Starting phenix.real_space_refine on Fri Feb 16 09:38:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r77_24294/02_2024/7r77_24294_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r77_24294/02_2024/7r77_24294.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r77_24294/02_2024/7r77_24294_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r77_24294/02_2024/7r77_24294_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r77_24294/02_2024/7r77_24294_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r77_24294/02_2024/7r77_24294.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r77_24294/02_2024/7r77_24294.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r77_24294/02_2024/7r77_24294_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r77_24294/02_2024/7r77_24294_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 24 5.49 5 S 70 5.16 5 C 9338 2.51 5 N 2709 2.21 5 O 2834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 309": "NH1" <-> "NH2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A ARG 592": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A ARG 781": "NH1" <-> "NH2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A GLU 863": "OE1" <-> "OE2" Residue "A GLU 865": "OE1" <-> "OE2" Residue "A ARG 867": "NH1" <-> "NH2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A ARG 877": "NH1" <-> "NH2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A ARG 923": "NH1" <-> "NH2" Residue "A ARG 925": "NH1" <-> "NH2" Residue "A GLU 938": "OE1" <-> "OE2" Residue "A GLU 1009": "OE1" <-> "OE2" Residue "A GLU 1048": "OE1" <-> "OE2" Residue "A ARG 1053": "NH1" <-> "NH2" Residue "A ARG 1064": "NH1" <-> "NH2" Residue "A ARG 1076": "NH1" <-> "NH2" Residue "A GLU 1101": "OE1" <-> "OE2" Residue "A GLU 1134": "OE1" <-> "OE2" Residue "A ARG 1179": "NH1" <-> "NH2" Residue "A GLU 1198": "OE1" <-> "OE2" Residue "A ARG 1210": "NH1" <-> "NH2" Residue "A GLU 1268": "OE1" <-> "OE2" Residue "A ARG 1273": "NH1" <-> "NH2" Residue "A ARG 1329": "NH1" <-> "NH2" Residue "A ARG 1353": "NH1" <-> "NH2" Residue "A ARG 1368": "NH1" <-> "NH2" Residue "A ARG 1406": "NH1" <-> "NH2" Residue "A ARG 1411": "NH1" <-> "NH2" Residue "A GLU 1418": "OE1" <-> "OE2" Residue "A GLU 1432": "OE1" <-> "OE2" Residue "A ARG 1445": "NH1" <-> "NH2" Residue "A ARG 1457": "NH1" <-> "NH2" Residue "A GLU 1487": "OE1" <-> "OE2" Residue "A GLU 1541": "OE1" <-> "OE2" Residue "A GLU 1556": "OE1" <-> "OE2" Residue "A GLU 1565": "OE1" <-> "OE2" Residue "A GLU 1573": "OE1" <-> "OE2" Residue "A ARG 1582": "NH1" <-> "NH2" Residue "A GLU 1593": "OE1" <-> "OE2" Residue "A ARG 1788": "NH1" <-> "NH2" Residue "A ARG 1802": "NH1" <-> "NH2" Residue "A GLU 1815": "OE1" <-> "OE2" Residue "A GLU 1856": "OE1" <-> "OE2" Residue "A GLU 1858": "OE1" <-> "OE2" Residue "A GLU 1888": "OE1" <-> "OE2" Residue "A ARG 1903": "NH1" <-> "NH2" Residue "A GLU 1941": "OE1" <-> "OE2" Residue "A GLU 1991": "OE1" <-> "OE2" Residue "A ARG 2036": "NH1" <-> "NH2" Residue "A GLU 2037": "OE1" <-> "OE2" Residue "A GLU 2080": "OE1" <-> "OE2" Residue "A GLU 2122": "OE1" <-> "OE2" Residue "A GLU 2141": "OE1" <-> "OE2" Residue "A ARG 2148": "NH1" <-> "NH2" Residue "A GLU 2167": "OE1" <-> "OE2" Residue "A PHE 2172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2176": "OE1" <-> "OE2" Residue "A ARG 2190": "NH1" <-> "NH2" Residue "A GLU 2297": "OE1" <-> "OE2" Residue "A GLU 2305": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14980 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 14464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1830, 14464 Classifications: {'peptide': 1830} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 88, 'TRANS': 1741} Chain breaks: 11 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' ZN': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3883 SG CYS A 817 65.967 70.429 59.010 1.00 26.78 S ATOM 3898 SG CYS A 819 63.523 67.857 59.085 1.00 30.19 S ATOM 4052 SG CYS A 840 64.629 70.291 62.140 1.00 27.50 S ATOM 4073 SG CYS A 843 67.026 67.639 61.788 1.00 30.66 S ATOM 6739 SG CYS A1200 35.062 39.965 34.272 1.00 59.77 S ATOM 7299 SG CYS A1271 35.622 36.983 35.898 1.00 70.35 S ATOM 7325 SG CYS A1274 37.968 39.423 35.974 1.00 53.10 S ATOM 3988 SG CYS A 832 74.246 81.825 60.784 1.00 28.82 S ATOM 4012 SG CYS A 835 76.389 80.860 57.365 1.00 29.36 S ATOM 5839 SG CYS A1065 78.003 80.945 60.453 1.00 30.34 S ATOM 12714 SG CYS A2081 88.599 80.915 82.593 1.00 75.53 S ATOM 12901 SG CYS A2107 85.651 82.602 81.187 1.00 56.57 S ATOM 12844 SG CYS A2099 85.323 67.384 84.585 1.00 44.10 S ATOM 13017 SG CYS A2123 89.315 67.024 82.960 1.00 54.15 S Time building chain proxies: 8.26, per 1000 atoms: 0.55 Number of scatterers: 14980 At special positions: 0 Unit cell: (120.232, 110.656, 124.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 S 70 16.00 P 24 15.00 O 2834 8.00 N 2709 7.00 C 9338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.12 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2401 " pdb="ZN ZN A2401 " - pdb=" SG CYS A 817 " pdb="ZN ZN A2401 " - pdb=" SG CYS A 819 " pdb="ZN ZN A2401 " - pdb=" SG CYS A 840 " pdb="ZN ZN A2401 " - pdb=" SG CYS A 843 " pdb=" ZN A2402 " pdb="ZN ZN A2402 " - pdb=" ND1 HIS A1348 " pdb="ZN ZN A2402 " - pdb=" SG CYS A1271 " pdb="ZN ZN A2402 " - pdb=" SG CYS A1200 " pdb="ZN ZN A2402 " - pdb=" SG CYS A1274 " pdb=" ZN A2403 " pdb="ZN ZN A2403 " - pdb=" SG CYS A 832 " pdb="ZN ZN A2403 " - pdb=" SG CYS A 835 " pdb="ZN ZN A2403 " - pdb=" ND1 HIS A 849 " pdb="ZN ZN A2403 " - pdb=" SG CYS A1065 " pdb=" ZN A2404 " pdb="ZN ZN A2404 " - pdb=" SG CYS A2081 " pdb="ZN ZN A2404 " - pdb=" ND1 HIS A2083 " pdb="ZN ZN A2404 " - pdb=" SG CYS A2107 " pdb=" ZN A2405 " pdb="ZN ZN A2405 " - pdb=" SG CYS A2123 " pdb="ZN ZN A2405 " - pdb=" SG CYS A2099 " Number of angles added : 12 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 15 sheets defined 36.6% alpha, 11.5% beta 9 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 8.63 Creating SS restraints... Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 333 through 341 removed outlier: 3.535A pdb=" N VAL A 336 " --> pdb=" O PRO A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 374 Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 488 through 497 Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 535 through 545 Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 564 through 579 Processing helix chain 'A' and resid 591 through 603 removed outlier: 3.944A pdb=" N ARG A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 632 No H-bonds generated for 'chain 'A' and resid 629 through 632' Processing helix chain 'A' and resid 637 through 653 removed outlier: 3.898A pdb=" N ASP A 653 " --> pdb=" O ARG A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 709 removed outlier: 3.853A pdb=" N GLN A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 736 through 749 Processing helix chain 'A' and resid 760 through 780 Processing helix chain 'A' and resid 803 through 813 Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 883 through 895 Processing helix chain 'A' and resid 903 through 917 Processing helix chain 'A' and resid 970 through 974 Processing helix chain 'A' and resid 1020 through 1024 Processing helix chain 'A' and resid 1045 through 1050 Processing helix chain 'A' and resid 1190 through 1194 Processing helix chain 'A' and resid 1232 through 1242 removed outlier: 7.126A pdb=" N ASN A1237 " --> pdb=" O SER A1233 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR A1238 " --> pdb=" O HIS A1234 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN A1242 " --> pdb=" O THR A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1249 removed outlier: 4.484A pdb=" N ARG A1249 " --> pdb=" O TRP A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1307 through 1318 Processing helix chain 'A' and resid 1343 through 1353 Processing helix chain 'A' and resid 1407 through 1421 removed outlier: 3.532A pdb=" N ARG A1411 " --> pdb=" O LYS A1407 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A1412 " --> pdb=" O GLU A1408 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP A1415 " --> pdb=" O ARG A1411 " (cutoff:3.500A) Processing helix chain 'A' and resid 1470 through 1481 Processing helix chain 'A' and resid 1508 through 1518 Proline residue: A1512 - end of helix removed outlier: 3.609A pdb=" N ARG A1517 " --> pdb=" O ASN A1513 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A1518 " --> pdb=" O GLU A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1539 through 1542 No H-bonds generated for 'chain 'A' and resid 1539 through 1542' Processing helix chain 'A' and resid 1552 through 1556 Processing helix chain 'A' and resid 1558 through 1568 Processing helix chain 'A' and resid 1582 through 1600 Processing helix chain 'A' and resid 1714 through 1716 No H-bonds generated for 'chain 'A' and resid 1714 through 1716' Processing helix chain 'A' and resid 1735 through 1740 Processing helix chain 'A' and resid 1758 through 1768 Processing helix chain 'A' and resid 1782 through 1791 removed outlier: 4.516A pdb=" N ASP A1791 " --> pdb=" O ALA A1787 " (cutoff:3.500A) Processing helix chain 'A' and resid 1794 through 1802 removed outlier: 3.813A pdb=" N PHE A1801 " --> pdb=" O LYS A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1807 through 1824 Processing helix chain 'A' and resid 1848 through 1863 removed outlier: 3.781A pdb=" N VAL A1853 " --> pdb=" O SER A1849 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A1854 " --> pdb=" O GLU A1850 " (cutoff:3.500A) Processing helix chain 'A' and resid 1877 through 1889 removed outlier: 5.324A pdb=" N ALA A1889 " --> pdb=" O ARG A1885 " (cutoff:3.500A) Processing helix chain 'A' and resid 1896 through 1905 Processing helix chain 'A' and resid 1923 through 1960 removed outlier: 3.686A pdb=" N LYS A1960 " --> pdb=" O TRP A1956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1972 through 1980 Processing helix chain 'A' and resid 1990 through 2002 Processing helix chain 'A' and resid 2028 through 2067 Processing helix chain 'A' and resid 2070 through 2077 removed outlier: 3.641A pdb=" N VAL A2075 " --> pdb=" O ASP A2071 " (cutoff:3.500A) Processing helix chain 'A' and resid 2106 through 2114 removed outlier: 3.652A pdb=" N LYS A2110 " --> pdb=" O LYS A2106 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA A2111 " --> pdb=" O CYS A2107 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2131 No H-bonds generated for 'chain 'A' and resid 2129 through 2131' Processing helix chain 'A' and resid 2135 through 2138 No H-bonds generated for 'chain 'A' and resid 2135 through 2138' Processing helix chain 'A' and resid 2151 through 2162 Processing helix chain 'A' and resid 2176 through 2188 removed outlier: 4.079A pdb=" N GLY A2180 " --> pdb=" O ASP A2177 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A2184 " --> pdb=" O LYS A2181 " (cutoff:3.500A) Processing helix chain 'A' and resid 2202 through 2210 Processing helix chain 'A' and resid 2252 through 2266 removed outlier: 3.871A pdb=" N VAL A2266 " --> pdb=" O ALA A2262 " (cutoff:3.500A) Processing helix chain 'A' and resid 2286 through 2302 removed outlier: 3.515A pdb=" N LYS A2299 " --> pdb=" O ARG A2295 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A2300 " --> pdb=" O THR A2296 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A2302 " --> pdb=" O LEU A2298 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 500 through 508 removed outlier: 6.474A pdb=" N LEU A 434 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLU A 481 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA A 436 " --> pdb=" O GLU A 481 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR A 351 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 663 through 665 Processing sheet with id= C, first strand: chain 'A' and resid 830 through 832 Processing sheet with id= D, first strand: chain 'A' and resid 876 through 879 Processing sheet with id= E, first strand: chain 'A' and resid 1146 through 1148 removed outlier: 3.922A pdb=" N ALA A 980 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TRP A 933 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR A 926 " --> pdb=" O VAL A 936 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLU A 938 " --> pdb=" O PHE A 924 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N PHE A 924 " --> pdb=" O GLU A 938 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1136 through 1144 removed outlier: 3.542A pdb=" N GLU A1009 " --> pdb=" O SER A1042 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1016 through 1018 Processing sheet with id= H, first strand: chain 'A' and resid 1088 through 1092 removed outlier: 3.628A pdb=" N ASP A1092 " --> pdb=" O ARG A1103 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG A1103 " --> pdb=" O ASP A1092 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1182 through 1184 removed outlier: 6.547A pdb=" N ILE A1339 " --> pdb=" O LEU A1206 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER A1208 " --> pdb=" O PHE A1337 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE A1337 " --> pdb=" O SER A1208 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG A1210 " --> pdb=" O GLY A1335 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY A1335 " --> pdb=" O ARG A1210 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1364 through 1371 Processing sheet with id= K, first strand: chain 'A' and resid 1429 through 1431 Processing sheet with id= L, first strand: chain 'A' and resid 1458 through 1462 removed outlier: 6.561A pdb=" N ARG A1746 " --> pdb=" O GLY A1459 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE A1461 " --> pdb=" O ARG A1746 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE A1748 " --> pdb=" O ILE A1461 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE A1548 " --> pdb=" O ILE A1501 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL A1503 " --> pdb=" O ILE A1548 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N MET A1550 " --> pdb=" O VAL A1503 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1837 through 1844 removed outlier: 6.248A pdb=" N VAL A2275 " --> pdb=" O VAL A1838 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N HIS A1840 " --> pdb=" O VAL A2275 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE A2277 " --> pdb=" O HIS A1840 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N HIS A1842 " --> pdb=" O ILE A2277 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ARG A2279 " --> pdb=" O HIS A1842 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N PHE A1844 " --> pdb=" O ARG A2279 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU A2281 " --> pdb=" O PHE A1844 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 2094 through 2096 Processing sheet with id= O, first strand: chain 'A' and resid 2170 through 2173 removed outlier: 7.027A pdb=" N LEU A2221 " --> pdb=" O VAL A2171 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N LEU A2173 " --> pdb=" O LEU A2221 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU A2223 " --> pdb=" O LEU A2173 " (cutoff:3.500A) No H-bonds generated for sheet with id= O 527 hydrogen bonds defined for protein. 1497 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 7.21 Time building geometry restraints manager: 6.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2464 1.30 - 1.43: 4053 1.43 - 1.56: 8665 1.56 - 1.69: 49 1.69 - 1.83: 100 Bond restraints: 15331 Sorted by residual: bond pdb=" C2' 5CM B 30 " pdb=" C1' 5CM B 30 " ideal model delta sigma weight residual 1.521 1.314 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C3' 5CM B 30 " pdb=" C2' 5CM B 30 " ideal model delta sigma weight residual 1.323 1.524 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C3' 5CM B 30 " pdb=" O3' 5CM B 30 " ideal model delta sigma weight residual 1.460 1.329 0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" C1' 5CM B 30 " pdb=" N1 5CM B 30 " ideal model delta sigma weight residual 1.321 1.406 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" N ARG A 846 " pdb=" CA ARG A 846 " ideal model delta sigma weight residual 1.461 1.495 -0.034 9.20e-03 1.18e+04 1.39e+01 ... (remaining 15326 not shown) Histogram of bond angle deviations from ideal: 98.17 - 105.35: 407 105.35 - 112.53: 8378 112.53 - 119.72: 4754 119.72 - 126.90: 7011 126.90 - 134.08: 305 Bond angle restraints: 20855 Sorted by residual: angle pdb=" N PRO A 847 " pdb=" CA PRO A 847 " pdb=" C PRO A 847 " ideal model delta sigma weight residual 112.47 99.64 12.83 2.06e+00 2.36e-01 3.88e+01 angle pdb=" C PRO A 847 " pdb=" N GLU A 848 " pdb=" CA GLU A 848 " ideal model delta sigma weight residual 123.23 114.00 9.23 1.57e+00 4.06e-01 3.45e+01 angle pdb=" N ASP A1533 " pdb=" CA ASP A1533 " pdb=" C ASP A1533 " ideal model delta sigma weight residual 114.62 108.43 6.19 1.14e+00 7.69e-01 2.94e+01 angle pdb=" C VAL A2102 " pdb=" N ALA A2103 " pdb=" CA ALA A2103 " ideal model delta sigma weight residual 121.90 115.61 6.29 1.26e+00 6.30e-01 2.49e+01 angle pdb=" CA TRP A1574 " pdb=" CB TRP A1574 " pdb=" CG TRP A1574 " ideal model delta sigma weight residual 113.60 122.13 -8.53 1.90e+00 2.77e-01 2.02e+01 ... (remaining 20850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 7974 17.56 - 35.12: 952 35.12 - 52.68: 252 52.68 - 70.24: 76 70.24 - 87.81: 18 Dihedral angle restraints: 9272 sinusoidal: 3956 harmonic: 5316 Sorted by residual: dihedral pdb=" CA THR A2087 " pdb=" C THR A2087 " pdb=" N ASN A2088 " pdb=" CA ASN A2088 " ideal model delta harmonic sigma weight residual 180.00 155.44 24.56 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA TRP A 626 " pdb=" C TRP A 626 " pdb=" N THR A 627 " pdb=" CA THR A 627 " ideal model delta harmonic sigma weight residual -180.00 -156.76 -23.24 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA GLN A2124 " pdb=" C GLN A2124 " pdb=" N ALA A2125 " pdb=" CA ALA A2125 " ideal model delta harmonic sigma weight residual -180.00 -156.79 -23.21 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 9269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1815 0.056 - 0.112: 431 0.112 - 0.168: 71 0.168 - 0.225: 9 0.225 - 0.281: 3 Chirality restraints: 2329 Sorted by residual: chirality pdb=" CA PRO A 847 " pdb=" N PRO A 847 " pdb=" C PRO A 847 " pdb=" CB PRO A 847 " both_signs ideal model delta sigma weight residual False 2.72 3.00 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA SER A2015 " pdb=" N SER A2015 " pdb=" C SER A2015 " pdb=" CB SER A2015 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ILE A1554 " pdb=" N ILE A1554 " pdb=" C ILE A1554 " pdb=" CB ILE A1554 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 2326 not shown) Planarity restraints: 2610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 846 " 0.099 5.00e-02 4.00e+02 1.52e-01 3.69e+01 pdb=" N PRO A 847 " -0.263 5.00e-02 4.00e+02 pdb=" CA PRO A 847 " 0.088 5.00e-02 4.00e+02 pdb=" CD PRO A 847 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A2011 " -0.083 5.00e-02 4.00e+02 1.25e-01 2.49e+01 pdb=" N PRO A2012 " 0.216 5.00e-02 4.00e+02 pdb=" CA PRO A2012 " -0.067 5.00e-02 4.00e+02 pdb=" CD PRO A2012 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A2088 " -0.055 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO A2089 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A2089 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A2089 " -0.046 5.00e-02 4.00e+02 ... (remaining 2607 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 325 2.65 - 3.21: 14229 3.21 - 3.78: 22600 3.78 - 4.34: 31056 4.34 - 4.90: 50677 Nonbonded interactions: 118887 Sorted by model distance: nonbonded pdb=" N2 DG B 25 " pdb=" O2 DC D 12 " model vdw 2.090 2.496 nonbonded pdb=" OD2 ASP A 562 " pdb=" NE2 GLN A 822 " model vdw 2.095 2.520 nonbonded pdb=" OG SER A1019 " pdb=" OG1 THR A1033 " model vdw 2.131 2.440 nonbonded pdb=" OG1 THR A 613 " pdb=" OE2 GLU A 644 " model vdw 2.137 2.440 nonbonded pdb=" OG SER A1893 " pdb=" N LYS A1894 " model vdw 2.151 2.520 ... (remaining 118882 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 4.560 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 50.500 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.011 0.207 15331 Z= 0.731 Angle : 0.941 13.984 20855 Z= 0.543 Chirality : 0.051 0.281 2329 Planarity : 0.007 0.152 2610 Dihedral : 17.173 87.806 5802 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 1.40 % Allowed : 11.66 % Favored : 86.93 % 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: -3.14 (0.17), residues: 1806 helix: -1.35 (0.17), residues: 693 sheet: -1.51 (0.27), residues: 296 loop : -2.97 (0.18), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A1222 HIS 0.012 0.002 HIS A 597 PHE 0.026 0.003 PHE A1337 TYR 0.040 0.003 TYR A2149 ARG 0.013 0.001 ARG A 548 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 1.802 Fit side-chains REVERT: A 442 ASP cc_start: 0.7638 (t0) cc_final: 0.7246 (t0) REVERT: A 1250 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 1378 PRO cc_start: 0.6588 (Cg_endo) cc_final: 0.6310 (Cg_exo) REVERT: A 1470 THR cc_start: 0.8248 (p) cc_final: 0.8040 (m) REVERT: A 1563 ARG cc_start: 0.7537 (tpt170) cc_final: 0.7255 (tpp-160) REVERT: A 1567 LEU cc_start: 0.7989 (mt) cc_final: 0.7704 (mt) outliers start: 22 outliers final: 10 residues processed: 163 average time/residue: 1.5622 time to fit residues: 276.9016 Evaluate side-chains 108 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 794 ASP Chi-restraints excluded: chain A residue 846 ARG Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 2220 VAL Chi-restraints excluded: chain A residue 2221 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 HIS A 565 ASN A 629 ASN A 732 ASN A 780 ASN A 802 ASN A 833 GLN A 857 GLN A 907 GLN A 977 HIS A1234 HIS A1342 ASN A1379 GLN A1397 GLN A1409 GLN A1810 HIS A1827 GLN A1940 GLN A2009 ASN A2101 HIS A2115 GLN A2124 GLN A2131 ASN A2211 GLN ** A2278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15331 Z= 0.267 Angle : 0.626 11.342 20855 Z= 0.323 Chirality : 0.042 0.237 2329 Planarity : 0.005 0.080 2610 Dihedral : 12.840 67.700 2257 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.63 % Allowed : 17.46 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.19), residues: 1806 helix: 0.11 (0.19), residues: 693 sheet: -0.80 (0.28), residues: 313 loop : -2.50 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2304 HIS 0.006 0.001 HIS A 816 PHE 0.021 0.002 PHE A1518 TYR 0.026 0.002 TYR A2269 ARG 0.007 0.000 ARG A1718 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 122 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 ASP cc_start: 0.7453 (t0) cc_final: 0.7055 (t0) REVERT: A 778 VAL cc_start: 0.8634 (p) cc_final: 0.8282 (m) REVERT: A 795 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6621 (tp) REVERT: A 1250 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7868 (mp) REVERT: A 1373 HIS cc_start: 0.7974 (OUTLIER) cc_final: 0.6640 (p-80) REVERT: A 1378 PRO cc_start: 0.5983 (Cg_endo) cc_final: 0.5664 (Cg_exo) REVERT: A 1470 THR cc_start: 0.8195 (p) cc_final: 0.7765 (m) REVERT: A 1716 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7324 (ptt) REVERT: A 1963 PHE cc_start: 0.6356 (OUTLIER) cc_final: 0.4510 (m-10) REVERT: A 1970 ARG cc_start: 0.7683 (mmm160) cc_final: 0.7421 (mmp80) REVERT: A 2304 TRP cc_start: 0.6817 (OUTLIER) cc_final: 0.6188 (t60) outliers start: 57 outliers final: 27 residues processed: 170 average time/residue: 1.0769 time to fit residues: 206.8542 Evaluate side-chains 128 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 95 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1574 TRP Chi-restraints excluded: chain A residue 1716 MET Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1782 VAL Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1866 MET Chi-restraints excluded: chain A residue 1963 PHE Chi-restraints excluded: chain A residue 2031 VAL Chi-restraints excluded: chain A residue 2087 THR Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 46 optimal weight: 0.0770 chunk 168 optimal weight: 7.9990 chunk 181 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 135 optimal weight: 0.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15331 Z= 0.200 Angle : 0.573 9.718 20855 Z= 0.293 Chirality : 0.040 0.236 2329 Planarity : 0.005 0.071 2610 Dihedral : 12.528 65.792 2246 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.63 % Allowed : 19.82 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.19), residues: 1806 helix: 0.82 (0.20), residues: 696 sheet: -0.55 (0.29), residues: 310 loop : -2.25 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2304 HIS 0.004 0.001 HIS A1217 PHE 0.013 0.001 PHE A1337 TYR 0.017 0.001 TYR A2269 ARG 0.007 0.000 ARG A 940 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 124 time to evaluate : 1.731 Fit side-chains REVERT: A 442 ASP cc_start: 0.7286 (t0) cc_final: 0.6925 (t0) REVERT: A 778 VAL cc_start: 0.8648 (p) cc_final: 0.8315 (m) REVERT: A 1250 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7774 (mp) REVERT: A 1373 HIS cc_start: 0.7981 (OUTLIER) cc_final: 0.6767 (p-80) REVERT: A 1378 PRO cc_start: 0.5971 (Cg_endo) cc_final: 0.5553 (Cg_exo) REVERT: A 1470 THR cc_start: 0.8076 (p) cc_final: 0.7757 (m) REVERT: A 1550 MET cc_start: 0.7508 (tpp) cc_final: 0.7285 (tpp) REVERT: A 1565 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7686 (mt-10) REVERT: A 2269 TYR cc_start: 0.5550 (t80) cc_final: 0.5312 (t80) REVERT: A 2304 TRP cc_start: 0.6710 (OUTLIER) cc_final: 0.5646 (t60) outliers start: 57 outliers final: 27 residues processed: 174 average time/residue: 1.0654 time to fit residues: 209.3912 Evaluate side-chains 127 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 97 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1574 TRP Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 2031 VAL Chi-restraints excluded: chain A residue 2159 LEU Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 178 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN A1067 GLN A1711 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 15331 Z= 0.395 Angle : 0.666 10.880 20855 Z= 0.342 Chirality : 0.044 0.224 2329 Planarity : 0.006 0.066 2610 Dihedral : 12.770 67.814 2246 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 4.91 % Allowed : 21.10 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.19), residues: 1806 helix: 0.72 (0.20), residues: 696 sheet: -0.38 (0.30), residues: 296 loop : -2.23 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A2304 HIS 0.007 0.001 HIS A 849 PHE 0.020 0.002 PHE A1337 TYR 0.018 0.002 TYR A 513 ARG 0.008 0.001 ARG A1587 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 98 time to evaluate : 1.789 Fit side-chains REVERT: A 357 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: A 442 ASP cc_start: 0.7389 (t0) cc_final: 0.7012 (t0) REVERT: A 778 VAL cc_start: 0.8709 (p) cc_final: 0.8360 (m) REVERT: A 795 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6716 (tp) REVERT: A 1250 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7991 (mp) REVERT: A 1373 HIS cc_start: 0.8014 (OUTLIER) cc_final: 0.6502 (p-80) REVERT: A 1378 PRO cc_start: 0.6071 (Cg_endo) cc_final: 0.5778 (Cg_exo) REVERT: A 1470 THR cc_start: 0.8137 (p) cc_final: 0.7838 (m) REVERT: A 1565 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7701 (mt-10) REVERT: A 1782 VAL cc_start: 0.8117 (OUTLIER) cc_final: 0.7881 (t) REVERT: A 2304 TRP cc_start: 0.6900 (OUTLIER) cc_final: 0.5894 (t60) outliers start: 77 outliers final: 38 residues processed: 166 average time/residue: 0.9772 time to fit residues: 185.5956 Evaluate side-chains 139 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 95 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1150 CYS Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1522 MET Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1714 LEU Chi-restraints excluded: chain A residue 1728 THR Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1782 VAL Chi-restraints excluded: chain A residue 1866 MET Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2140 VAL Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1818 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15331 Z= 0.251 Angle : 0.601 9.760 20855 Z= 0.304 Chirality : 0.041 0.205 2329 Planarity : 0.005 0.060 2610 Dihedral : 12.591 66.476 2246 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.91 % Allowed : 21.86 % Favored : 73.23 % 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: -0.86 (0.20), residues: 1806 helix: 1.03 (0.20), residues: 695 sheet: -0.35 (0.31), residues: 290 loop : -2.14 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2304 HIS 0.004 0.001 HIS A1217 PHE 0.015 0.002 PHE A1337 TYR 0.028 0.002 TYR A2269 ARG 0.007 0.000 ARG A1718 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 99 time to evaluate : 1.708 Fit side-chains REVERT: A 357 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: A 442 ASP cc_start: 0.7310 (t0) cc_final: 0.6943 (t0) REVERT: A 778 VAL cc_start: 0.8677 (p) cc_final: 0.8362 (m) REVERT: A 795 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6642 (tp) REVERT: A 1224 ARG cc_start: 0.7076 (mmt90) cc_final: 0.6775 (mmt90) REVERT: A 1250 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7977 (mp) REVERT: A 1373 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.6792 (p-80) REVERT: A 1378 PRO cc_start: 0.6131 (Cg_endo) cc_final: 0.5914 (Cg_exo) REVERT: A 1470 THR cc_start: 0.8102 (p) cc_final: 0.7831 (m) REVERT: A 1782 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7810 (t) REVERT: A 2304 TRP cc_start: 0.6767 (OUTLIER) cc_final: 0.5524 (t60) outliers start: 77 outliers final: 43 residues processed: 166 average time/residue: 1.0462 time to fit residues: 196.8060 Evaluate side-chains 142 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 93 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 794 ASP Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1782 VAL Chi-restraints excluded: chain A residue 1866 MET Chi-restraints excluded: chain A residue 2039 THR Chi-restraints excluded: chain A residue 2087 THR Chi-restraints excluded: chain A residue 2098 CYS Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2140 VAL Chi-restraints excluded: chain A residue 2173 LEU Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 148 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15331 Z= 0.267 Angle : 0.604 10.185 20855 Z= 0.307 Chirality : 0.041 0.207 2329 Planarity : 0.005 0.056 2610 Dihedral : 12.557 66.329 2246 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 4.97 % Allowed : 22.31 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.79 (0.20), residues: 1806 helix: 1.11 (0.20), residues: 697 sheet: -0.28 (0.31), residues: 290 loop : -2.15 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2304 HIS 0.005 0.001 HIS A 849 PHE 0.015 0.002 PHE A1337 TYR 0.017 0.002 TYR A2269 ARG 0.008 0.000 ARG A2268 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 103 time to evaluate : 1.842 Fit side-chains REVERT: A 357 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: A 442 ASP cc_start: 0.7294 (t0) cc_final: 0.6932 (t0) REVERT: A 778 VAL cc_start: 0.8682 (p) cc_final: 0.8372 (m) REVERT: A 795 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6646 (tp) REVERT: A 943 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7741 (mtm) REVERT: A 1250 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7978 (mp) REVERT: A 1373 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.6945 (p-80) REVERT: A 1378 PRO cc_start: 0.6227 (Cg_endo) cc_final: 0.5936 (Cg_exo) REVERT: A 1470 THR cc_start: 0.8087 (p) cc_final: 0.7807 (m) REVERT: A 1782 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7875 (t) REVERT: A 2304 TRP cc_start: 0.6878 (OUTLIER) cc_final: 0.5467 (t60) outliers start: 78 outliers final: 51 residues processed: 170 average time/residue: 0.9156 time to fit residues: 178.5527 Evaluate side-chains 153 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 95 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 794 ASP Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1150 CYS Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1522 MET Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1728 THR Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1782 VAL Chi-restraints excluded: chain A residue 1866 MET Chi-restraints excluded: chain A residue 2039 THR Chi-restraints excluded: chain A residue 2087 THR Chi-restraints excluded: chain A residue 2098 CYS Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2140 VAL Chi-restraints excluded: chain A residue 2173 LEU Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 99 optimal weight: 0.6980 chunk 178 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN ** A 791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15331 Z= 0.267 Angle : 0.603 9.875 20855 Z= 0.307 Chirality : 0.041 0.207 2329 Planarity : 0.005 0.056 2610 Dihedral : 12.528 66.182 2246 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.72 % Allowed : 22.43 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.20), residues: 1806 helix: 1.20 (0.20), residues: 695 sheet: -0.44 (0.31), residues: 299 loop : -2.07 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1574 HIS 0.006 0.001 HIS A 849 PHE 0.019 0.002 PHE A2253 TYR 0.018 0.002 TYR A2269 ARG 0.008 0.000 ARG A2268 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 102 time to evaluate : 1.822 Fit side-chains REVERT: A 357 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: A 442 ASP cc_start: 0.7126 (t0) cc_final: 0.6785 (t0) REVERT: A 778 VAL cc_start: 0.8675 (p) cc_final: 0.8368 (m) REVERT: A 795 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6646 (tp) REVERT: A 1250 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7914 (mp) REVERT: A 1373 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.6942 (p-80) REVERT: A 1378 PRO cc_start: 0.6271 (Cg_endo) cc_final: 0.5992 (Cg_exo) REVERT: A 1470 THR cc_start: 0.8068 (p) cc_final: 0.7779 (m) REVERT: A 1782 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7887 (t) REVERT: A 2304 TRP cc_start: 0.6876 (OUTLIER) cc_final: 0.5454 (t60) outliers start: 74 outliers final: 56 residues processed: 164 average time/residue: 0.9522 time to fit residues: 180.0496 Evaluate side-chains 158 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 96 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1150 CYS Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1354 LEU Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1522 MET Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1714 LEU Chi-restraints excluded: chain A residue 1728 THR Chi-restraints excluded: chain A residue 1763 SER Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1782 VAL Chi-restraints excluded: chain A residue 1866 MET Chi-restraints excluded: chain A residue 2039 THR Chi-restraints excluded: chain A residue 2087 THR Chi-restraints excluded: chain A residue 2098 CYS Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2140 VAL Chi-restraints excluded: chain A residue 2173 LEU Chi-restraints excluded: chain A residue 2207 LEU Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 chunk 121 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1906 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15331 Z= 0.270 Angle : 0.609 9.773 20855 Z= 0.310 Chirality : 0.041 0.211 2329 Planarity : 0.005 0.055 2610 Dihedral : 12.512 66.180 2246 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 5.10 % Allowed : 22.24 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.68 (0.20), residues: 1806 helix: 1.24 (0.20), residues: 695 sheet: -0.42 (0.31), residues: 300 loop : -2.04 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1574 HIS 0.006 0.001 HIS A 849 PHE 0.017 0.002 PHE A2253 TYR 0.020 0.002 TYR A2269 ARG 0.008 0.000 ARG A2268 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 103 time to evaluate : 1.848 Fit side-chains REVERT: A 357 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: A 442 ASP cc_start: 0.7127 (t0) cc_final: 0.6782 (t0) REVERT: A 778 VAL cc_start: 0.8677 (p) cc_final: 0.8368 (m) REVERT: A 795 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6634 (tp) REVERT: A 1250 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7974 (mp) REVERT: A 1373 HIS cc_start: 0.7992 (OUTLIER) cc_final: 0.6939 (p-80) REVERT: A 1378 PRO cc_start: 0.6259 (Cg_endo) cc_final: 0.5979 (Cg_exo) REVERT: A 1470 THR cc_start: 0.8124 (p) cc_final: 0.7756 (m) REVERT: A 1496 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8112 (mp) REVERT: A 2269 TYR cc_start: 0.5745 (t80) cc_final: 0.5454 (t80) REVERT: A 2304 TRP cc_start: 0.6878 (OUTLIER) cc_final: 0.5463 (t60) outliers start: 80 outliers final: 57 residues processed: 169 average time/residue: 0.9763 time to fit residues: 188.3155 Evaluate side-chains 156 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 93 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1150 CYS Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1354 LEU Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1496 LEU Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1522 MET Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1714 LEU Chi-restraints excluded: chain A residue 1728 THR Chi-restraints excluded: chain A residue 1763 SER Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1866 MET Chi-restraints excluded: chain A residue 1939 CYS Chi-restraints excluded: chain A residue 2039 THR Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2087 THR Chi-restraints excluded: chain A residue 2098 CYS Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2140 VAL Chi-restraints excluded: chain A residue 2173 LEU Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2266 VAL Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 chunk 130 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 165 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15331 Z= 0.189 Angle : 0.594 13.895 20855 Z= 0.296 Chirality : 0.040 0.263 2329 Planarity : 0.005 0.053 2610 Dihedral : 12.301 64.696 2246 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.14 % Allowed : 23.65 % Favored : 72.21 % 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 (0.20), residues: 1806 helix: 1.47 (0.20), residues: 701 sheet: -0.31 (0.31), residues: 298 loop : -1.99 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A1574 HIS 0.004 0.001 HIS A 849 PHE 0.017 0.001 PHE A2253 TYR 0.024 0.001 TYR A2269 ARG 0.011 0.000 ARG A2268 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 113 time to evaluate : 1.751 Fit side-chains REVERT: A 357 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: A 442 ASP cc_start: 0.7029 (t0) cc_final: 0.6715 (t0) REVERT: A 778 VAL cc_start: 0.8654 (p) cc_final: 0.8373 (m) REVERT: A 795 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6562 (tp) REVERT: A 1250 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7778 (mp) REVERT: A 1373 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.7015 (p-80) REVERT: A 1378 PRO cc_start: 0.6035 (Cg_endo) cc_final: 0.5730 (Cg_exo) REVERT: A 1496 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8098 (mp) REVERT: A 1775 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7161 (pm20) REVERT: A 2225 MET cc_start: 0.8342 (tpp) cc_final: 0.8132 (mmp) REVERT: A 2268 ARG cc_start: 0.7038 (mmm-85) cc_final: 0.6691 (mtp-110) REVERT: A 2304 TRP cc_start: 0.6572 (OUTLIER) cc_final: 0.5540 (t60) outliers start: 65 outliers final: 40 residues processed: 170 average time/residue: 0.9333 time to fit residues: 182.4272 Evaluate side-chains 145 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 98 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1496 LEU Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1714 LEU Chi-restraints excluded: chain A residue 1728 THR Chi-restraints excluded: chain A residue 1763 SER Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1793 THR Chi-restraints excluded: chain A residue 1939 CYS Chi-restraints excluded: chain A residue 2039 THR Chi-restraints excluded: chain A residue 2087 THR Chi-restraints excluded: chain A residue 2140 VAL Chi-restraints excluded: chain A residue 2173 LEU Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2266 VAL Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 184 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 HIS ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1342 ASN A1792 GLN A1811 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 15331 Z= 0.561 Angle : 0.779 11.482 20855 Z= 0.394 Chirality : 0.048 0.324 2329 Planarity : 0.006 0.057 2610 Dihedral : 12.874 68.740 2244 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.89 % Allowed : 24.28 % Favored : 71.83 % 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: -0.94 (0.20), residues: 1806 helix: 0.85 (0.20), residues: 697 sheet: -0.41 (0.30), residues: 303 loop : -2.10 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1574 HIS 0.009 0.002 HIS A 849 PHE 0.025 0.003 PHE A1337 TYR 0.022 0.003 TYR A2149 ARG 0.010 0.001 ARG A 714 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 95 time to evaluate : 1.653 Fit side-chains REVERT: A 357 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: A 442 ASP cc_start: 0.7232 (t0) cc_final: 0.6865 (t0) REVERT: A 778 VAL cc_start: 0.8733 (p) cc_final: 0.8407 (m) REVERT: A 795 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6807 (tp) REVERT: A 1250 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8008 (mp) REVERT: A 1373 HIS cc_start: 0.7966 (OUTLIER) cc_final: 0.6638 (p-80) REVERT: A 1378 PRO cc_start: 0.6226 (Cg_endo) cc_final: 0.6015 (Cg_exo) REVERT: A 2304 TRP cc_start: 0.7051 (OUTLIER) cc_final: 0.5798 (t60) outliers start: 61 outliers final: 45 residues processed: 146 average time/residue: 1.0163 time to fit residues: 169.3962 Evaluate side-chains 143 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 93 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 724 ASP Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1150 CYS Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1714 LEU Chi-restraints excluded: chain A residue 1728 THR Chi-restraints excluded: chain A residue 1763 SER Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1894 LYS Chi-restraints excluded: chain A residue 1939 CYS Chi-restraints excluded: chain A residue 2031 VAL Chi-restraints excluded: chain A residue 2039 THR Chi-restraints excluded: chain A residue 2087 THR Chi-restraints excluded: chain A residue 2098 CYS Chi-restraints excluded: chain A residue 2140 VAL Chi-restraints excluded: chain A residue 2173 LEU Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2266 VAL Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1342 ASN A1792 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.127554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.104182 restraints weight = 25883.038| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.12 r_work: 0.3287 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15331 Z= 0.199 Angle : 0.626 12.605 20855 Z= 0.309 Chirality : 0.041 0.346 2329 Planarity : 0.005 0.052 2610 Dihedral : 12.397 65.856 2244 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.06 % Allowed : 25.24 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1806 helix: 1.37 (0.20), residues: 695 sheet: -0.36 (0.30), residues: 311 loop : -2.02 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A1574 HIS 0.003 0.001 HIS A1217 PHE 0.016 0.001 PHE A2253 TYR 0.029 0.002 TYR A2269 ARG 0.010 0.000 ARG A1100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4316.73 seconds wall clock time: 78 minutes 20.31 seconds (4700.31 seconds total)