REVERT: A 1244 MET cc_start: 0.7225 (mtm) cc_final: 0.6993 (mtm) REVERT: A 1700 SER cc_start: 0.8872 (m) cc_final: 0.8572 (t) REVERT: A 2162 ASP cc_start: 0.7392 (t0) cc_final: 0.7074 (t70) REVERT: A 2470 ILE cc_start: 0.8921 (mm) cc_final: 0.8670 (mm) REVERT: A 2637 ASP cc_start: 0.8589 (m-30) cc_final: 0.8191 (m-30) outliers start: 21 outliers final: 12 residues processed: 177 average time/residue: 0.2911 time to fit residues: 85.6756 Evaluate side-chains 167 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 2.202 ------------------------------------------------------------------------------- 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 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 1166 GLU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1643 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 0 optimal weight: 8.9990 chunk 237 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 140 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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** ** A1585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 GLN ** 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 = 0.3643 r_free = 0.3643 target = 0.106470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.079842 restraints weight = 86348.338| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 4.42 r_work: 0.3037 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 21116 Z= 0.172 Angle : 0.663 10.302 28683 Z= 0.349 Chirality : 0.044 0.187 3154 Planarity : 0.005 0.095 3756 Dihedral : 5.259 35.366 2920 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.99 % Allowed : 9.89 % Favored : 89.13 % Rotamer: Outliers : 1.46 % Allowed : 9.44 % Favored : 89.09 % 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: -0.85 (0.17), residues: 2636 helix: 1.02 (0.16), residues: 1154 sheet: -0.09 (0.30), residues: 315 loop : -2.46 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 255 HIS 0.009 0.001 HIS A 772 PHE 0.032 0.001 PHE A2215 TYR 0.015 0.001 TYR A2667 ARG 0.004 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 947) hydrogen bonds : angle 4.70933 ( 2803) covalent geometry : bond 0.00394 (21116) covalent geometry : angle 0.66316 (28683) *********************** 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 187 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 2.205 Fit side-chains revert: symmetry clash REVERT: A 216 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8748 (mp0) REVERT: A 294 GLU cc_start: 0.8882 (tp30) cc_final: 0.8183 (tp30) REVERT: A 435 MET cc_start: 0.6411 (mpp) cc_final: 0.5990 (mpp) REVERT: A 446 MET cc_start: 0.7544 (ttm) cc_final: 0.7246 (ttp) REVERT: A 504 MET cc_start: 0.7914 (tpp) cc_final: 0.7572 (mmt) REVERT: A 767 GLU cc_start: 0.8298 (tp30) cc_final: 0.7936 (tp30) REVERT: A 841 PHE cc_start: 0.6950 (t80) cc_final: 0.6722 (t80) REVERT: A 911 MET cc_start: 0.7028 (pmm) cc_final: 0.6723 (pmm) REVERT: A 1029 GLU cc_start: 0.8672 (pt0) cc_final: 0.8386 (pm20) REVERT: A 1121 ASP cc_start: 0.8067 (t0) cc_final: 0.7850 (t0) REVERT: A 1166 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: A 1167 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: A 1571 MET cc_start: 0.9156 (ttp) cc_final: 0.8955 (tmm) REVERT: A 1700 SER cc_start: 0.8923 (m) cc_final: 0.8605 (t) REVERT: A 2162 ASP cc_start: 0.7425 (t0) cc_final: 0.7059 (t70) REVERT: A 2637 ASP cc_start: 0.8626 (m-30) cc_final: 0.8232 (m-30) outliers start: 28 outliers final: 18 residues processed: 176 average time/residue: 0.2893 time to fit residues: 85.0200 Evaluate side-chains 172 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ASP 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 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 848 LEU Chi-restraints excluded: chain A residue 1166 GLU 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 2565 THR 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 223 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 59 optimal weight: 0.2980 chunk 110 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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** ** A1585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 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 = 0.3653 r_free = 0.3653 target = 0.106741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.079519 restraints weight = 108589.591| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 5.02 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 21116 Z= 0.149 Angle : 0.638 10.145 28683 Z= 0.335 Chirality : 0.043 0.186 3154 Planarity : 0.005 0.095 3756 Dihedral : 5.174 35.645 2920 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.99 % Allowed : 9.51 % Favored : 89.51 % Rotamer: Outliers : 1.70 % Allowed : 10.01 % Favored : 88.29 % 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: -0.74 (0.17), residues: 2636 helix: 1.17 (0.16), residues: 1143 sheet: -0.07 (0.30), residues: 309 loop : -2.41 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 936 HIS 0.009 0.001 HIS A 772 PHE 0.034 0.001 PHE A2215 TYR 0.016 0.001 TYR A 73 ARG 0.003 0.000 ARG A1788 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 947) hydrogen bonds : angle 4.56739 ( 2803) covalent geometry : bond 0.00339 (21116) covalent geometry : angle 0.63801 (28683) *********************** 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 193 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 2.330 Fit side-chains REVERT: A 216 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8665 (mp0) REVERT: A 255 TRP cc_start: 0.7544 (OUTLIER) cc_final: 0.7018 (t-100) REVERT: A 294 GLU cc_start: 0.8392 (tp30) cc_final: 0.7643 (tp30) REVERT: A 435 MET cc_start: 0.6144 (mpp) cc_final: 0.5750 (mpp) REVERT: A 446 MET cc_start: 0.7582 (ttm) cc_final: 0.7272 (ttp) REVERT: A 767 GLU cc_start: 0.8186 (tp30) cc_final: 0.7850 (tp30) REVERT: A 841 PHE cc_start: 0.6967 (t80) cc_final: 0.6737 (t80) REVERT: A 911 MET cc_start: 0.6835 (pmm) cc_final: 0.6549 (pmm) REVERT: A 1029 GLU cc_start: 0.8500 (pt0) cc_final: 0.8194 (pm20) REVERT: A 1166 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: A 1167 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.7987 (tm-30) REVERT: A 1700 SER cc_start: 0.8861 (m) cc_final: 0.8539 (t) REVERT: A 2162 ASP cc_start: 0.7310 (t0) cc_final: 0.6902 (t70) REVERT: A 2294 MET cc_start: 0.8366 (tmm) cc_final: 0.8154 (tmm) REVERT: A 2637 ASP cc_start: 0.8469 (m-30) cc_final: 0.8179 (m-30) outliers start: 33 outliers final: 23 residues processed: 178 average time/residue: 0.2939 time to fit residues: 87.8325 Evaluate side-chains 179 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 297 ASP 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 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 848 LEU Chi-restraints excluded: chain A residue 1166 GLU 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 1677 ILE Chi-restraints excluded: chain A residue 2307 MET Chi-restraints excluded: chain A residue 2362 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 2655 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 175 optimal weight: 0.9990 chunk 139 optimal weight: 0.0040 chunk 245 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 230 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 255 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.106544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.078964 restraints weight = 109785.649| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 5.10 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 21116 Z= 0.159 Angle : 0.645 11.186 28683 Z= 0.338 Chirality : 0.043 0.192 3154 Planarity : 0.005 0.094 3756 Dihedral : 5.151 34.616 2920 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.04 % Favored : 89.13 % Rotamer: Outliers : 1.75 % Allowed : 10.91 % Favored : 87.35 % 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: -0.74 (0.17), residues: 2636 helix: 1.20 (0.16), residues: 1145 sheet: -0.09 (0.30), residues: 303 loop : -2.43 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 936 HIS 0.008 0.001 HIS A 772 PHE 0.034 0.001 PHE A2215 TYR 0.017 0.001 TYR A1345 ARG 0.003 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 947) hydrogen bonds : angle 4.52869 ( 2803) covalent geometry : bond 0.00362 (21116) covalent geometry : angle 0.64508 (28683) *********************** 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 190 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 2.179 Fit side-chains REVERT: A 216 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8676 (mp0) REVERT: A 255 TRP cc_start: 0.7611 (OUTLIER) cc_final: 0.7234 (t-100) REVERT: A 285 MET cc_start: 0.9255 (tpp) cc_final: 0.8921 (tpp) REVERT: A 294 GLU cc_start: 0.8478 (tp30) cc_final: 0.7682 (tp30) REVERT: A 446 MET cc_start: 0.7490 (ttm) cc_final: 0.7168 (ttp) REVERT: A 767 GLU cc_start: 0.8212 (tp30) cc_final: 0.7868 (tp30) REVERT: A 841 PHE cc_start: 0.6790 (t80) cc_final: 0.6536 (t80) REVERT: A 911 MET cc_start: 0.6812 (pmm) cc_final: 0.6537 (pmm) REVERT: A 1029 GLU cc_start: 0.8526 (pt0) cc_final: 0.8231 (pm20) REVERT: A 1163 ARG cc_start: 0.8798 (mpt-90) cc_final: 0.7525 (mmm160) REVERT: A 1166 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: A 1167 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.7965 (tm-30) REVERT: A 1635 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.8072 (t0) REVERT: A 1700 SER cc_start: 0.8903 (m) cc_final: 0.8540 (t) REVERT: A 2162 ASP cc_start: 0.7294 (t0) cc_final: 0.6869 (t70) REVERT: A 2637 ASP cc_start: 0.8515 (m-30) cc_final: 0.8225 (m-30) outliers start: 34 outliers final: 19 residues processed: 177 average time/residue: 0.2862 time to fit residues: 82.9839 Evaluate side-chains 176 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 297 ASP 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 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 1166 GLU 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 2307 MET Chi-restraints excluded: chain A residue 2362 MET Chi-restraints excluded: chain A residue 2446 VAL Chi-restraints excluded: chain A residue 2565 THR 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 130 optimal weight: 0.1980 chunk 124 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** A1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 HIS A1585 GLN ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.108250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.080881 restraints weight = 94708.205| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 4.75 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 21116 Z= 0.126 Angle : 0.626 11.878 28683 Z= 0.327 Chirality : 0.043 0.198 3154 Planarity : 0.004 0.094 3756 Dihedral : 5.040 34.682 2920 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.35 % Favored : 89.85 % Rotamer: Outliers : 1.46 % Allowed : 11.05 % Favored : 87.49 % 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: -0.65 (0.17), residues: 2636 helix: 1.31 (0.16), residues: 1139 sheet: -0.07 (0.30), residues: 303 loop : -2.39 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 936 HIS 0.009 0.001 HIS A 772 PHE 0.032 0.001 PHE A2215 TYR 0.015 0.001 TYR A 73 ARG 0.005 0.000 ARG A1275 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 947) hydrogen bonds : angle 4.42730 ( 2803) covalent geometry : bond 0.00281 (21116) covalent geometry : angle 0.62630 (28683) *********************** 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 191 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 2.341 Fit side-chains revert: symmetry clash REVERT: A 216 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8640 (mp0) REVERT: A 255 TRP cc_start: 0.7770 (OUTLIER) cc_final: 0.7292 (t-100) REVERT: A 285 MET cc_start: 0.9165 (tpp) cc_final: 0.8888 (tpp) REVERT: A 294 GLU cc_start: 0.8333 (tp30) cc_final: 0.7744 (tp30) REVERT: A 767 GLU cc_start: 0.8071 (tp30) cc_final: 0.7726 (tp30) REVERT: A 841 PHE cc_start: 0.6855 (t80) cc_final: 0.6614 (t80) REVERT: A 911 MET cc_start: 0.6749 (pmm) cc_final: 0.6511 (pmm) REVERT: A 1029 GLU cc_start: 0.8462 (pt0) cc_final: 0.8157 (pm20) REVERT: A 1166 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: A 1167 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: A 1244 MET cc_start: 0.6915 (mtm) cc_final: 0.6661 (mtm) REVERT: A 1700 SER cc_start: 0.8818 (m) cc_final: 0.8481 (t) REVERT: A 1906 MET cc_start: 0.8799 (ttm) cc_final: 0.8507 (mtp) REVERT: A 2162 ASP cc_start: 0.7199 (t0) cc_final: 0.6782 (t70) REVERT: A 2637 ASP cc_start: 0.8439 (m-30) cc_final: 0.8173 (m-30) outliers start: 28 outliers final: 19 residues processed: 178 average time/residue: 0.3189 time to fit residues: 93.3057 Evaluate side-chains 175 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 297 ASP 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 1166 GLU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1635 ASP Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 2362 MET Chi-restraints excluded: chain A residue 2446 VAL Chi-restraints excluded: chain A residue 2565 THR 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 40 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 192 optimal weight: 0.7980 chunk 217 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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** ** A2080 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 = 0.3663 r_free = 0.3663 target = 0.107603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.080117 restraints weight = 99243.066| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 4.75 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 21116 Z= 0.154 Angle : 0.638 11.687 28683 Z= 0.334 Chirality : 0.043 0.191 3154 Planarity : 0.004 0.093 3756 Dihedral : 5.048 34.520 2920 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.84 % Allowed : 9.70 % Favored : 89.47 % Rotamer: Outliers : 1.51 % Allowed : 11.85 % 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: -0.66 (0.17), residues: 2636 helix: 1.29 (0.16), residues: 1146 sheet: -0.12 (0.30), residues: 309 loop : -2.40 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 936 HIS 0.008 0.001 HIS A 772 PHE 0.034 0.001 PHE A2215 TYR 0.017 0.001 TYR A 73 ARG 0.005 0.000 ARG A1376 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 947) hydrogen bonds : angle 4.44331 ( 2803) covalent geometry : bond 0.00352 (21116) covalent geometry : angle 0.63819 (28683) *********************** 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 181 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 2.455 Fit side-chains REVERT: A 216 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8627 (mp0) REVERT: A 255 TRP cc_start: 0.7750 (OUTLIER) cc_final: 0.7227 (t-100) REVERT: A 285 MET cc_start: 0.9226 (tpp) cc_final: 0.8882 (tpp) REVERT: A 294 GLU cc_start: 0.8377 (tp30) cc_final: 0.7622 (tp30) REVERT: A 460 ASN cc_start: 0.8822 (m-40) cc_final: 0.8226 (m-40) REVERT: A 767 GLU cc_start: 0.8107 (tp30) cc_final: 0.7759 (tp30) REVERT: A 841 PHE cc_start: 0.6938 (t80) cc_final: 0.6701 (t80) REVERT: A 911 MET cc_start: 0.6660 (pmm) cc_final: 0.6413 (pmm) REVERT: A 1029 GLU cc_start: 0.8454 (pt0) cc_final: 0.8165 (pm20) REVERT: A 1163 ARG cc_start: 0.8858 (mpt-90) cc_final: 0.7533 (mmm160) REVERT: A 1166 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: A 1167 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: A 1484 MET cc_start: 0.7935 (mtt) cc_final: 0.7723 (mtt) REVERT: A 1700 SER cc_start: 0.8860 (m) cc_final: 0.8506 (t) REVERT: A 2162 ASP cc_start: 0.7170 (t0) cc_final: 0.6876 (t70) REVERT: A 2294 MET cc_start: 0.8182 (tmm) cc_final: 0.6858 (tmm) REVERT: A 2637 ASP cc_start: 0.8437 (m-30) cc_final: 0.8168 (m-30) outliers start: 29 outliers final: 22 residues processed: 170 average time/residue: 0.3012 time to fit residues: 84.0768 Evaluate side-chains 179 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 297 ASP 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 745 PHE 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 823 PHE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1635 ASP Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1666 THR Chi-restraints excluded: chain A residue 1677 ILE Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 2178 VAL Chi-restraints excluded: chain A residue 2362 MET Chi-restraints excluded: chain A residue 2446 VAL Chi-restraints excluded: chain A residue 2565 THR 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 129 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 198 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 GLN ** 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 = 0.3643 r_free = 0.3643 target = 0.106052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.078486 restraints weight = 91736.899| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 4.63 r_work: 0.3024 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 21116 Z= 0.182 Angle : 0.666 11.931 28683 Z= 0.349 Chirality : 0.044 0.217 3154 Planarity : 0.005 0.093 3756 Dihedral : 5.149 34.285 2920 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.77 % Favored : 89.43 % Rotamer: Outliers : 1.46 % Allowed : 12.04 % Favored : 86.50 % 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: -0.73 (0.17), residues: 2636 helix: 1.23 (0.16), residues: 1152 sheet: -0.29 (0.30), residues: 314 loop : -2.41 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 936 HIS 0.008 0.001 HIS A2086 PHE 0.035 0.001 PHE A2215 TYR 0.014 0.001 TYR A2667 ARG 0.006 0.000 ARG A1376 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 947) hydrogen bonds : angle 4.50970 ( 2803) covalent geometry : bond 0.00420 (21116) covalent geometry : angle 0.66588 (28683) *********************** 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 182 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 2.224 Fit side-chains REVERT: A 255 TRP cc_start: 0.7942 (OUTLIER) cc_final: 0.7481 (t-100) REVERT: A 294 GLU cc_start: 0.8871 (tp30) cc_final: 0.8101 (tp30) REVERT: A 460 ASN cc_start: 0.8867 (m-40) cc_final: 0.8312 (m-40) REVERT: A 767 GLU cc_start: 0.8194 (tp30) cc_final: 0.7855 (tp30) REVERT: A 821 TRP cc_start: 0.7292 (m-10) cc_final: 0.7084 (m-10) REVERT: A 841 PHE cc_start: 0.6870 (t80) cc_final: 0.6636 (t80) REVERT: A 911 MET cc_start: 0.6814 (pmm) cc_final: 0.6557 (pmm) REVERT: A 1162 HIS cc_start: 0.7728 (OUTLIER) cc_final: 0.6875 (m-70) REVERT: A 1163 ARG cc_start: 0.8967 (mpt-90) cc_final: 0.7690 (mmm160) REVERT: A 1166 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: A 1167 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: A 1635 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8189 (t0) REVERT: A 1700 SER cc_start: 0.9039 (m) cc_final: 0.8677 (t) REVERT: A 2162 ASP cc_start: 0.7371 (t0) cc_final: 0.7024 (t70) REVERT: A 2184 ILE cc_start: 0.8908 (mt) cc_final: 0.8450 (tp) REVERT: A 2294 MET cc_start: 0.8385 (tmm) cc_final: 0.7024 (tmm) REVERT: A 2637 ASP cc_start: 0.8710 (m-30) cc_final: 0.8454 (m-30) REVERT: A 2671 TYR cc_start: 0.8947 (m-80) cc_final: 0.8678 (m-80) outliers start: 28 outliers final: 21 residues processed: 173 average time/residue: 0.2940 time to fit residues: 83.3915 Evaluate side-chains 176 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 297 ASP 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 745 PHE 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 823 PHE Chi-restraints excluded: chain A residue 1162 HIS Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1635 ASP Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1666 THR Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 2178 VAL Chi-restraints excluded: chain A residue 2362 MET Chi-restraints excluded: chain A residue 2433 LEU 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 170 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 240 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 237 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 166 optimal weight: 0.0980 chunk 239 optimal weight: 1.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- 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 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 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 = 0.3654 r_free = 0.3654 target = 0.107178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.080441 restraints weight = 81958.029| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 4.34 r_work: 0.3056 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 21116 Z= 0.149 Angle : 0.642 11.725 28683 Z= 0.335 Chirality : 0.043 0.186 3154 Planarity : 0.004 0.093 3756 Dihedral : 5.089 34.312 2920 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.96 % Favored : 89.24 % Rotamer: Outliers : 1.37 % Allowed : 12.28 % Favored : 86.36 % 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: -0.67 (0.17), residues: 2636 helix: 1.31 (0.16), residues: 1144 sheet: -0.21 (0.30), residues: 309 loop : -2.41 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 936 HIS 0.008 0.001 HIS A 772 PHE 0.038 0.001 PHE A2215 TYR 0.016 0.001 TYR A 73 ARG 0.005 0.000 ARG A1376 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 947) hydrogen bonds : angle 4.43866 ( 2803) covalent geometry : bond 0.00339 (21116) covalent geometry : angle 0.64234 (28683) ********************** 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 179 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 2.674 Fit side-chains revert: symmetry clash REVERT: A 255 TRP cc_start: 0.7897 (OUTLIER) cc_final: 0.7494 (t-100) REVERT: A 285 MET cc_start: 0.9345 (tpp) cc_final: 0.8920 (tpp) REVERT: A 294 GLU cc_start: 0.8763 (tp30) cc_final: 0.8027 (tp30) REVERT: A 460 ASN cc_start: 0.8817 (m-40) cc_final: 0.8297 (m-40) REVERT: A 767 GLU cc_start: 0.8162 (tp30) cc_final: 0.7815 (tp30) REVERT: A 841 PHE cc_start: 0.6938 (t80) cc_final: 0.6716 (t80) REVERT: A 911 MET cc_start: 0.6884 (pmm) cc_final: 0.6640 (pmm) REVERT: A 1029 GLU cc_start: 0.8557 (pt0) cc_final: 0.8269 (pm20) REVERT: A 1163 ARG cc_start: 0.8953 (mpt-90) cc_final: 0.7673 (mmm160) REVERT: A 1166 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: A 1167 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.7981 (tm-30) REVERT: A 1700 SER cc_start: 0.8993 (m) cc_final: 0.8641 (t) REVERT: A 2162 ASP cc_start: 0.7389 (t0) cc_final: 0.7045 (t70) REVERT: A 2294 MET cc_start: 0.8383 (tmm) cc_final: 0.7021 (tmm) REVERT: A 2637 ASP cc_start: 0.8663 (m-30) cc_final: 0.8413 (m-30) REVERT: A 2671 TYR cc_start: 0.8906 (m-80) cc_final: 0.8612 (m-80) outliers start: 26 outliers final: 21 residues processed: 170 average time/residue: 0.3005 time to fit residues: 84.0462 Evaluate side-chains 178 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 297 ASP 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 745 PHE 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 823 PHE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1635 ASP Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1666 THR Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 2178 VAL Chi-restraints excluded: chain A residue 2362 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 193 optimal weight: 0.0060 chunk 228 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.109347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.081799 restraints weight = 97809.440| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 4.77 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 21116 Z= 0.122 Angle : 0.626 12.302 28683 Z= 0.326 Chirality : 0.043 0.230 3154 Planarity : 0.004 0.093 3756 Dihedral : 4.954 34.530 2920 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.43 % Favored : 89.81 % Rotamer: Outliers : 1.13 % Allowed : 12.46 % Favored : 86.40 % 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: 1145 sheet: -0.13 (0.30), residues: 308 loop : -2.34 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 936 HIS 0.008 0.001 HIS A 772 PHE 0.036 0.001 PHE A2215 TYR 0.019 0.001 TYR A 73 ARG 0.008 0.000 ARG A2174 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 947) hydrogen bonds : angle 4.33491 ( 2803) covalent geometry : bond 0.00274 (21116) covalent geometry : angle 0.62582 (28683) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8708.88 seconds wall clock time: 151 minutes 36.93 seconds (9096.93 seconds total)