Starting phenix.real_space_refine on Thu Sep 18 23:03:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rf9_19116/09_2025/8rf9_19116.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rf9_19116/09_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_19116/09_2025/8rf9_19116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rf9_19116/09_2025/8rf9_19116.map" model { file = "/net/cci-nas-00/data/ceres_data/8rf9_19116/09_2025/8rf9_19116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rf9_19116/09_2025/8rf9_19116.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 6, 'TYR:plan': 1, 'GLU:plan': 7, 'GLN:plan1': 4, 'ASP:plan': 9, 'HIS:plan': 1, 'TRP:plan': 2, 'PHE:plan': 4, 'ASN:plan1': 3} 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: {'ARG:plan': 6, 'TYR:plan': 1, 'GLU:plan': 7, 'GLN:plan1': 4, 'ASP:plan': 9, 'HIS:plan': 1, 'TRP:plan': 2, 'PHE:plan': 4, 'ASN:plan1': 3} 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: 8.44, per 1000 atoms: 0.41 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: 1.44 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.16 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: 5.88 Time building geometry restraints manager: 2.05 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.880 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.360 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG A1120 TYR 0.029 0.001 TYR A2237 PHE 0.019 0.001 PHE A 447 TRP 0.064 0.002 TRP A 821 HIS 0.017 0.001 HIS A 772 Details of bonding type rmsd covalent geometry : bond 0.00332 (21116) covalent geometry : angle 0.70010 (28683) hydrogen bonds : bond 0.20209 ( 947) hydrogen bonds : angle 6.88549 ( 2803) *********************** 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 : 0.772 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: 0.7678 (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: 0.1324 time to fit residues: 44.8737 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 : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 A1503 HIS ** A1585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2225 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.111324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.084853 restraints weight = 79712.849| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 4.29 r_work: 0.3140 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 21116 Z= 0.167 Angle : 0.694 11.241 28683 Z= 0.366 Chirality : 0.045 0.187 3154 Planarity : 0.005 0.091 3756 Dihedral : 5.231 34.574 2920 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 1.06 % Allowed : 9.47 % Favored : 89.47 % Rotamer: Outliers : 0.76 % Allowed : 6.47 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.17), residues: 2636 helix: 1.04 (0.16), residues: 1144 sheet: 0.19 (0.30), residues: 309 loop : -2.44 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 763 TYR 0.023 0.002 TYR A2237 PHE 0.029 0.001 PHE A2215 TRP 0.038 0.002 TRP A 255 HIS 0.014 0.001 HIS A 772 Details of bonding type rmsd covalent geometry : bond 0.00371 (21116) covalent geometry : angle 0.69448 (28683) hydrogen bonds : bond 0.04895 ( 947) hydrogen bonds : angle 5.09775 ( 2803) *********************** 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 193 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8917 (tp30) cc_final: 0.8252 (tp30) REVERT: A 435 MET cc_start: 0.6919 (mpp) cc_final: 0.6387 (mpp) REVERT: A 704 ASP cc_start: 0.8484 (m-30) cc_final: 0.8227 (m-30) REVERT: A 911 MET cc_start: 0.6834 (pmm) cc_final: 0.6538 (pmm) REVERT: A 1700 SER cc_start: 0.8923 (m) cc_final: 0.8570 (t) REVERT: A 2162 ASP cc_start: 0.7555 (t0) cc_final: 0.7290 (t70) REVERT: A 2470 ILE cc_start: 0.8896 (mm) cc_final: 0.8622 (mm) REVERT: A 2637 ASP cc_start: 0.8550 (m-30) cc_final: 0.8267 (m-30) outliers start: 13 outliers final: 8 residues processed: 185 average time/residue: 0.1461 time to fit residues: 43.6227 Evaluate side-chains 168 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 762 THR Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 821 TRP Chi-restraints excluded: chain A residue 848 LEU 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 232 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 214 optimal weight: 0.0010 chunk 202 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 199 optimal weight: 20.0000 chunk 130 optimal weight: 0.7980 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 A1585 GLN ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.109224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.081800 restraints weight = 107031.151| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 5.02 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1336 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= 0.129 Angle : 0.639 10.608 28683 Z= 0.335 Chirality : 0.043 0.213 3154 Planarity : 0.005 0.094 3756 Dihedral : 5.109 35.744 2920 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 1.03 % Allowed : 9.01 % Favored : 89.96 % Rotamer: Outliers : 0.80 % Allowed : 8.17 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.17), residues: 2636 helix: 1.11 (0.16), residues: 1144 sheet: 0.22 (0.31), residues: 304 loop : -2.41 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 770 TYR 0.021 0.001 TYR A 822 PHE 0.027 0.001 PHE A2215 TRP 0.047 0.002 TRP A 255 HIS 0.012 0.001 HIS A 772 Details of bonding type rmsd covalent geometry : bond 0.00280 (21116) covalent geometry : angle 0.63902 (28683) hydrogen bonds : bond 0.04134 ( 947) hydrogen bonds : angle 4.75861 ( 2803) *********************** 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 186 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8274 (tp30) cc_final: 0.7722 (tp30) REVERT: A 704 ASP cc_start: 0.8755 (m-30) cc_final: 0.8492 (m-30) REVERT: A 911 MET cc_start: 0.6914 (pmm) cc_final: 0.6614 (pmm) REVERT: A 1166 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: A 1167 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.7966 (tm-30) REVERT: A 1244 MET cc_start: 0.6931 (mtm) cc_final: 0.6717 (mtm) REVERT: A 1700 SER cc_start: 0.8684 (m) cc_final: 0.8398 (t) REVERT: A 2135 CYS cc_start: 0.8433 (m) cc_final: 0.8212 (m) REVERT: A 2162 ASP cc_start: 0.7196 (t0) cc_final: 0.6880 (t70) REVERT: A 2470 ILE cc_start: 0.8826 (mm) cc_final: 0.8589 (mm) REVERT: A 2637 ASP cc_start: 0.8427 (m-30) cc_final: 0.7990 (m-30) outliers start: 14 outliers final: 11 residues processed: 178 average time/residue: 0.1342 time to fit residues: 38.8636 Evaluate side-chains 172 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 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 2655 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 234 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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** A1439 ASN ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 GLN ** 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 = 0.3627 r_free = 0.3627 target = 0.105062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.078014 restraints weight = 95664.205| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 4.69 r_work: 0.3006 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 21116 Z= 0.219 Angle : 0.697 10.137 28683 Z= 0.368 Chirality : 0.046 0.190 3154 Planarity : 0.005 0.095 3756 Dihedral : 5.288 35.643 2920 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 1.03 % Allowed : 10.08 % Favored : 88.90 % Rotamer: Outliers : 1.42 % Allowed : 8.69 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.17), residues: 2636 helix: 1.07 (0.16), residues: 1149 sheet: -0.09 (0.30), residues: 319 loop : -2.44 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1376 TYR 0.018 0.002 TYR A 139 PHE 0.031 0.002 PHE A2215 TRP 0.060 0.002 TRP A 255 HIS 0.009 0.001 HIS A2086 Details of bonding type rmsd covalent geometry : bond 0.00504 (21116) covalent geometry : angle 0.69677 (28683) hydrogen bonds : bond 0.04553 ( 947) hydrogen bonds : angle 4.77917 ( 2803) *********************** 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 188 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 133 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8576 (tpp) REVERT: A 216 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8746 (mp0) REVERT: A 435 MET cc_start: 0.6395 (mpp) cc_final: 0.5962 (mpp) REVERT: A 446 MET cc_start: 0.7578 (ttm) cc_final: 0.7356 (ttp) REVERT: A 606 PHE cc_start: 0.7290 (OUTLIER) cc_final: 0.6879 (m-80) REVERT: A 607 LEU cc_start: 0.7521 (mt) cc_final: 0.7013 (mt) REVERT: A 841 PHE cc_start: 0.6865 (t80) cc_final: 0.6647 (t80) REVERT: A 911 MET cc_start: 0.7125 (pmm) cc_final: 0.6810 (pmm) REVERT: A 1029 GLU cc_start: 0.8681 (pt0) cc_final: 0.8383 (pm20) REVERT: A 1166 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: A 1167 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: A 1700 SER cc_start: 0.8904 (m) cc_final: 0.8609 (t) REVERT: A 1812 GLU cc_start: 0.8374 (mp0) cc_final: 0.8160 (pm20) REVERT: A 2162 ASP cc_start: 0.7426 (t0) cc_final: 0.7057 (t70) REVERT: A 2184 ILE cc_start: 0.8848 (mt) cc_final: 0.8421 (tp) REVERT: A 2637 ASP cc_start: 0.8640 (m-30) cc_final: 0.8251 (m-30) outliers start: 27 outliers final: 18 residues processed: 176 average time/residue: 0.1391 time to fit residues: 40.5406 Evaluate side-chains 173 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET 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 606 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 821 TRP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1635 ASP Chi-restraints excluded: chain A residue 2362 MET Chi-restraints excluded: chain A residue 2433 LEU 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 72 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 127 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 200 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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** ** 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 = 0.3635 r_free = 0.3635 target = 0.105989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.078366 restraints weight = 108068.726| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 4.94 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1766 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= 0.191 Angle : 0.672 10.001 28683 Z= 0.355 Chirality : 0.045 0.194 3154 Planarity : 0.005 0.095 3756 Dihedral : 5.277 35.412 2920 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.95 % Allowed : 9.73 % Favored : 89.32 % Rotamer: Outliers : 1.75 % Allowed : 9.73 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.17), residues: 2636 helix: 1.13 (0.16), residues: 1146 sheet: -0.21 (0.30), residues: 314 loop : -2.49 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1376 TYR 0.016 0.001 TYR A1345 PHE 0.036 0.002 PHE A 838 TRP 0.030 0.001 TRP A1122 HIS 0.009 0.001 HIS A 772 Details of bonding type rmsd covalent geometry : bond 0.00439 (21116) covalent geometry : angle 0.67164 (28683) hydrogen bonds : bond 0.04256 ( 947) hydrogen bonds : angle 4.65701 ( 2803) *********************** 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 189 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 133 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8421 (tpp) REVERT: A 216 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8669 (mp0) REVERT: A 255 TRP cc_start: 0.7535 (OUTLIER) cc_final: 0.7082 (t-100) REVERT: A 435 MET cc_start: 0.6140 (mpp) cc_final: 0.5775 (mpp) REVERT: A 504 MET cc_start: 0.7537 (tpp) cc_final: 0.7280 (mmt) REVERT: A 606 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6927 (m-80) REVERT: A 607 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.6993 (mt) REVERT: A 767 GLU cc_start: 0.8248 (tp30) cc_final: 0.7885 (tp30) REVERT: A 841 PHE cc_start: 0.6814 (t80) cc_final: 0.6559 (t80) REVERT: A 911 MET cc_start: 0.6875 (pmm) cc_final: 0.6581 (pmm) REVERT: A 1029 GLU cc_start: 0.8512 (pt0) cc_final: 0.8205 (pm20) REVERT: A 1163 ARG cc_start: 0.8860 (mpt-90) cc_final: 0.7614 (mmm160) REVERT: A 1166 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: A 1167 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: A 1347 MET cc_start: 0.8655 (mmm) cc_final: 0.7704 (tpt) REVERT: A 1484 MET cc_start: 0.7771 (mtt) cc_final: 0.7368 (mtt) REVERT: A 1700 SER cc_start: 0.8835 (m) cc_final: 0.8479 (t) REVERT: A 2162 ASP cc_start: 0.7291 (t0) cc_final: 0.6909 (t70) REVERT: A 2294 MET cc_start: 0.8415 (tmm) cc_final: 0.8187 (tmm) REVERT: A 2637 ASP cc_start: 0.8474 (m-30) cc_final: 0.8085 (m-30) outliers start: 34 outliers final: 21 residues processed: 173 average time/residue: 0.1391 time to fit residues: 39.8525 Evaluate side-chains 177 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET 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 606 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 1367 ILE 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 2565 THR Chi-restraints excluded: chain A residue 2599 ASP Chi-restraints excluded: chain A residue 2623 LEU Chi-restraints excluded: chain A residue 2643 LEU 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 43 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 152 optimal weight: 0.4980 chunk 116 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 218 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 178 optimal weight: 0.0470 chunk 7 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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** ** 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 = 0.3679 r_free = 0.3679 target = 0.108311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.081291 restraints weight = 92983.763| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 4.70 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1879 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= 0.123 Angle : 0.625 11.308 28683 Z= 0.327 Chirality : 0.042 0.203 3154 Planarity : 0.004 0.095 3756 Dihedral : 5.043 34.873 2920 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.39 % Favored : 89.73 % Rotamer: Outliers : 1.61 % Allowed : 10.20 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.17), residues: 2636 helix: 1.33 (0.16), residues: 1134 sheet: -0.05 (0.31), residues: 304 loop : -2.43 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1376 TYR 0.020 0.001 TYR A1345 PHE 0.030 0.001 PHE A2215 TRP 0.032 0.001 TRP A 936 HIS 0.009 0.001 HIS A 772 Details of bonding type rmsd covalent geometry : bond 0.00271 (21116) covalent geometry : angle 0.62500 (28683) hydrogen bonds : bond 0.03668 ( 947) hydrogen bonds : angle 4.44711 ( 2803) *********************** 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 196 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.844 Fit side-chains REVERT: A 133 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8563 (tpp) REVERT: A 216 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8633 (mp0) REVERT: A 255 TRP cc_start: 0.7593 (OUTLIER) cc_final: 0.7158 (t-100) REVERT: A 285 MET cc_start: 0.9144 (tpp) cc_final: 0.8942 (tpp) REVERT: A 294 GLU cc_start: 0.8343 (tp30) cc_final: 0.7755 (tp30) REVERT: A 435 MET cc_start: 0.6054 (mpp) cc_final: 0.5728 (mpp) REVERT: A 460 ASN cc_start: 0.8798 (m-40) cc_final: 0.8218 (m-40) REVERT: A 504 MET cc_start: 0.7626 (tpp) cc_final: 0.7017 (mmt) REVERT: A 607 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7197 (mt) REVERT: A 767 GLU cc_start: 0.8147 (tp30) cc_final: 0.7816 (tp30) REVERT: A 841 PHE cc_start: 0.6905 (t80) cc_final: 0.6679 (t80) REVERT: A 911 MET cc_start: 0.6861 (pmm) cc_final: 0.6577 (pmm) REVERT: A 1163 ARG cc_start: 0.8847 (mpt-90) cc_final: 0.7458 (mmm160) REVERT: A 1166 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: A 1167 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: A 1700 SER cc_start: 0.8851 (m) cc_final: 0.8486 (t) REVERT: A 1906 MET cc_start: 0.8762 (ttm) cc_final: 0.8392 (mtp) REVERT: A 2162 ASP cc_start: 0.7099 (t0) cc_final: 0.6674 (t70) REVERT: A 2294 MET cc_start: 0.8359 (tmm) cc_final: 0.8106 (tmm) REVERT: A 2637 ASP cc_start: 0.8430 (m-30) cc_final: 0.8154 (m-30) outliers start: 31 outliers final: 17 residues processed: 183 average time/residue: 0.1293 time to fit residues: 39.3945 Evaluate side-chains 178 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET 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 1367 ILE Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 2307 MET 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 101 optimal weight: 4.9990 chunk 159 optimal weight: 0.6980 chunk 219 optimal weight: 0.7980 chunk 247 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 191 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.107493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.081319 restraints weight = 71479.573| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 4.05 r_work: 0.3075 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1972 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 : 0.645 11.669 28683 Z= 0.338 Chirality : 0.044 0.195 3154 Planarity : 0.005 0.094 3756 Dihedral : 5.028 33.935 2920 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.62 % Favored : 89.51 % Rotamer: Outliers : 1.46 % Allowed : 10.72 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.17), residues: 2636 helix: 1.31 (0.16), residues: 1143 sheet: -0.02 (0.31), residues: 303 loop : -2.42 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1275 TYR 0.016 0.001 TYR A 73 PHE 0.034 0.001 PHE A2215 TRP 0.030 0.001 TRP A 936 HIS 0.008 0.001 HIS A 772 Details of bonding type rmsd covalent geometry : bond 0.00351 (21116) covalent geometry : angle 0.64545 (28683) hydrogen bonds : bond 0.03857 ( 947) hydrogen bonds : angle 4.45956 ( 2803) *********************** 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 183 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.886 Fit side-chains REVERT: A 216 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8677 (mp0) REVERT: A 255 TRP cc_start: 0.7941 (OUTLIER) cc_final: 0.7403 (t-100) REVERT: A 294 GLU cc_start: 0.8786 (tp30) cc_final: 0.8070 (tp30) REVERT: A 446 MET cc_start: 0.7444 (ttm) cc_final: 0.7226 (ttp) REVERT: A 460 ASN cc_start: 0.8885 (m-40) cc_final: 0.8344 (m-40) REVERT: A 607 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7159 (mt) REVERT: A 767 GLU cc_start: 0.8213 (tp30) cc_final: 0.7877 (tp30) REVERT: A 841 PHE cc_start: 0.6888 (t80) cc_final: 0.6673 (t80) REVERT: A 911 MET cc_start: 0.7040 (pmm) cc_final: 0.6746 (pmm) REVERT: A 988 PHE cc_start: 0.6644 (m-10) cc_final: 0.6425 (m-10) REVERT: A 1163 ARG cc_start: 0.8836 (mpt-90) cc_final: 0.7491 (mmm160) REVERT: A 1166 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: A 1167 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: A 1347 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8242 (tmm) REVERT: A 1700 SER cc_start: 0.8995 (m) cc_final: 0.8639 (t) REVERT: A 1906 MET cc_start: 0.8797 (ttm) cc_final: 0.8478 (mtp) REVERT: A 2162 ASP cc_start: 0.7278 (t0) cc_final: 0.6845 (t70) REVERT: A 2294 MET cc_start: 0.8586 (tmm) cc_final: 0.8333 (tmm) REVERT: A 2637 ASP cc_start: 0.8661 (m-30) cc_final: 0.8408 (m-30) outliers start: 28 outliers final: 20 residues processed: 168 average time/residue: 0.1333 time to fit residues: 37.0413 Evaluate side-chains 177 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 1347 MET 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 2307 MET Chi-restraints excluded: chain A residue 2362 MET Chi-restraints excluded: chain A residue 2565 THR Chi-restraints excluded: chain A residue 2599 ASP Chi-restraints excluded: chain A residue 2623 LEU Chi-restraints excluded: chain A residue 2655 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 21 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 247 optimal weight: 0.9980 chunk 199 optimal weight: 0.1980 chunk 169 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 246 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.109015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.081619 restraints weight = 95372.252| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 4.71 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2070 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= 0.128 Angle : 0.632 11.370 28683 Z= 0.329 Chirality : 0.043 0.198 3154 Planarity : 0.004 0.094 3756 Dihedral : 4.971 34.826 2920 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.20 % Favored : 89.92 % Rotamer: Outliers : 1.42 % Allowed : 11.33 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.17), residues: 2636 helix: 1.40 (0.16), residues: 1136 sheet: 0.03 (0.31), residues: 302 loop : -2.41 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2660 TYR 0.016 0.001 TYR A 73 PHE 0.036 0.001 PHE A 838 TRP 0.032 0.001 TRP A 936 HIS 0.008 0.001 HIS A 772 Details of bonding type rmsd covalent geometry : bond 0.00288 (21116) covalent geometry : angle 0.63151 (28683) hydrogen bonds : bond 0.03619 ( 947) hydrogen bonds : angle 4.39281 ( 2803) *********************** 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 188 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 216 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8615 (mp0) REVERT: A 255 TRP cc_start: 0.7762 (OUTLIER) cc_final: 0.7201 (t-100) REVERT: A 285 MET cc_start: 0.9170 (tpp) cc_final: 0.8939 (tpp) REVERT: A 294 GLU cc_start: 0.8388 (tp30) cc_final: 0.7817 (tp30) REVERT: A 446 MET cc_start: 0.7350 (ttm) cc_final: 0.7140 (ttp) REVERT: A 460 ASN cc_start: 0.8835 (m-40) cc_final: 0.8294 (m-40) REVERT: A 607 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7092 (mt) REVERT: A 767 GLU cc_start: 0.8078 (tp30) cc_final: 0.7739 (tp30) REVERT: A 841 PHE cc_start: 0.6902 (t80) cc_final: 0.6678 (t80) REVERT: A 911 MET cc_start: 0.6676 (pmm) cc_final: 0.6426 (pmm) REVERT: A 1163 ARG cc_start: 0.8797 (mpt-90) cc_final: 0.7451 (mmm160) REVERT: A 1166 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: A 1167 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: A 1347 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7278 (tmm) REVERT: A 1700 SER cc_start: 0.8812 (m) cc_final: 0.8458 (t) REVERT: A 2162 ASP cc_start: 0.7040 (t0) cc_final: 0.6637 (t70) REVERT: A 2294 MET cc_start: 0.8293 (tmm) cc_final: 0.8060 (tmm) REVERT: A 2470 ILE cc_start: 0.8770 (mm) cc_final: 0.8496 (mm) REVERT: A 2637 ASP cc_start: 0.8504 (m-30) cc_final: 0.8240 (m-30) REVERT: A 2671 TYR cc_start: 0.8764 (m-80) cc_final: 0.8498 (m-80) outliers start: 27 outliers final: 19 residues processed: 174 average time/residue: 0.1323 time to fit residues: 37.5170 Evaluate side-chains 181 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 823 PHE Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1347 MET 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 2307 MET Chi-restraints excluded: chain A residue 2362 MET Chi-restraints excluded: chain A residue 2565 THR Chi-restraints excluded: chain A residue 2599 ASP Chi-restraints excluded: chain A residue 2623 LEU Chi-restraints excluded: chain A residue 2655 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 58 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 216 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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** ** 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 = 0.3650 r_free = 0.3650 target = 0.106498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.079439 restraints weight = 101582.340| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 4.88 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2117 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= 0.168 Angle : 0.657 12.009 28683 Z= 0.343 Chirality : 0.044 0.189 3154 Planarity : 0.005 0.093 3756 Dihedral : 5.029 34.389 2920 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.92 % Favored : 89.28 % Rotamer: Outliers : 1.27 % Allowed : 11.85 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.17), residues: 2636 helix: 1.30 (0.16), residues: 1152 sheet: -0.09 (0.30), residues: 306 loop : -2.39 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2660 TYR 0.014 0.001 TYR A 73 PHE 0.037 0.001 PHE A2215 TRP 0.030 0.001 TRP A 936 HIS 0.008 0.001 HIS A 772 Details of bonding type rmsd covalent geometry : bond 0.00387 (21116) covalent geometry : angle 0.65699 (28683) hydrogen bonds : bond 0.03916 ( 947) hydrogen bonds : angle 4.44373 ( 2803) *********************** 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 181 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.882 Fit side-chains REVERT: A 216 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8634 (mp0) REVERT: A 255 TRP cc_start: 0.7784 (OUTLIER) cc_final: 0.7252 (t-100) REVERT: A 294 GLU cc_start: 0.8456 (tp30) cc_final: 0.7631 (tp30) REVERT: A 446 MET cc_start: 0.7385 (ttm) cc_final: 0.7071 (ttp) REVERT: A 460 ASN cc_start: 0.8835 (m-40) cc_final: 0.8289 (m-40) REVERT: A 607 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7107 (mt) REVERT: A 767 GLU cc_start: 0.8147 (tp30) cc_final: 0.7794 (tp30) REVERT: A 821 TRP cc_start: 0.7260 (m-10) cc_final: 0.7024 (m-10) REVERT: A 824 MET cc_start: 0.8024 (ptt) cc_final: 0.7730 (ttp) REVERT: A 841 PHE cc_start: 0.6891 (t80) cc_final: 0.6663 (t80) REVERT: A 911 MET cc_start: 0.6659 (pmm) cc_final: 0.6411 (pmm) REVERT: A 1163 ARG cc_start: 0.8847 (mpt-90) cc_final: 0.7502 (mmm160) REVERT: A 1166 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: A 1167 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.7954 (tm-30) REVERT: A 1347 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7457 (tmm) REVERT: A 1700 SER cc_start: 0.8896 (m) cc_final: 0.8527 (t) REVERT: A 2162 ASP cc_start: 0.7201 (t0) cc_final: 0.6888 (t70) REVERT: A 2294 MET cc_start: 0.8304 (tmm) cc_final: 0.8044 (tmm) REVERT: A 2470 ILE cc_start: 0.8784 (mm) cc_final: 0.8500 (mm) REVERT: A 2637 ASP cc_start: 0.8548 (m-30) cc_final: 0.8292 (m-30) outliers start: 24 outliers final: 18 residues processed: 170 average time/residue: 0.1382 time to fit residues: 38.6893 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 : 0.740 ------------------------------------------------------------------------------- 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 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 1347 MET 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 2307 MET Chi-restraints excluded: chain A residue 2362 MET 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 72 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 258 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 223 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 132 optimal weight: 0.3980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.107409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.080720 restraints weight = 87299.218| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 4.52 r_work: 0.3063 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2179 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= 0.140 Angle : 0.639 11.835 28683 Z= 0.333 Chirality : 0.043 0.239 3154 Planarity : 0.004 0.093 3756 Dihedral : 4.991 34.486 2920 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.32 % Favored : 89.89 % Rotamer: Outliers : 1.27 % Allowed : 11.95 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.17), residues: 2636 helix: 1.35 (0.16), residues: 1144 sheet: -0.03 (0.31), residues: 302 loop : -2.38 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2660 TYR 0.016 0.001 TYR A 73 PHE 0.036 0.001 PHE A2215 TRP 0.032 0.001 TRP A 936 HIS 0.008 0.001 HIS A 772 Details of bonding type rmsd covalent geometry : bond 0.00319 (21116) covalent geometry : angle 0.63888 (28683) hydrogen bonds : bond 0.03740 ( 947) hydrogen bonds : angle 4.38981 ( 2803) ********************** 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 177 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 216 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8680 (mp0) REVERT: A 255 TRP cc_start: 0.7879 (OUTLIER) cc_final: 0.7339 (t-100) REVERT: A 285 MET cc_start: 0.9332 (tpp) cc_final: 0.8896 (tpp) REVERT: A 294 GLU cc_start: 0.8793 (tp30) cc_final: 0.8056 (tp30) REVERT: A 446 MET cc_start: 0.7302 (ttm) cc_final: 0.6972 (ttp) REVERT: A 460 ASN cc_start: 0.8864 (m-40) cc_final: 0.8362 (m-40) REVERT: A 607 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7189 (mt) REVERT: A 767 GLU cc_start: 0.8164 (tp30) cc_final: 0.7812 (tp30) REVERT: A 841 PHE cc_start: 0.6879 (t80) cc_final: 0.6667 (t80) REVERT: A 911 MET cc_start: 0.6930 (pmm) cc_final: 0.6673 (pmm) REVERT: A 1163 ARG cc_start: 0.8926 (mpt-90) cc_final: 0.7621 (mmm160) REVERT: A 1166 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: A 1167 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.7982 (tm-30) REVERT: A 1700 SER cc_start: 0.8977 (m) cc_final: 0.8623 (t) REVERT: A 2162 ASP cc_start: 0.7311 (t0) cc_final: 0.7006 (t70) REVERT: A 2184 ILE cc_start: 0.8922 (mt) cc_final: 0.8479 (tp) REVERT: A 2294 MET cc_start: 0.8538 (tmm) cc_final: 0.8285 (tmm) REVERT: A 2470 ILE cc_start: 0.8817 (mm) cc_final: 0.8516 (mm) REVERT: A 2637 ASP cc_start: 0.8685 (m-30) cc_final: 0.8439 (m-30) outliers start: 24 outliers final: 17 residues processed: 166 average time/residue: 0.1370 time to fit residues: 37.2722 Evaluate side-chains 172 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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 1635 ASP Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1666 THR Chi-restraints excluded: chain A residue 2307 MET Chi-restraints excluded: chain A residue 2362 MET 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 248 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 228 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 136 optimal weight: 0.0370 chunk 50 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.3862 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.107462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.080282 restraints weight = 89173.089| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 4.49 r_work: 0.3051 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2214 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= 0.160 Angle : 0.649 12.085 28683 Z= 0.340 Chirality : 0.044 0.258 3154 Planarity : 0.004 0.092 3756 Dihedral : 5.026 34.326 2920 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.89 % Favored : 89.35 % Rotamer: Outliers : 1.27 % Allowed : 11.85 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.17), residues: 2636 helix: 1.36 (0.16), residues: 1143 sheet: -0.07 (0.31), residues: 303 loop : -2.39 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2660 TYR 0.015 0.001 TYR A 73 PHE 0.037 0.001 PHE A2215 TRP 0.030 0.001 TRP A 936 HIS 0.008 0.001 HIS A 772 Details of bonding type rmsd covalent geometry : bond 0.00367 (21116) covalent geometry : angle 0.64928 (28683) hydrogen bonds : bond 0.03845 ( 947) hydrogen bonds : angle 4.40815 ( 2803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4107.16 seconds wall clock time: 71 minutes 16.84 seconds (4276.84 seconds total)