Starting phenix.real_space_refine on Thu Jun 19 23:39:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p52_17440/06_2025/8p52_17440.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p52_17440/06_2025/8p52_17440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p52_17440/06_2025/8p52_17440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p52_17440/06_2025/8p52_17440.map" model { file = "/net/cci-nas-00/data/ceres_data/8p52_17440/06_2025/8p52_17440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p52_17440/06_2025/8p52_17440.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 54 5.16 5 C 14343 2.51 5 N 4022 2.21 5 O 4364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 182 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22783 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 22783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2914, 22783 Classifications: {'peptide': 2914} Link IDs: {'PTRANS': 97, 'TRANS': 2816} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 19 residue: pdb=" N ALA A 993 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 993 " occ=0.00 residue: pdb=" N ASP A1113 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP A1113 " occ=0.00 residue: pdb=" N GLN A1120 " occ=0.40 ... (7 atoms not shown) pdb=" NE2 GLN A1120 " occ=0.00 residue: pdb=" N ALA A1262 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A1262 " occ=0.00 residue: pdb=" N ASP A2674 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP A2674 " occ=0.00 residue: pdb=" N GLY A2675 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A2675 " occ=0.00 residue: pdb=" N LYS A2676 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A2676 " occ=0.00 residue: pdb=" N THR A2831 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR A2831 " occ=0.00 residue: pdb=" N VAL A2833 " occ=0.56 ... (5 atoms not shown) pdb=" CG2 VAL A2833 " occ=0.38 residue: pdb=" N ASP A2835 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP A2835 " occ=0.33 residue: pdb=" N VAL A2858 " occ=0.89 ... (5 atoms not shown) pdb=" CG2 VAL A2858 " occ=0.78 residue: pdb=" N SER A2859 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER A2859 " occ=0.00 ... (remaining 7 not shown) Time building chain proxies: 14.21, per 1000 atoms: 0.62 Number of scatterers: 22783 At special positions: 0 Unit cell: (180, 184.5, 162.9, 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 54 16.00 O 4364 8.00 N 4022 7.00 C 14343 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.97 Conformation dependent library (CDL) restraints added in 3.0 seconds 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5372 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 29 sheets defined 42.1% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.38 Creating SS restraints... Processing helix chain 'A' and resid 5 through 22 Processing helix chain 'A' and resid 35 through 55 removed outlier: 3.518A pdb=" N ASP A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.559A pdb=" N GLN A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 93 through 132 Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 147 through 170 removed outlier: 4.442A pdb=" N ALA A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 202 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 225 through 233 Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 296 through 301 removed outlier: 4.196A pdb=" N ARG A 300 " --> pdb=" O PRO A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 321 removed outlier: 3.529A pdb=" N TYR A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 378 through 390 Processing helix chain 'A' and resid 399 through 405 Processing helix chain 'A' and resid 418 through 425 Processing helix chain 'A' and resid 465 through 489 removed outlier: 3.688A pdb=" N SER A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 500 through 517 removed outlier: 3.832A pdb=" N ARG A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 541 through 558 Processing helix chain 'A' and resid 561 through 573 removed outlier: 3.518A pdb=" N ARG A 567 " --> pdb=" O PRO A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 584 removed outlier: 6.192A pdb=" N ALA A 577 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 598 removed outlier: 4.074A pdb=" N ASP A 590 " --> pdb=" O TYR A 586 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA A 592 " --> pdb=" O GLN A 588 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLN A 593 " --> pdb=" O SER A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 611 through 623 removed outlier: 3.648A pdb=" N GLN A 615 " --> pdb=" O GLU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 653 Processing helix chain 'A' and resid 654 through 658 Processing helix chain 'A' and resid 659 through 664 Processing helix chain 'A' and resid 665 through 674 Processing helix chain 'A' and resid 675 through 698 removed outlier: 3.872A pdb=" N ARG A 691 " --> pdb=" O PHE A 687 " (cutoff:3.500A) Proline residue: A 692 - end of helix removed outlier: 3.542A pdb=" N PHE A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 731 Processing helix chain 'A' and resid 735 through 740 removed outlier: 3.559A pdb=" N ARG A 740 " --> pdb=" O GLN A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 756 removed outlier: 4.110A pdb=" N SER A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR A 754 " --> pdb=" O LYS A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 773 Processing helix chain 'A' and resid 781 through 789 Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 800 through 818 Processing helix chain 'A' and resid 823 through 834 removed outlier: 4.921A pdb=" N VAL A 829 " --> pdb=" O GLU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 857 removed outlier: 3.602A pdb=" N GLU A 855 " --> pdb=" O LYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 878 removed outlier: 3.892A pdb=" N ARG A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) Proline residue: A 875 - end of helix Processing helix chain 'A' and resid 879 through 881 No H-bonds generated for 'chain 'A' and resid 879 through 881' Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 930 through 937 Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 949 through 953 Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 1052 through 1056 Processing helix chain 'A' and resid 1065 through 1069 Processing helix chain 'A' and resid 1125 through 1152 removed outlier: 3.863A pdb=" N GLN A1133 " --> pdb=" O ARG A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1209 removed outlier: 4.624A pdb=" N ALA A1178 " --> pdb=" O PRO A1174 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TRP A1179 " --> pdb=" O ALA A1175 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A1190 " --> pdb=" O VAL A1186 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP A1193 " --> pdb=" O ARG A1189 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN A1196 " --> pdb=" O ALA A1192 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU A1197 " --> pdb=" O ASP A1193 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A1200 " --> pdb=" O GLN A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1259 removed outlier: 4.110A pdb=" N ILE A1217 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLN A1219 " --> pdb=" O ASP A1215 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLN A1220 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR A1237 " --> pdb=" O ALA A1233 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL A1238 " --> pdb=" O GLN A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1263 Processing helix chain 'A' and resid 1281 through 1289 Processing helix chain 'A' and resid 1298 through 1307 removed outlier: 3.788A pdb=" N SER A1302 " --> pdb=" O GLY A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1331 Processing helix chain 'A' and resid 1335 through 1358 Processing helix chain 'A' and resid 1361 through 1372 removed outlier: 3.861A pdb=" N PHE A1365 " --> pdb=" O GLN A1361 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER A1366 " --> pdb=" O THR A1362 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A1367 " --> pdb=" O ALA A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1396 removed outlier: 3.916A pdb=" N GLY A1395 " --> pdb=" O ASP A1391 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG A1396 " --> pdb=" O ARG A1392 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1391 through 1396' Processing helix chain 'A' and resid 1396 through 1429 removed outlier: 3.588A pdb=" N ARG A1402 " --> pdb=" O TYR A1398 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A1406 " --> pdb=" O ARG A1402 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N GLU A1413 " --> pdb=" O ALA A1409 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ALA A1414 " --> pdb=" O SER A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1443 Processing helix chain 'A' and resid 1448 through 1454 removed outlier: 3.550A pdb=" N VAL A1452 " --> pdb=" O ASN A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1473 Processing helix chain 'A' and resid 1515 through 1528 removed outlier: 3.506A pdb=" N GLN A1525 " --> pdb=" O ARG A1521 " (cutoff:3.500A) Processing helix chain 'A' and resid 1531 through 1536 Processing helix chain 'A' and resid 1553 through 1558 removed outlier: 3.708A pdb=" N ALA A1558 " --> pdb=" O THR A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1576 through 1599 removed outlier: 3.645A pdb=" N GLU A1588 " --> pdb=" O ARG A1584 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A1599 " --> pdb=" O GLU A1595 " (cutoff:3.500A) Processing helix chain 'A' and resid 1600 through 1630 removed outlier: 3.702A pdb=" N GLN A1608 " --> pdb=" O SER A1604 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1643 Processing helix chain 'A' and resid 1672 through 1691 removed outlier: 4.473A pdb=" N ARG A1678 " --> pdb=" O PHE A1674 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS A1684 " --> pdb=" O PHE A1680 " (cutoff:3.500A) Processing helix chain 'A' and resid 1709 through 1735 removed outlier: 4.485A pdb=" N ASN A1715 " --> pdb=" O VAL A1711 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A1719 " --> pdb=" O ASN A1715 " (cutoff:3.500A) Processing helix chain 'A' and resid 1743 through 1757 removed outlier: 4.266A pdb=" N ALA A1747 " --> pdb=" O ASP A1743 " (cutoff:3.500A) Processing helix chain 'A' and resid 1766 through 1779 Processing helix chain 'A' and resid 1788 through 1809 removed outlier: 3.737A pdb=" N GLY A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A1800 " --> pdb=" O LEU A1796 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY A1805 " --> pdb=" O ASN A1801 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL A1806 " --> pdb=" O GLU A1802 " (cutoff:3.500A) Processing helix chain 'A' and resid 1837 through 1848 Processing helix chain 'A' and resid 1873 through 1907 removed outlier: 3.712A pdb=" N GLY A1877 " --> pdb=" O GLY A1873 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE A1878 " --> pdb=" O LEU A1874 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A1884 " --> pdb=" O ALA A1880 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP A1891 " --> pdb=" O ALA A1887 " (cutoff:3.500A) Processing helix chain 'A' and resid 1981 through 1985 Processing helix chain 'A' and resid 2028 through 2036 removed outlier: 3.546A pdb=" N ILE A2032 " --> pdb=" O GLY A2028 " (cutoff:3.500A) Processing helix chain 'A' and resid 2083 through 2087 removed outlier: 3.917A pdb=" N HIS A2087 " --> pdb=" O LYS A2084 " (cutoff:3.500A) Processing helix chain 'A' and resid 2194 through 2211 removed outlier: 3.505A pdb=" N LYS A2206 " --> pdb=" O SER A2202 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A2207 " --> pdb=" O ASP A2203 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS A2208 " --> pdb=" O LEU A2204 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A2209 " --> pdb=" O ALA A2205 " (cutoff:3.500A) Processing helix chain 'A' and resid 2248 through 2252 Processing helix chain 'A' and resid 2339 through 2347 removed outlier: 3.795A pdb=" N LEU A2345 " --> pdb=" O ALA A2341 " (cutoff:3.500A) Processing helix chain 'A' and resid 2358 through 2364 Processing helix chain 'A' and resid 2365 through 2367 No H-bonds generated for 'chain 'A' and resid 2365 through 2367' Processing helix chain 'A' and resid 2369 through 2374 Processing helix chain 'A' and resid 2529 through 2534 Processing helix chain 'A' and resid 2538 through 2543 removed outlier: 3.638A pdb=" N ASP A2542 " --> pdb=" O HIS A2538 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2546 No H-bonds generated for 'chain 'A' and resid 2544 through 2546' Processing helix chain 'A' and resid 2583 through 2587 removed outlier: 3.688A pdb=" N HIS A2587 " --> pdb=" O GLN A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2617 through 2625 Processing helix chain 'A' and resid 2683 through 2691 Processing helix chain 'A' and resid 2693 through 2705 Processing helix chain 'A' and resid 2822 through 2829 Processing helix chain 'A' and resid 2883 through 2889 removed outlier: 3.960A pdb=" N VAL A2887 " --> pdb=" O SER A2884 " (cutoff:3.500A) Processing helix chain 'A' and resid 2905 through 2915 removed outlier: 4.053A pdb=" N LEU A2915 " --> pdb=" O GLY A2911 " (cutoff:3.500A) Processing helix chain 'A' and resid 2916 through 2919 Processing helix chain 'A' and resid 2925 through 2931 removed outlier: 3.585A pdb=" N GLU A2930 " --> pdb=" O PRO A2926 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 236 removed outlier: 7.568A pdb=" N GLU A 234 " --> pdb=" O ARG A 241 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG A 241 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 236 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ASN A 274 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN A 274 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE A 359 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 339 removed outlier: 5.877A pdb=" N ILE A 359 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN A 274 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ASN A 274 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 307 " --> pdb=" O ILE A 398 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 261 Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA5, first strand: chain 'A' and resid 450 through 454 Processing sheet with id=AA6, first strand: chain 'A' and resid 720 through 722 Processing sheet with id=AA7, first strand: chain 'A' and resid 946 through 948 removed outlier: 6.787A pdb=" N LEU A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 963 " --> pdb=" O THR A 979 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE A1022 " --> pdb=" O PRO A 992 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR A1025 " --> pdb=" O ALA A1081 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ALA A1081 " --> pdb=" O THR A1025 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU A1078 " --> pdb=" O GLN A1097 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 946 through 948 removed outlier: 6.787A pdb=" N LEU A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 963 " --> pdb=" O THR A 979 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE A1022 " --> pdb=" O PRO A 992 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR A1025 " --> pdb=" O ALA A1081 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ALA A1081 " --> pdb=" O THR A1025 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU A1078 " --> pdb=" O GLN A1097 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1009 through 1014 removed outlier: 6.822A pdb=" N SER A1037 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL A1060 " --> pdb=" O SER A1037 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1376 through 1379 removed outlier: 4.287A pdb=" N PHE A1376 " --> pdb=" O ALA A1512 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1457 through 1462 removed outlier: 5.016A pdb=" N GLY A1459 " --> pdb=" O LEU A1549 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A1549 " --> pdb=" O GLY A1459 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1636 through 1638 Processing sheet with id=AB4, first strand: chain 'A' and resid 1636 through 1638 Processing sheet with id=AB5, first strand: chain 'A' and resid 1692 through 1695 Processing sheet with id=AB6, first strand: chain 'A' and resid 1911 through 1913 removed outlier: 6.678A pdb=" N LEU A1920 " --> pdb=" O ILE A2002 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP A2121 " --> pdb=" O LEU A2162 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A2164 " --> pdb=" O TRP A2121 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A2123 " --> pdb=" O VAL A2164 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N VAL A2161 " --> pdb=" O VAL A2173 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A2173 " --> pdb=" O VAL A2161 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1990 through 1992 removed outlier: 6.459A pdb=" N GLN A1937 " --> pdb=" O LEU A1931 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU A1931 " --> pdb=" O GLN A1937 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP A1939 " --> pdb=" O LYS A1929 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LYS A1929 " --> pdb=" O GLU A2067 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N VAL A2069 " --> pdb=" O LYS A1929 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU A1931 " --> pdb=" O VAL A2069 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU A2144 " --> pdb=" O LYS A2147 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A2132 " --> pdb=" O GLY A2143 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1977 through 1978 removed outlier: 6.970A pdb=" N TYR A1944 " --> pdb=" O ILE A2011 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N TYR A2013 " --> pdb=" O TYR A1944 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N TYR A1946 " --> pdb=" O TYR A2013 " (cutoff:3.500A) removed outlier: 11.677A pdb=" N TYR A2015 " --> pdb=" O TYR A1946 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS A2008 " --> pdb=" O VAL A2062 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A2056 " --> pdb=" O GLU A2014 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N MET A2016 " --> pdb=" O ILE A2054 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ILE A2054 " --> pdb=" O MET A2016 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A2052 " --> pdb=" O PHE A2045 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE A2045 " --> pdb=" O GLU A2052 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1977 through 1978 removed outlier: 6.970A pdb=" N TYR A1944 " --> pdb=" O ILE A2011 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N TYR A2013 " --> pdb=" O TYR A1944 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N TYR A1946 " --> pdb=" O TYR A2013 " (cutoff:3.500A) removed outlier: 11.677A pdb=" N TYR A2015 " --> pdb=" O TYR A1946 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS A2008 " --> pdb=" O VAL A2062 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A2056 " --> pdb=" O GLU A2014 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N MET A2016 " --> pdb=" O ILE A2054 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ILE A2054 " --> pdb=" O MET A2016 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N TYR A2214 " --> pdb=" O ARG A2055 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A2057 " --> pdb=" O TYR A2214 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL A2216 " --> pdb=" O ILE A2057 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N HIS A2059 " --> pdb=" O VAL A2216 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A2240 " --> pdb=" O PHE A2231 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1948 through 1949 Processing sheet with id=AC2, first strand: chain 'A' and resid 2253 through 2258 removed outlier: 4.891A pdb=" N LEU A2254 " --> pdb=" O TYR A2265 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N TYR A2265 " --> pdb=" O LEU A2254 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A2261 " --> pdb=" O MET A2258 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2285 through 2286 removed outlier: 6.941A pdb=" N GLN A2285 " --> pdb=" O ILE A2382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 2295 through 2303 removed outlier: 5.628A pdb=" N GLY A2295 " --> pdb=" O ARG A2314 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ARG A2314 " --> pdb=" O GLY A2295 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE A2297 " --> pdb=" O ARG A2312 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ARG A2312 " --> pdb=" O ILE A2297 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A2307 " --> pdb=" O ILE A2326 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLU A2321 " --> pdb=" O ALA A2336 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA A2336 " --> pdb=" O GLU A2321 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY A2323 " --> pdb=" O VAL A2334 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N MET A2331 " --> pdb=" O THR A2385 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA A2387 " --> pdb=" O MET A2331 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU A2333 " --> pdb=" O ALA A2387 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU A2389 " --> pdb=" O LEU A2333 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N SER A2335 " --> pdb=" O LEU A2389 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR A2391 " --> pdb=" O SER A2335 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL A2400 " --> pdb=" O ASP A2396 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 2445 through 2451 removed outlier: 5.762A pdb=" N LEU A2446 " --> pdb=" O TYR A2462 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR A2462 " --> pdb=" O LEU A2446 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLY A2448 " --> pdb=" O PHE A2460 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE A2460 " --> pdb=" O GLY A2448 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A2468 " --> pdb=" O SER A2463 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU A2469 " --> pdb=" O VAL A2490 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 2495 through 2501 removed outlier: 4.790A pdb=" N LEU A2505 " --> pdb=" O LEU A2517 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A2517 " --> pdb=" O LEU A2505 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A2515 " --> pdb=" O VAL A2507 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG A2513 " --> pdb=" O THR A2509 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A2514 " --> pdb=" O ALA A2526 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N SER A2524 " --> pdb=" O THR A2552 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N ALA A2554 " --> pdb=" O SER A2524 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ALA A2526 " --> pdb=" O ALA A2554 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL A2569 " --> pdb=" O VAL A2555 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 2589 through 2590 removed outlier: 3.723A pdb=" N LYS A2609 " --> pdb=" O GLU A2604 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 2649 through 2655 removed outlier: 6.718A pdb=" N THR A2662 " --> pdb=" O LYS A2650 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA A2652 " --> pdb=" O ARG A2660 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG A2660 " --> pdb=" O ALA A2652 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLN A2654 " --> pdb=" O GLY A2658 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY A2658 " --> pdb=" O GLN A2654 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A2667 " --> pdb=" O THR A2663 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU A2670 " --> pdb=" O LEU A2679 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU A2679 " --> pdb=" O LEU A2670 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR A2672 " --> pdb=" O LEU A2677 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU A2677 " --> pdb=" O THR A2672 " (cutoff:3.500A) removed outlier: 11.881A pdb=" N VAL A2710 " --> pdb=" O GLN A2678 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL A2680 " --> pdb=" O VAL A2710 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A2712 " --> pdb=" O VAL A2680 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A2682 " --> pdb=" O THR A2712 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN A2719 " --> pdb=" O ILE A2732 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 2742 through 2746 removed outlier: 3.551A pdb=" N ILE A2744 " --> pdb=" O TYR A2754 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N TYR A2754 " --> pdb=" O ILE A2744 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLN A2765 " --> pdb=" O LYS A2773 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LYS A2773 " --> pdb=" O GLN A2765 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 2779 through 2783 removed outlier: 4.184A pdb=" N ASP A2779 " --> pdb=" O GLN A2790 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 2819 through 2821 removed outlier: 6.813A pdb=" N TYR A2819 " --> pdb=" O ILE A2848 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ALA A2850 " --> pdb=" O TYR A2819 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N LEU A2821 " --> pdb=" O ALA A2850 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N ASP A2852 " --> pdb=" O LEU A2821 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE A2847 " --> pdb=" O ASP A2895 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLU A2897 " --> pdb=" O ILE A2847 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N LEU A2849 " --> pdb=" O GLU A2897 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 3135 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: 18.67 Time building geometry restraints manager: 7.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7643 1.34 - 1.46: 2962 1.46 - 1.57: 12515 1.57 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 23225 Sorted by residual: bond pdb=" CZ ARG A1573 " pdb=" NH2 ARG A1573 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 8.89e+00 bond pdb=" N ARG A1573 " pdb=" CA ARG A1573 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.44e-02 4.82e+03 6.49e+00 bond pdb=" CA GLU A1575 " pdb=" C GLU A1575 " ideal model delta sigma weight residual 1.526 1.552 -0.027 1.36e-02 5.41e+03 3.92e+00 bond pdb=" CD ARG A1530 " pdb=" NE ARG A1530 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.58e+00 bond pdb=" CZ ARG A1573 " pdb=" NH1 ARG A1573 " ideal model delta sigma weight residual 1.323 1.301 0.022 1.40e-02 5.10e+03 2.46e+00 ... (remaining 23220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 30115 1.41 - 2.82: 1152 2.82 - 4.23: 161 4.23 - 5.64: 43 5.64 - 7.04: 7 Bond angle restraints: 31478 Sorted by residual: angle pdb=" CA ARG A1573 " pdb=" C ARG A1573 " pdb=" N PHE A1574 " ideal model delta sigma weight residual 115.71 121.07 -5.36 1.60e+00 3.91e-01 1.12e+01 angle pdb=" N LYS A2880 " pdb=" CA LYS A2880 " pdb=" C LYS A2880 " ideal model delta sigma weight residual 110.41 114.30 -3.89 1.18e+00 7.18e-01 1.09e+01 angle pdb=" CA GLU A1575 " pdb=" C GLU A1575 " pdb=" N GLU A1576 " ideal model delta sigma weight residual 115.21 119.38 -4.17 1.33e+00 5.65e-01 9.83e+00 angle pdb=" N GLN A1660 " pdb=" CA GLN A1660 " pdb=" C GLN A1660 " ideal model delta sigma weight residual 109.81 116.42 -6.61 2.21e+00 2.05e-01 8.94e+00 angle pdb=" CA GLN A2484 " pdb=" CB GLN A2484 " pdb=" CG GLN A2484 " ideal model delta sigma weight residual 114.10 120.01 -5.91 2.00e+00 2.50e-01 8.73e+00 ... (remaining 31473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12813 17.94 - 35.88: 860 35.88 - 53.83: 130 53.83 - 71.77: 57 71.77 - 89.71: 30 Dihedral angle restraints: 13890 sinusoidal: 5504 harmonic: 8386 Sorted by residual: dihedral pdb=" CA ARG A2238 " pdb=" C ARG A2238 " pdb=" N MET A2239 " pdb=" CA MET A2239 " ideal model delta harmonic sigma weight residual -180.00 -150.67 -29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA GLY A2592 " pdb=" C GLY A2592 " pdb=" N PHE A2593 " pdb=" CA PHE A2593 " ideal model delta harmonic sigma weight residual 180.00 -150.70 -29.30 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA MET A2239 " pdb=" C MET A2239 " pdb=" N LEU A2240 " pdb=" CA LEU A2240 " ideal model delta harmonic sigma weight residual 180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 13887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2523 0.040 - 0.080: 708 0.080 - 0.120: 218 0.120 - 0.160: 37 0.160 - 0.201: 7 Chirality restraints: 3493 Sorted by residual: chirality pdb=" CA ILE A2920 " pdb=" N ILE A2920 " pdb=" C ILE A2920 " pdb=" CB ILE A2920 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLN A2213 " pdb=" N GLN A2213 " pdb=" C GLN A2213 " pdb=" CB GLN A2213 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" CB ILE A2297 " pdb=" CA ILE A2297 " pdb=" CG1 ILE A2297 " pdb=" CG2 ILE A2297 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.56e-01 ... (remaining 3490 not shown) Planarity restraints: 4152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A1572 " 0.019 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C THR A1572 " -0.062 2.00e-02 2.50e+03 pdb=" O THR A1572 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG A1573 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A1722 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C ALA A1722 " -0.056 2.00e-02 2.50e+03 pdb=" O ALA A1722 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU A1723 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1651 " 0.003 2.00e-02 2.50e+03 2.26e-02 1.02e+01 pdb=" CG TYR A1651 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR A1651 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR A1651 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A1651 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR A1651 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A1651 " -0.031 2.00e-02 2.50e+03 pdb=" OH TYR A1651 " 0.031 2.00e-02 2.50e+03 ... (remaining 4149 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 669 2.71 - 3.26: 23675 3.26 - 3.81: 34472 3.81 - 4.35: 44815 4.35 - 4.90: 74623 Nonbonded interactions: 178254 Sorted by model distance: nonbonded pdb=" O LEU A 144 " pdb=" OH TYR A 196 " model vdw 2.166 3.040 nonbonded pdb=" O PHE A2290 " pdb=" NH1 ARG A2311 " model vdw 2.196 3.120 nonbonded pdb=" OG SER A1054 " pdb=" OD2 ASP A1065 " model vdw 2.246 3.040 nonbonded pdb=" OG1 THR A1953 " pdb=" OD2 ASP A1966 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR A1137 " pdb=" OE2 GLU A1241 " model vdw 2.268 3.040 ... (remaining 178249 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=0.00 max=1.00 mean=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 6.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.040 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 67.010 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5428 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 : 0.002 0.039 23225 Z= 0.132 Angle : 0.633 7.044 31478 Z= 0.366 Chirality : 0.042 0.201 3493 Planarity : 0.008 0.094 4152 Dihedral : 13.730 89.711 8518 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.14), residues: 2910 helix: -1.54 (0.13), residues: 1099 sheet: -0.69 (0.21), residues: 498 loop : -1.55 (0.16), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 556 HIS 0.007 0.001 HIS A2211 PHE 0.020 0.001 PHE A1808 TYR 0.034 0.004 TYR A1651 ARG 0.024 0.003 ARG A 817 Details of bonding type rmsd hydrogen bonds : bond 0.17692 ( 1077) hydrogen bonds : angle 7.08588 ( 3135) covalent geometry : bond 0.00230 (23225) covalent geometry : angle 0.63336 (31478) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.6979 (ttm) cc_final: 0.6123 (tpt) REVERT: A 794 LEU cc_start: 0.9029 (mt) cc_final: 0.8826 (mp) REVERT: A 901 LEU cc_start: 0.8177 (mt) cc_final: 0.7946 (mt) REVERT: A 1230 TYR cc_start: 0.6604 (t80) cc_final: 0.6170 (t80) REVERT: A 1478 MET cc_start: 0.7856 (mmt) cc_final: 0.7490 (mmp) REVERT: A 1561 PRO cc_start: 0.8705 (Cg_exo) cc_final: 0.8498 (Cg_endo) REVERT: A 1685 MET cc_start: 0.7460 (tpp) cc_final: 0.7162 (mmm) REVERT: A 2346 SER cc_start: 0.8549 (t) cc_final: 0.8173 (p) REVERT: A 2825 MET cc_start: 0.7791 (tmm) cc_final: 0.7474 (tmm) REVERT: A 2852 ASP cc_start: 0.6905 (m-30) cc_final: 0.6530 (p0) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.4066 time to fit residues: 226.7138 Evaluate side-chains 169 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 0.9980 chunk 220 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 228 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 264 optimal weight: 0.7980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 63 HIS A 85 GLN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN A1052 ASN A1142 HIS A1196 GLN A1223 GLN A1234 GLN ** A1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1535 HIS A1691 HIS A1995 HIS ** A2181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.100403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.077758 restraints weight = 79678.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.078602 restraints weight = 50213.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.078802 restraints weight = 39539.348| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 544 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 539 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 23225 Z= 0.164 Angle : 0.674 11.903 31478 Z= 0.355 Chirality : 0.044 0.179 3493 Planarity : 0.004 0.046 4152 Dihedral : 5.930 28.897 3194 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.08 % Allowed : 6.55 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 2910 helix: 0.52 (0.16), residues: 1097 sheet: -0.51 (0.21), residues: 516 loop : -0.83 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A2532 HIS 0.006 0.001 HIS A 119 PHE 0.021 0.002 PHE A1727 TYR 0.028 0.002 TYR A 443 ARG 0.008 0.001 ARG A 236 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 1077) hydrogen bonds : angle 5.03371 ( 3135) covalent geometry : bond 0.00367 (23225) covalent geometry : angle 0.67360 (31478) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7844 (ttm) cc_final: 0.6670 (tpt) REVERT: A 443 TYR cc_start: 0.7179 (m-10) cc_final: 0.6950 (m-10) REVERT: A 564 LEU cc_start: 0.8744 (tt) cc_final: 0.8518 (tp) REVERT: A 757 PHE cc_start: 0.8164 (m-80) cc_final: 0.7779 (m-10) REVERT: A 1105 MET cc_start: 0.6148 (tpp) cc_final: 0.5911 (tpp) REVERT: A 1325 MET cc_start: 0.8127 (mtm) cc_final: 0.7812 (ttp) REVERT: A 1478 MET cc_start: 0.7737 (mmt) cc_final: 0.7450 (mmm) REVERT: A 1488 MET cc_start: 0.8118 (mmm) cc_final: 0.7803 (mmt) REVERT: A 1523 MET cc_start: 0.8849 (mtp) cc_final: 0.8645 (mtm) REVERT: A 1557 MET cc_start: 0.8109 (tpp) cc_final: 0.7670 (tpp) REVERT: A 2346 SER cc_start: 0.8596 (t) cc_final: 0.8313 (p) outliers start: 26 outliers final: 14 residues processed: 199 average time/residue: 0.3715 time to fit residues: 120.4099 Evaluate side-chains 145 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2920 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 60 optimal weight: 4.9990 chunk 200 optimal weight: 0.9990 chunk 246 optimal weight: 0.0970 chunk 99 optimal weight: 0.0070 chunk 282 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 chunk 235 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 432 GLN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2181 GLN ** A2200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.098533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.077232 restraints weight = 79559.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.076826 restraints weight = 49102.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.077711 restraints weight = 44537.544| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 539 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 563 | |-----------------------------------------------------------------------------| r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23225 Z= 0.111 Angle : 0.581 11.384 31478 Z= 0.304 Chirality : 0.041 0.181 3493 Planarity : 0.004 0.076 4152 Dihedral : 5.287 26.939 3194 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.24 % Allowed : 7.51 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 2910 helix: 1.09 (0.16), residues: 1093 sheet: -0.28 (0.22), residues: 518 loop : -0.70 (0.18), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2570 HIS 0.005 0.001 HIS A 119 PHE 0.022 0.001 PHE A2241 TYR 0.022 0.001 TYR A 443 ARG 0.009 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 1077) hydrogen bonds : angle 4.65007 ( 3135) covalent geometry : bond 0.00227 (23225) covalent geometry : angle 0.58059 (31478) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7791 (ttm) cc_final: 0.6644 (tpt) REVERT: A 443 TYR cc_start: 0.7050 (m-10) cc_final: 0.6814 (m-10) REVERT: A 564 LEU cc_start: 0.8696 (tt) cc_final: 0.8473 (tp) REVERT: A 677 GLU cc_start: 0.7982 (mp0) cc_final: 0.7607 (tp30) REVERT: A 692 PRO cc_start: 0.8002 (Cg_exo) cc_final: 0.7766 (Cg_endo) REVERT: A 1325 MET cc_start: 0.8127 (mtm) cc_final: 0.7837 (ttp) REVERT: A 1478 MET cc_start: 0.7706 (mmt) cc_final: 0.7407 (mmm) REVERT: A 1488 MET cc_start: 0.8037 (mmm) cc_final: 0.7660 (mmm) REVERT: A 1557 MET cc_start: 0.8057 (tpp) cc_final: 0.7653 (tpp) REVERT: A 2346 SER cc_start: 0.8421 (t) cc_final: 0.8133 (p) REVERT: A 2364 ARG cc_start: 0.6742 (ttt180) cc_final: 0.6134 (tpp80) outliers start: 30 outliers final: 19 residues processed: 174 average time/residue: 0.3322 time to fit residues: 96.5343 Evaluate side-chains 148 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 1764 VAL Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2453 LEU Chi-restraints excluded: chain A residue 2851 VAL Chi-restraints excluded: chain A residue 2920 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 3 optimal weight: 0.4980 chunk 138 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1339 GLN ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2636 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.098820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.074990 restraints weight = 79710.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.075702 restraints weight = 51664.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.076684 restraints weight = 38396.147| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 563 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 567 | |-----------------------------------------------------------------------------| r_final: 0.3627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23225 Z= 0.128 Angle : 0.575 11.666 31478 Z= 0.300 Chirality : 0.042 0.177 3493 Planarity : 0.004 0.048 4152 Dihedral : 4.982 26.298 3194 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.46 % Rotamer: Outliers : 1.78 % Allowed : 8.34 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2910 helix: 1.25 (0.16), residues: 1100 sheet: -0.40 (0.22), residues: 531 loop : -0.75 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2273 HIS 0.005 0.001 HIS A 119 PHE 0.020 0.001 PHE A2241 TYR 0.019 0.001 TYR A 196 ARG 0.005 0.000 ARG A 679 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 1077) hydrogen bonds : angle 4.54428 ( 3135) covalent geometry : bond 0.00281 (23225) covalent geometry : angle 0.57487 (31478) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.8458 (m-40) cc_final: 0.8253 (m-40) REVERT: A 99 TYR cc_start: 0.7830 (t80) cc_final: 0.7402 (t80) REVERT: A 130 MET cc_start: 0.7785 (ttm) cc_final: 0.6635 (tpt) REVERT: A 533 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7187 (m110) REVERT: A 564 LEU cc_start: 0.8708 (tt) cc_final: 0.8486 (tp) REVERT: A 593 GLN cc_start: 0.9000 (tt0) cc_final: 0.8730 (mt0) REVERT: A 638 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7574 (pt0) REVERT: A 676 ASN cc_start: 0.8797 (m-40) cc_final: 0.8486 (t0) REVERT: A 677 GLU cc_start: 0.8043 (mp0) cc_final: 0.7603 (tp30) REVERT: A 1325 MET cc_start: 0.8127 (mtm) cc_final: 0.7832 (ttp) REVERT: A 2346 SER cc_start: 0.8463 (t) cc_final: 0.8189 (p) REVERT: A 2924 GLU cc_start: 0.7043 (pm20) cc_final: 0.6801 (pm20) outliers start: 43 outliers final: 25 residues processed: 181 average time/residue: 0.3372 time to fit residues: 102.5263 Evaluate side-chains 156 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1688 LEU Chi-restraints excluded: chain A residue 1764 VAL Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1827 VAL Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2851 VAL Chi-restraints excluded: chain A residue 2920 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 66 optimal weight: 0.9980 chunk 236 optimal weight: 10.0000 chunk 40 optimal weight: 0.0770 chunk 171 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 217 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN A 164 GLN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 HIS A1765 GLN A1883 GLN ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2483 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.096997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.071920 restraints weight = 80308.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.073265 restraints weight = 50702.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.073598 restraints weight = 35753.670| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 567 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 567 | |-----------------------------------------------------------------------------| r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23225 Z= 0.160 Angle : 0.594 10.931 31478 Z= 0.311 Chirality : 0.043 0.205 3493 Planarity : 0.004 0.067 4152 Dihedral : 4.998 27.648 3194 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.71 % Favored : 96.25 % Rotamer: Outliers : 1.95 % Allowed : 9.66 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2910 helix: 1.31 (0.16), residues: 1105 sheet: -0.52 (0.21), residues: 539 loop : -0.83 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A2273 HIS 0.010 0.001 HIS A 119 PHE 0.017 0.002 PHE A1479 TYR 0.025 0.002 TYR A 602 ARG 0.015 0.001 ARG A 595 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 1077) hydrogen bonds : angle 4.59938 ( 3135) covalent geometry : bond 0.00363 (23225) covalent geometry : angle 0.59412 (31478) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7850 (ttm) cc_final: 0.6686 (tpt) REVERT: A 160 LYS cc_start: 0.8721 (tttm) cc_final: 0.8168 (tppt) REVERT: A 195 ARG cc_start: 0.8566 (mmp80) cc_final: 0.8211 (mmp80) REVERT: A 233 MET cc_start: 0.7609 (mpp) cc_final: 0.7351 (mpp) REVERT: A 397 THR cc_start: 0.5407 (m) cc_final: 0.5196 (p) REVERT: A 533 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7338 (m110) REVERT: A 593 GLN cc_start: 0.9037 (tt0) cc_final: 0.8686 (mt0) REVERT: A 676 ASN cc_start: 0.8803 (m-40) cc_final: 0.8501 (t0) REVERT: A 677 GLU cc_start: 0.8116 (mp0) cc_final: 0.7642 (tp30) REVERT: A 731 ASN cc_start: 0.8449 (m-40) cc_final: 0.8025 (m110) REVERT: A 809 MET cc_start: 0.8139 (ttp) cc_final: 0.7836 (mtp) REVERT: A 1325 MET cc_start: 0.8174 (mtm) cc_final: 0.7880 (ttp) REVERT: A 1478 MET cc_start: 0.7994 (mmm) cc_final: 0.7605 (mmm) outliers start: 47 outliers final: 32 residues processed: 168 average time/residue: 0.3272 time to fit residues: 92.4581 Evaluate side-chains 153 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 1022 PHE Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1764 VAL Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1827 VAL Chi-restraints excluded: chain A residue 1964 VAL Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2800 MET Chi-restraints excluded: chain A residue 2851 VAL Chi-restraints excluded: chain A residue 2920 ILE Chi-restraints excluded: chain A residue 2929 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 2 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 chunk 258 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 29 optimal weight: 0.1980 chunk 189 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 81 GLN ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 945 HIS A1765 GLN ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.095932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.072000 restraints weight = 79551.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.072679 restraints weight = 51268.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.073398 restraints weight = 38689.304| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 567 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 572 | |-----------------------------------------------------------------------------| r_final: 0.3553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23225 Z= 0.172 Angle : 0.595 10.341 31478 Z= 0.312 Chirality : 0.043 0.193 3493 Planarity : 0.004 0.053 4152 Dihedral : 4.974 28.186 3194 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.05 % Favored : 95.91 % Rotamer: Outliers : 1.99 % Allowed : 10.54 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2910 helix: 1.30 (0.16), residues: 1104 sheet: -0.62 (0.21), residues: 551 loop : -0.94 (0.18), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A2273 HIS 0.015 0.001 HIS A 119 PHE 0.016 0.002 PHE A2590 TYR 0.018 0.002 TYR A2313 ARG 0.006 0.000 ARG A2370 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 1077) hydrogen bonds : angle 4.60786 ( 3135) covalent geometry : bond 0.00392 (23225) covalent geometry : angle 0.59473 (31478) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7278 (tm-30) cc_final: 0.6951 (tm-30) REVERT: A 87 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6819 (tmm) REVERT: A 130 MET cc_start: 0.7859 (ttm) cc_final: 0.6735 (tpt) REVERT: A 195 ARG cc_start: 0.8432 (mmp80) cc_final: 0.8152 (mmp80) REVERT: A 482 LYS cc_start: 0.8702 (mmmt) cc_final: 0.8176 (tppt) REVERT: A 491 MET cc_start: 0.5562 (tpt) cc_final: 0.5277 (tpt) REVERT: A 533 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7341 (m110) REVERT: A 676 ASN cc_start: 0.8743 (m-40) cc_final: 0.8521 (t0) REVERT: A 677 GLU cc_start: 0.8146 (mp0) cc_final: 0.7708 (tp30) REVERT: A 731 ASN cc_start: 0.8389 (m-40) cc_final: 0.8066 (m110) REVERT: A 809 MET cc_start: 0.8197 (ttp) cc_final: 0.7911 (mtp) REVERT: A 1325 MET cc_start: 0.8146 (mtm) cc_final: 0.7879 (ttp) REVERT: A 1478 MET cc_start: 0.7998 (mmm) cc_final: 0.7562 (mmm) REVERT: A 2825 MET cc_start: 0.7575 (tmm) cc_final: 0.7182 (tmm) REVERT: A 2924 GLU cc_start: 0.7307 (pm20) cc_final: 0.7040 (pm20) outliers start: 48 outliers final: 32 residues processed: 166 average time/residue: 0.4338 time to fit residues: 122.8934 Evaluate side-chains 154 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1022 PHE Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1764 VAL Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1827 VAL Chi-restraints excluded: chain A residue 1964 VAL Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2800 MET Chi-restraints excluded: chain A residue 2851 VAL Chi-restraints excluded: chain A residue 2920 ILE Chi-restraints excluded: chain A residue 2929 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 248 optimal weight: 0.6980 chunk 196 optimal weight: 0.1980 chunk 187 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 202 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN A1765 GLN ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.096235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.071434 restraints weight = 79555.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.072916 restraints weight = 50945.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.072893 restraints weight = 35272.541| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 572 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 573 | |-----------------------------------------------------------------------------| r_final: 0.3539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23225 Z= 0.131 Angle : 0.564 11.345 31478 Z= 0.296 Chirality : 0.042 0.201 3493 Planarity : 0.004 0.049 4152 Dihedral : 4.812 27.045 3194 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.01 % Rotamer: Outliers : 1.66 % Allowed : 11.32 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.16), residues: 2910 helix: 1.40 (0.16), residues: 1104 sheet: -0.58 (0.21), residues: 551 loop : -0.94 (0.18), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 556 HIS 0.020 0.001 HIS A 119 PHE 0.015 0.001 PHE A2241 TYR 0.013 0.001 TYR A2313 ARG 0.005 0.000 ARG A2055 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 1077) hydrogen bonds : angle 4.54087 ( 3135) covalent geometry : bond 0.00289 (23225) covalent geometry : angle 0.56385 (31478) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7365 (tm-30) cc_final: 0.6980 (tm-30) REVERT: A 87 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6829 (tmm) REVERT: A 124 TRP cc_start: 0.7329 (t60) cc_final: 0.6745 (t60) REVERT: A 130 MET cc_start: 0.7939 (ttm) cc_final: 0.6819 (tpt) REVERT: A 195 ARG cc_start: 0.8510 (mmp80) cc_final: 0.8254 (mmp80) REVERT: A 482 LYS cc_start: 0.8660 (mmmt) cc_final: 0.8140 (tppt) REVERT: A 491 MET cc_start: 0.5229 (tpt) cc_final: 0.4993 (tpt) REVERT: A 533 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7377 (m110) REVERT: A 676 ASN cc_start: 0.8815 (m-40) cc_final: 0.8540 (t0) REVERT: A 677 GLU cc_start: 0.8225 (mp0) cc_final: 0.7732 (tp30) REVERT: A 731 ASN cc_start: 0.8337 (m-40) cc_final: 0.8055 (m110) REVERT: A 809 MET cc_start: 0.8209 (ttp) cc_final: 0.7951 (mtp) REVERT: A 1105 MET cc_start: 0.6482 (tpp) cc_final: 0.5709 (ttp) REVERT: A 1325 MET cc_start: 0.8186 (mtm) cc_final: 0.7836 (ptp) REVERT: A 1478 MET cc_start: 0.8049 (mmm) cc_final: 0.7584 (mmm) REVERT: A 2133 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7705 (mt) REVERT: A 2825 MET cc_start: 0.7599 (tmm) cc_final: 0.7147 (tmm) REVERT: A 2924 GLU cc_start: 0.7209 (pm20) cc_final: 0.6944 (pm20) outliers start: 40 outliers final: 29 residues processed: 164 average time/residue: 0.3300 time to fit residues: 92.0648 Evaluate side-chains 152 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 1022 PHE Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1764 VAL Chi-restraints excluded: chain A residue 1765 GLN Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1827 VAL Chi-restraints excluded: chain A residue 1964 VAL Chi-restraints excluded: chain A residue 2133 ILE Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2445 VAL Chi-restraints excluded: chain A residue 2800 MET Chi-restraints excluded: chain A residue 2920 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 289 optimal weight: 0.7980 chunk 262 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 108 optimal weight: 0.0370 chunk 228 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 chunk 209 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 overall best weight: 0.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN A1765 GLN ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2538 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.096393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.073481 restraints weight = 79419.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.073978 restraints weight = 46889.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.073884 restraints weight = 41208.553| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 573 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 578 | |-----------------------------------------------------------------------------| r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23225 Z= 0.120 Angle : 0.551 11.731 31478 Z= 0.289 Chirality : 0.041 0.279 3493 Planarity : 0.004 0.048 4152 Dihedral : 4.705 26.181 3194 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 1.87 % Allowed : 11.41 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2910 helix: 1.47 (0.16), residues: 1104 sheet: -0.52 (0.22), residues: 551 loop : -0.95 (0.18), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 556 HIS 0.022 0.001 HIS A 119 PHE 0.015 0.001 PHE A2241 TYR 0.011 0.001 TYR A2313 ARG 0.007 0.000 ARG A2055 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 1077) hydrogen bonds : angle 4.48112 ( 3135) covalent geometry : bond 0.00264 (23225) covalent geometry : angle 0.55132 (31478) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7447 (tm-30) cc_final: 0.7107 (tm-30) REVERT: A 87 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6792 (tmm) REVERT: A 124 TRP cc_start: 0.7420 (t60) cc_final: 0.6696 (t60) REVERT: A 130 MET cc_start: 0.7910 (ttm) cc_final: 0.6795 (tpt) REVERT: A 232 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6479 (tpp) REVERT: A 482 LYS cc_start: 0.8579 (mmmt) cc_final: 0.8058 (tppt) REVERT: A 491 MET cc_start: 0.5352 (tpt) cc_final: 0.5104 (tpt) REVERT: A 533 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7425 (m110) REVERT: A 676 ASN cc_start: 0.8787 (m-40) cc_final: 0.8518 (t0) REVERT: A 677 GLU cc_start: 0.8213 (mp0) cc_final: 0.7720 (tp30) REVERT: A 725 ASP cc_start: 0.8632 (t70) cc_final: 0.8221 (t0) REVERT: A 731 ASN cc_start: 0.8319 (m-40) cc_final: 0.8088 (m110) REVERT: A 809 MET cc_start: 0.8196 (ttp) cc_final: 0.7949 (mtp) REVERT: A 1325 MET cc_start: 0.8129 (mtm) cc_final: 0.7851 (ptp) REVERT: A 1478 MET cc_start: 0.8043 (mmm) cc_final: 0.7599 (mmm) REVERT: A 2133 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7774 (mt) REVERT: A 2924 GLU cc_start: 0.7142 (pm20) cc_final: 0.6915 (pm20) outliers start: 45 outliers final: 36 residues processed: 166 average time/residue: 0.4066 time to fit residues: 115.7445 Evaluate side-chains 160 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 3.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 904 GLN Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1022 PHE Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1764 VAL Chi-restraints excluded: chain A residue 1765 GLN Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1827 VAL Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2133 ILE Chi-restraints excluded: chain A residue 2191 GLN Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2445 VAL Chi-restraints excluded: chain A residue 2453 LEU Chi-restraints excluded: chain A residue 2547 THR Chi-restraints excluded: chain A residue 2800 MET Chi-restraints excluded: chain A residue 2920 ILE Chi-restraints excluded: chain A residue 2929 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 7 optimal weight: 8.9990 chunk 203 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 254 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 GLN A1196 GLN A2058 HIS ** A2181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2366 ASN A2497 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.093768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.070548 restraints weight = 79527.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.071032 restraints weight = 49009.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.070982 restraints weight = 39424.017| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 578 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 577 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 23225 Z= 0.240 Angle : 0.680 10.952 31478 Z= 0.357 Chirality : 0.045 0.194 3493 Planarity : 0.005 0.052 4152 Dihedral : 5.248 30.246 3194 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.09 % Favored : 94.88 % Rotamer: Outliers : 1.91 % Allowed : 12.11 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.16), residues: 2910 helix: 1.18 (0.16), residues: 1099 sheet: -0.77 (0.21), residues: 562 loop : -1.17 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A2273 HIS 0.024 0.001 HIS A 119 PHE 0.021 0.002 PHE A2590 TYR 0.022 0.002 TYR A2313 ARG 0.009 0.001 ARG A1596 Details of bonding type rmsd hydrogen bonds : bond 0.04632 ( 1077) hydrogen bonds : angle 4.85061 ( 3135) covalent geometry : bond 0.00549 (23225) covalent geometry : angle 0.68036 (31478) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7716 (tm-30) cc_final: 0.7457 (tm-30) REVERT: A 130 MET cc_start: 0.8021 (ttm) cc_final: 0.6904 (tpt) REVERT: A 232 MET cc_start: 0.7074 (OUTLIER) cc_final: 0.6549 (tpp) REVERT: A 482 LYS cc_start: 0.8569 (mmmt) cc_final: 0.8102 (mmtt) REVERT: A 491 MET cc_start: 0.5505 (tpt) cc_final: 0.5253 (tpt) REVERT: A 533 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7351 (m110) REVERT: A 676 ASN cc_start: 0.8792 (m-40) cc_final: 0.8575 (t0) REVERT: A 677 GLU cc_start: 0.8288 (mp0) cc_final: 0.7801 (tp30) REVERT: A 1105 MET cc_start: 0.6561 (tpp) cc_final: 0.5804 (ttp) REVERT: A 1325 MET cc_start: 0.8210 (mtm) cc_final: 0.7865 (ptp) REVERT: A 1478 MET cc_start: 0.8090 (mmm) cc_final: 0.7656 (mmm) REVERT: A 2133 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7809 (mt) REVERT: A 2311 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6551 (ttt90) outliers start: 46 outliers final: 37 residues processed: 164 average time/residue: 0.3222 time to fit residues: 87.6775 Evaluate side-chains 157 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 904 GLN Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1022 PHE Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1825 ASN Chi-restraints excluded: chain A residue 1827 VAL Chi-restraints excluded: chain A residue 1964 VAL Chi-restraints excluded: chain A residue 1978 ILE Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2133 ILE Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2311 ARG Chi-restraints excluded: chain A residue 2359 ILE Chi-restraints excluded: chain A residue 2445 VAL Chi-restraints excluded: chain A residue 2453 LEU Chi-restraints excluded: chain A residue 2547 THR Chi-restraints excluded: chain A residue 2800 MET Chi-restraints excluded: chain A residue 2920 ILE Chi-restraints excluded: chain A residue 2929 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 231 optimal weight: 0.9980 chunk 255 optimal weight: 0.9980 chunk 268 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 284 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 107 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS A 707 HIS ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2613 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.095535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.072622 restraints weight = 79686.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.073317 restraints weight = 45743.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.073245 restraints weight = 41605.628| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 577 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 577 | |-----------------------------------------------------------------------------| r_final: 0.3551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23225 Z= 0.123 Angle : 0.585 11.610 31478 Z= 0.303 Chirality : 0.042 0.167 3493 Planarity : 0.004 0.048 4152 Dihedral : 4.797 26.553 3194 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 1.37 % Allowed : 12.82 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2910 helix: 1.38 (0.16), residues: 1104 sheet: -0.60 (0.22), residues: 544 loop : -1.07 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2273 HIS 0.023 0.001 HIS A2861 PHE 0.015 0.001 PHE A2241 TYR 0.013 0.001 TYR A 475 ARG 0.007 0.000 ARG A 758 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 1077) hydrogen bonds : angle 4.53648 ( 3135) covalent geometry : bond 0.00270 (23225) covalent geometry : angle 0.58522 (31478) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7648 (tm-30) cc_final: 0.7365 (tm-30) REVERT: A 87 MET cc_start: 0.7184 (ttm) cc_final: 0.6967 (ptt) REVERT: A 124 TRP cc_start: 0.7467 (t60) cc_final: 0.6740 (t60) REVERT: A 130 MET cc_start: 0.7990 (ttm) cc_final: 0.6874 (tpt) REVERT: A 195 ARG cc_start: 0.8434 (mmp80) cc_final: 0.8229 (mmp80) REVERT: A 225 PRO cc_start: 0.7305 (Cg_exo) cc_final: 0.7092 (Cg_endo) REVERT: A 232 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6473 (tpp) REVERT: A 481 GLU cc_start: 0.8064 (pt0) cc_final: 0.7474 (pt0) REVERT: A 491 MET cc_start: 0.5307 (tpt) cc_final: 0.5020 (tpt) REVERT: A 533 ASN cc_start: 0.8117 (OUTLIER) cc_final: 0.7443 (m110) REVERT: A 677 GLU cc_start: 0.8241 (mp0) cc_final: 0.7769 (tp30) REVERT: A 809 MET cc_start: 0.8220 (ttp) cc_final: 0.8002 (mtp) REVERT: A 1105 MET cc_start: 0.6501 (tpp) cc_final: 0.5776 (ttp) REVERT: A 1325 MET cc_start: 0.8131 (mtm) cc_final: 0.7895 (ptp) REVERT: A 1478 MET cc_start: 0.8031 (mmm) cc_final: 0.7601 (mmm) REVERT: A 2133 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7823 (mt) REVERT: A 2237 ASP cc_start: 0.5945 (p0) cc_final: 0.5652 (p0) outliers start: 33 outliers final: 30 residues processed: 149 average time/residue: 0.3205 time to fit residues: 81.9589 Evaluate side-chains 147 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 904 GLN Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1022 PHE Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1807 LEU Chi-restraints excluded: chain A residue 1827 VAL Chi-restraints excluded: chain A residue 1964 VAL Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2133 ILE Chi-restraints excluded: chain A residue 2191 GLN Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2359 ILE Chi-restraints excluded: chain A residue 2445 VAL Chi-restraints excluded: chain A residue 2453 LEU Chi-restraints excluded: chain A residue 2547 THR Chi-restraints excluded: chain A residue 2920 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 188 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 283 optimal weight: 0.6980 chunk 262 optimal weight: 0.8980 chunk 268 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 272 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2181 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 = 0.4080 r_free = 0.4080 target = 0.097296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.073647 restraints weight = 79219.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.074695 restraints weight = 48746.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.075465 restraints weight = 35478.228| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 577 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 580 | |-----------------------------------------------------------------------------| r_final: 0.3610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23225 Z= 0.122 Angle : 0.578 11.710 31478 Z= 0.300 Chirality : 0.042 0.186 3493 Planarity : 0.004 0.047 4152 Dihedral : 4.662 25.460 3194 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.33 % Favored : 95.64 % Rotamer: Outliers : 1.66 % Allowed : 12.94 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.16), residues: 2910 helix: 1.45 (0.16), residues: 1102 sheet: -0.50 (0.22), residues: 544 loop : -1.03 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 556 HIS 0.025 0.001 HIS A 119 PHE 0.021 0.001 PHE A 480 TYR 0.012 0.001 TYR A 602 ARG 0.009 0.000 ARG A 503 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 1077) hydrogen bonds : angle 4.46555 ( 3135) covalent geometry : bond 0.00268 (23225) covalent geometry : angle 0.57760 (31478) =============================================================================== Job complete usr+sys time: 9638.84 seconds wall clock time: 169 minutes 48.90 seconds (10188.90 seconds total)