Starting phenix.real_space_refine on Fri Feb 16 11:53:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r78_24295/02_2024/7r78_24295_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r78_24295/02_2024/7r78_24295.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r78_24295/02_2024/7r78_24295_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r78_24295/02_2024/7r78_24295_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r78_24295/02_2024/7r78_24295_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r78_24295/02_2024/7r78_24295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r78_24295/02_2024/7r78_24295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r78_24295/02_2024/7r78_24295_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r78_24295/02_2024/7r78_24295_updated.pdb" } resolution = 3.5 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= 0.005 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: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 20 5.49 5 Mg 1 5.21 5 S 72 5.16 5 C 9483 2.51 5 N 2756 2.21 5 O 2901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A GLU 637": "OE1" <-> "OE2" Residue "A ARG 703": "NH1" <-> "NH2" Residue "A GLU 723": "OE1" <-> "OE2" Residue "A GLU 756": "OE1" <-> "OE2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A ARG 781": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 846": "NH1" <-> "NH2" Residue "A GLU 860": "OE1" <-> "OE2" Residue "A ARG 867": "NH1" <-> "NH2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A ARG 877": "NH1" <-> "NH2" Residue "A GLU 921": "OE1" <-> "OE2" Residue "A ARG 923": "NH1" <-> "NH2" Residue "A PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1046": "OE1" <-> "OE2" Residue "A ARG 1053": "NH1" <-> "NH2" Residue "A ARG 1064": "NH1" <-> "NH2" Residue "A ARG 1076": "NH1" <-> "NH2" Residue "A ARG 1179": "NH1" <-> "NH2" Residue "A ARG 1210": "NH1" <-> "NH2" Residue "A GLU 1219": "OE1" <-> "OE2" Residue "A ARG 1223": "NH1" <-> "NH2" Residue "A ARG 1224": "NH1" <-> "NH2" Residue "A ARG 1249": "NH1" <-> "NH2" Residue "A ARG 1286": "NH1" <-> "NH2" Residue "A GLU 1309": "OE1" <-> "OE2" Residue "A GLU 1314": "OE1" <-> "OE2" Residue "A ARG 1329": "NH1" <-> "NH2" Residue "A ARG 1338": "NH1" <-> "NH2" Residue "A ARG 1368": "NH1" <-> "NH2" Residue "A ARG 1382": "NH1" <-> "NH2" Residue "A GLU 1399": "OE1" <-> "OE2" Residue "A ARG 1445": "NH1" <-> "NH2" Residue "A ARG 1457": "NH1" <-> "NH2" Residue "A GLU 1536": "OE1" <-> "OE2" Residue "A ARG 1563": "NH1" <-> "NH2" Residue "A ARG 1572": "NH1" <-> "NH2" Residue "A GLU 1726": "OE1" <-> "OE2" Residue "A ARG 1813": "NH1" <-> "NH2" Residue "A GLU 1856": "OE1" <-> "OE2" Residue "A GLU 1858": "OE1" <-> "OE2" Residue "A GLU 1865": "OE1" <-> "OE2" Residue "A ARG 1869": "NH1" <-> "NH2" Residue "A GLU 1888": "OE1" <-> "OE2" Residue "A ARG 1903": "NH1" <-> "NH2" Residue "A ARG 1934": "NH1" <-> "NH2" Residue "A ARG 1945": "NH1" <-> "NH2" Residue "A ARG 2036": "NH1" <-> "NH2" Residue "A ARG 2043": "NH1" <-> "NH2" Residue "A GLU 2048": "OE1" <-> "OE2" Residue "A ARG 2057": "NH1" <-> "NH2" Residue "A GLU 2080": "OE1" <-> "OE2" Residue "A ARG 2116": "NH1" <-> "NH2" Residue "A GLU 2141": "OE1" <-> "OE2" Residue "A GLU 2184": "OE1" <-> "OE2" Residue "A ARG 2190": "NH1" <-> "NH2" Residue "A ARG 2219": "NH1" <-> "NH2" Residue "A ARG 2265": "NH1" <-> "NH2" Residue "A ARG 2268": "NH1" <-> "NH2" Residue "A GLU 2297": "OE1" <-> "OE2" Residue "A GLU 2306": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15238 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 14810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1880, 14810 Classifications: {'peptide': 1880} Link IDs: {'PTRANS': 89, 'TRANS': 1790} Chain breaks: 6 Chain: "D" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "E" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 63 Unusual residues: {' MG': 1, ' ZN': 5, 'ANP': 1} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3945 SG CYS A 817 71.375 72.832 60.619 1.00 44.98 S ATOM 3960 SG CYS A 819 70.233 69.601 61.157 1.00 45.98 S ATOM 4114 SG CYS A 840 68.351 73.358 62.510 1.00 45.74 S ATOM 4050 SG CYS A 832 78.993 84.373 65.074 1.00 43.82 S ATOM 4074 SG CYS A 835 81.452 83.071 61.227 1.00 42.36 S ATOM 5901 SG CYS A1065 82.602 83.158 64.911 1.00 39.33 S ATOM 6801 SG CYS A1200 44.677 46.916 34.498 1.00 61.37 S ATOM 7361 SG CYS A1271 44.581 43.896 35.833 1.00 61.48 S ATOM 7387 SG CYS A1274 46.898 46.677 37.104 1.00 56.78 S ATOM 12993 SG CYS A2081 86.979 77.986 97.399 1.00 96.97 S ATOM 13123 SG CYS A2099 85.214 66.624 92.667 1.00 68.23 S ATOM 13255 SG CYS A2117 87.178 69.100 90.557 1.00 76.49 S ATOM 13296 SG CYS A2123 88.898 65.946 90.578 1.00 69.74 S Time building chain proxies: 9.01, per 1000 atoms: 0.59 Number of scatterers: 15238 At special positions: 0 Unit cell: (128.744, 111.72, 123.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 72 16.00 P 20 15.00 Mg 1 11.99 O 2901 8.00 N 2756 7.00 C 9483 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: 6.47 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2402 " pdb="ZN ZN A2402 " - pdb=" SG CYS A 819 " pdb="ZN ZN A2402 " - pdb=" SG CYS A 840 " pdb="ZN ZN A2402 " - pdb=" SG CYS A 817 " pdb=" ZN A2403 " pdb="ZN ZN A2403 " - pdb=" ND1 HIS A 849 " pdb="ZN ZN A2403 " - pdb=" SG CYS A1065 " pdb="ZN ZN A2403 " - pdb=" SG CYS A 832 " pdb="ZN ZN A2403 " - pdb=" SG CYS A 835 " pdb=" ZN A2404 " pdb="ZN ZN A2404 " - pdb=" SG CYS A1200 " pdb="ZN ZN A2404 " - pdb=" SG CYS A1271 " pdb="ZN ZN A2404 " - pdb=" SG CYS A1274 " pdb=" ZN A2405 " pdb="ZN ZN A2405 " - pdb=" SG CYS A2081 " pdb=" ZN A2406 " pdb="ZN ZN A2406 " - pdb=" SG CYS A2123 " pdb="ZN ZN A2406 " - pdb=" SG CYS A2117 " pdb="ZN ZN A2406 " - pdb=" SG CYS A2099 " Number of angles added : 3 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3558 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 16 sheets defined 33.3% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.03 Creating SS restraints... Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 336 through 342 removed outlier: 3.959A pdb=" N ARG A 340 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 373 Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 458 through 461 No H-bonds generated for 'chain 'A' and resid 458 through 461' Processing helix chain 'A' and resid 463 through 473 removed outlier: 3.752A pdb=" N GLN A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 535 through 545 Processing helix chain 'A' and resid 554 through 557 Processing helix chain 'A' and resid 564 through 573 removed outlier: 3.854A pdb=" N GLU A 572 " --> pdb=" O ARG A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 603 removed outlier: 4.039A pdb=" N ARG A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 634 removed outlier: 4.380A pdb=" N ALA A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 651 Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 702 through 708 Processing helix chain 'A' and resid 723 through 732 removed outlier: 3.698A pdb=" N ASN A 732 " --> pdb=" O ASP A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 749 Processing helix chain 'A' and resid 760 through 780 removed outlier: 3.619A pdb=" N VAL A 778 " --> pdb=" O ASP A 774 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 861 through 871 removed outlier: 3.822A pdb=" N GLY A 870 " --> pdb=" O LYS A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 895 Processing helix chain 'A' and resid 903 through 915 removed outlier: 3.596A pdb=" N ALA A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU A 915 " --> pdb=" O THR A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 974 No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 1020 through 1024 Processing helix chain 'A' and resid 1045 through 1049 Processing helix chain 'A' and resid 1188 through 1194 removed outlier: 3.686A pdb=" N SER A1192 " --> pdb=" O ALA A1188 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A1193 " --> pdb=" O SER A1189 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER A1194 " --> pdb=" O ALA A1190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1188 through 1194' Processing helix chain 'A' and resid 1238 through 1242 Processing helix chain 'A' and resid 1244 through 1247 No H-bonds generated for 'chain 'A' and resid 1244 through 1247' Processing helix chain 'A' and resid 1307 through 1316 Processing helix chain 'A' and resid 1343 through 1353 removed outlier: 3.781A pdb=" N ARG A1353 " --> pdb=" O ARG A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1421 Processing helix chain 'A' and resid 1469 through 1482 removed outlier: 4.658A pdb=" N SER A1482 " --> pdb=" O ALA A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1507 No H-bonds generated for 'chain 'A' and resid 1505 through 1507' Processing helix chain 'A' and resid 1510 through 1518 Processing helix chain 'A' and resid 1531 through 1535 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 1554 through 1557 No H-bonds generated for 'chain 'A' and resid 1554 through 1557' Processing helix chain 'A' and resid 1559 through 1568 Processing helix chain 'A' and resid 1584 through 1604 removed outlier: 4.596A pdb=" N GLU A1604 " --> pdb=" O LYS A1600 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1621 removed outlier: 3.597A pdb=" N GLU A1615 " --> pdb=" O MET A1611 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP A1616 " --> pdb=" O ARG A1612 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A1617 " --> pdb=" O ALA A1613 " (cutoff:3.500A) Processing helix chain 'A' and resid 1727 through 1729 No H-bonds generated for 'chain 'A' and resid 1727 through 1729' Processing helix chain 'A' and resid 1732 through 1740 removed outlier: 4.039A pdb=" N ALA A1737 " --> pdb=" O LYS A1733 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ARG A1740 " --> pdb=" O ALA A1736 " (cutoff:3.500A) Processing helix chain 'A' and resid 1758 through 1768 removed outlier: 3.685A pdb=" N ILE A1764 " --> pdb=" O ALA A1760 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE A1767 " --> pdb=" O SER A1763 " (cutoff:3.500A) Processing helix chain 'A' and resid 1794 through 1796 No H-bonds generated for 'chain 'A' and resid 1794 through 1796' Processing helix chain 'A' and resid 1807 through 1824 Processing helix chain 'A' and resid 1848 through 1863 Processing helix chain 'A' and resid 1882 through 1885 No H-bonds generated for 'chain 'A' and resid 1882 through 1885' Processing helix chain 'A' and resid 1896 through 1905 removed outlier: 3.512A pdb=" N ARG A1903 " --> pdb=" O ALA A1899 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N CYS A1905 " --> pdb=" O LEU A1901 " (cutoff:3.500A) Processing helix chain 'A' and resid 1921 through 1959 Processing helix chain 'A' and resid 1972 through 1981 removed outlier: 3.765A pdb=" N ALA A1978 " --> pdb=" O ALA A1974 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A1981 " --> pdb=" O ILE A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1983 through 1985 No H-bonds generated for 'chain 'A' and resid 1983 through 1985' Processing helix chain 'A' and resid 1990 through 2001 Processing helix chain 'A' and resid 2028 through 2067 removed outlier: 3.872A pdb=" N HIS A2040 " --> pdb=" O ARG A2036 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A2058 " --> pdb=" O ARG A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2069 through 2075 Processing helix chain 'A' and resid 2105 through 2114 removed outlier: 3.846A pdb=" N SER A2114 " --> pdb=" O LYS A2110 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2162 removed outlier: 3.603A pdb=" N VAL A2157 " --> pdb=" O LEU A2153 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN A2158 " --> pdb=" O GLU A2154 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A2159 " --> pdb=" O HIS A2155 " (cutoff:3.500A) Processing helix chain 'A' and resid 2176 through 2186 removed outlier: 4.786A pdb=" N GLY A2180 " --> pdb=" O ASP A2177 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU A2186 " --> pdb=" O SER A2183 " (cutoff:3.500A) Processing helix chain 'A' and resid 2202 through 2211 Processing helix chain 'A' and resid 2228 through 2230 No H-bonds generated for 'chain 'A' and resid 2228 through 2230' Processing helix chain 'A' and resid 2252 through 2265 Processing helix chain 'A' and resid 2287 through 2300 Processing sheet with id= A, first strand: chain 'A' and resid 404 through 406 removed outlier: 3.994A pdb=" N ILE A 404 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 385 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU A 347 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL A 383 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL A 349 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER A 385 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR A 351 " --> pdb=" O SER A 385 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 479 through 482 removed outlier: 3.652A pdb=" N ARG A 520 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 503 " --> pdb=" O PHE A 524 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 829 through 831 Processing sheet with id= D, first strand: chain 'A' and resid 876 through 878 Processing sheet with id= E, first strand: chain 'A' and resid 935 through 938 Processing sheet with id= F, first strand: chain 'A' and resid 1137 through 1144 removed outlier: 3.539A pdb=" N GLU A1038 " --> pdb=" O LYS A1013 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU A1072 " --> pdb=" O LEU A1062 " (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 1091 removed outlier: 3.558A pdb=" N ALA A1123 " --> pdb=" O PHE A1106 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1181 through 1183 removed outlier: 3.840A pdb=" N SER A1208 " --> pdb=" O ALA A1183 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A1339 " --> pdb=" O LEU A1206 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER A1208 " --> pdb=" O PHE A1337 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE A1337 " --> pdb=" O SER A1208 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG A1210 " --> pdb=" O GLY A1335 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY A1335 " --> pdb=" O ARG A1210 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL A1326 " --> pdb=" O ILE A1230 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1368 through 1371 removed outlier: 3.854A pdb=" N TRP A1444 " --> pdb=" O LEU A1439 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1429 through 1432 removed outlier: 3.693A pdb=" N PHE A1429 " --> pdb=" O VAL A1454 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1460 through 1462 removed outlier: 6.247A pdb=" N ILE A1748 " --> pdb=" O ILE A1461 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'A' and resid 1525 through 1528 removed outlier: 6.569A pdb=" N ILE A1547 " --> pdb=" O ILE A1526 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE A1528 " --> pdb=" O ILE A1547 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A1549 " --> pdb=" O ILE A1528 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N THR A1499 " --> pdb=" O ILE A1548 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N MET A1550 " --> pdb=" O THR A1499 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE A1501 " --> pdb=" O MET A1550 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG A1721 " --> pdb=" O LEU A1500 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL A1502 " --> pdb=" O ARG A1721 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A1723 " --> pdb=" O VAL A1502 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TYR A1745 " --> pdb=" O VAL A1722 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA A1724 " --> pdb=" O TYR A1745 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TRP A1747 " --> pdb=" O ALA A1724 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'A' and resid 1842 through 1844 Processing sheet with id= O, first strand: chain 'A' and resid 2093 through 2095 Processing sheet with id= P, first strand: chain 'A' and resid 2169 through 2173 434 hydrogen bonds defined for protein. 1254 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.04 Time building geometry restraints manager: 6.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4791 1.33 - 1.45: 2353 1.45 - 1.57: 8294 1.57 - 1.69: 38 1.69 - 1.81: 104 Bond restraints: 15580 Sorted by residual: bond pdb=" C3' 5CM D 30 " pdb=" C2' 5CM D 30 " ideal model delta sigma weight residual 1.323 1.517 -0.194 2.00e-02 2.50e+03 9.46e+01 bond pdb=" N3B ANP A2407 " pdb=" PG ANP A2407 " ideal model delta sigma weight residual 1.795 1.634 0.161 2.00e-02 2.50e+03 6.48e+01 bond pdb=" O4' 5CM D 30 " pdb=" C1' 5CM D 30 " ideal model delta sigma weight residual 1.587 1.430 0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" C4' 5CM D 30 " pdb=" O4' 5CM D 30 " ideal model delta sigma weight residual 1.279 1.430 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" C1' 5CM D 30 " pdb=" N1 5CM D 30 " ideal model delta sigma weight residual 1.321 1.465 -0.144 2.00e-02 2.50e+03 5.15e+01 ... (remaining 15575 not shown) Histogram of bond angle deviations from ideal: 98.63 - 105.73: 425 105.73 - 112.83: 8586 112.83 - 119.93: 5169 119.93 - 127.03: 6718 127.03 - 134.13: 276 Bond angle restraints: 21174 Sorted by residual: angle pdb=" N PRO A 861 " pdb=" CA PRO A 861 " pdb=" C PRO A 861 " ideal model delta sigma weight residual 113.65 105.93 7.72 1.35e+00 5.49e-01 3.27e+01 angle pdb=" N VAL A1442 " pdb=" CA VAL A1442 " pdb=" C VAL A1442 " ideal model delta sigma weight residual 110.05 105.85 4.20 1.09e+00 8.42e-01 1.48e+01 angle pdb=" C GLU A1604 " pdb=" N LYS A1605 " pdb=" CA LYS A1605 " ideal model delta sigma weight residual 121.54 128.74 -7.20 1.91e+00 2.74e-01 1.42e+01 angle pdb=" CA GLN A 635 " pdb=" C GLN A 635 " pdb=" N THR A 636 " ideal model delta sigma weight residual 115.49 110.91 4.58 1.24e+00 6.50e-01 1.37e+01 angle pdb=" N THR A 636 " pdb=" CA THR A 636 " pdb=" C THR A 636 " ideal model delta sigma weight residual 110.35 105.39 4.96 1.36e+00 5.41e-01 1.33e+01 ... (remaining 21169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.87: 9005 30.87 - 61.74: 405 61.74 - 92.62: 45 92.62 - 123.49: 0 123.49 - 154.36: 1 Dihedral angle restraints: 9456 sinusoidal: 3997 harmonic: 5459 Sorted by residual: dihedral pdb=" CA ASP A 501 " pdb=" C ASP A 501 " pdb=" N ALA A 502 " pdb=" CA ALA A 502 " ideal model delta harmonic sigma weight residual 180.00 153.84 26.16 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA SER A 444 " pdb=" C SER A 444 " pdb=" N ASN A 445 " pdb=" CA ASN A 445 " ideal model delta harmonic sigma weight residual 180.00 154.70 25.30 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA THR A 932 " pdb=" C THR A 932 " pdb=" N TRP A 933 " pdb=" CA TRP A 933 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 9453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1880 0.057 - 0.115: 421 0.115 - 0.172: 50 0.172 - 0.230: 2 0.230 - 0.287: 3 Chirality restraints: 2356 Sorted by residual: chirality pdb=" C3' ANP A2407 " pdb=" C2' ANP A2407 " pdb=" C4' ANP A2407 " pdb=" O3' ANP A2407 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA VAL A 859 " pdb=" N VAL A 859 " pdb=" C VAL A 859 " pdb=" CB VAL A 859 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA LEU A 881 " pdb=" N LEU A 881 " pdb=" C LEU A 881 " pdb=" CB LEU A 881 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2353 not shown) Planarity restraints: 2682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A2186 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.81e+00 pdb=" C LEU A2186 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU A2186 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A2187 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 858 " 0.013 2.00e-02 2.50e+03 2.76e-02 7.59e+00 pdb=" C ARG A 858 " -0.048 2.00e-02 2.50e+03 pdb=" O ARG A 858 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 859 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 635 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.42e+00 pdb=" C GLN A 635 " -0.047 2.00e-02 2.50e+03 pdb=" O GLN A 635 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 636 " 0.015 2.00e-02 2.50e+03 ... (remaining 2679 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 169 2.57 - 3.15: 13350 3.15 - 3.74: 22435 3.74 - 4.32: 30302 4.32 - 4.90: 50707 Nonbonded interactions: 116963 Sorted by model distance: nonbonded pdb=" O2B ANP A2407 " pdb="MG MG A2408 " model vdw 1.988 2.170 nonbonded pdb=" CD2 HIS A2101 " pdb="ZN ZN A2406 " model vdw 2.159 2.450 nonbonded pdb=" O THR A 519 " pdb=" NH1 ARG A 520 " model vdw 2.188 2.520 nonbonded pdb=" ND2 ASN A 897 " pdb=" OE2 GLU A1046 " model vdw 2.196 2.520 nonbonded pdb=" OE2 GLU A1420 " pdb=" NH2 ARG A1721 " model vdw 2.207 2.520 ... (remaining 116958 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.610 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 47.660 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 : 0.008 0.194 15580 Z= 0.571 Angle : 0.835 10.512 21174 Z= 0.464 Chirality : 0.048 0.287 2356 Planarity : 0.005 0.067 2682 Dihedral : 17.050 154.361 5898 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.08 % Favored : 86.92 % Rotamer: Outliers : 0.56 % Allowed : 12.32 % Favored : 87.12 % 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: -4.17 (0.16), residues: 1866 helix: -1.81 (0.17), residues: 661 sheet: -2.87 (0.29), residues: 207 loop : -3.54 (0.16), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 692 HIS 0.011 0.002 HIS A2240 PHE 0.030 0.002 PHE A1401 TYR 0.019 0.002 TYR A 395 ARG 0.008 0.001 ARG A 875 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 180 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 LYS cc_start: 0.8046 (mmtp) cc_final: 0.7750 (ptmt) REVERT: A 726 LEU cc_start: 0.8500 (mm) cc_final: 0.8227 (mm) REVERT: A 940 ARG cc_start: 0.7995 (ptm160) cc_final: 0.7442 (ttm-80) REVERT: A 1600 LYS cc_start: 0.7823 (tppt) cc_final: 0.7612 (tppp) REVERT: A 1798 PHE cc_start: 0.7505 (m-80) cc_final: 0.7124 (m-80) REVERT: A 2187 SER cc_start: 0.8530 (OUTLIER) cc_final: 0.8095 (p) outliers start: 9 outliers final: 6 residues processed: 189 average time/residue: 0.3627 time to fit residues: 95.0583 Evaluate side-chains 143 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2187 SER Chi-restraints excluded: chain A residue 2265 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 0.0020 chunk 148 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 overall best weight: 2.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 GLN ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 GLN A1202 HIS A1242 ASN A1261 HIS A1342 ASN A1348 HIS ** A1818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1859 HIS ** A1922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1940 GLN A2038 GLN A2101 HIS ** A2211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2271 GLN A2272 GLN ** A2276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15580 Z= 0.246 Angle : 0.627 7.997 21174 Z= 0.320 Chirality : 0.042 0.176 2356 Planarity : 0.005 0.059 2682 Dihedral : 12.589 161.014 2269 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 3.05 % Allowed : 14.56 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.18), residues: 1866 helix: -0.26 (0.20), residues: 660 sheet: -2.33 (0.31), residues: 217 loop : -3.00 (0.17), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1415 HIS 0.007 0.001 HIS A2240 PHE 0.019 0.002 PHE A1401 TYR 0.020 0.002 TYR A 926 ARG 0.005 0.000 ARG A 568 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 170 time to evaluate : 1.803 Fit side-chains revert: symmetry clash REVERT: A 490 LYS cc_start: 0.7972 (mmtp) cc_final: 0.7700 (ptmt) REVERT: A 507 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8586 (pp) REVERT: A 704 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7695 (mp0) REVERT: A 726 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8135 (mm) REVERT: A 771 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7533 (tm-30) REVERT: A 809 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8958 (tt) REVERT: A 940 ARG cc_start: 0.7885 (ptm160) cc_final: 0.7371 (ttm-80) REVERT: A 1098 GLU cc_start: 0.7119 (pt0) cc_final: 0.6811 (pt0) REVERT: A 1493 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8038 (pp) REVERT: A 1598 GLN cc_start: 0.8571 (tp40) cc_final: 0.8052 (tm-30) REVERT: A 1600 LYS cc_start: 0.7692 (tppt) cc_final: 0.7473 (tppp) REVERT: A 1735 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8725 (tt) outliers start: 49 outliers final: 23 residues processed: 201 average time/residue: 0.2743 time to fit residues: 82.9371 Evaluate side-chains 172 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1261 HIS Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1722 VAL Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1967 ASP Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2285 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 6.9990 chunk 53 optimal weight: 0.3980 chunk 142 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 171 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 170 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 HIS ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1217 HIS ** A1818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1966 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15580 Z= 0.177 Angle : 0.582 9.074 21174 Z= 0.294 Chirality : 0.040 0.179 2356 Planarity : 0.005 0.054 2682 Dihedral : 11.862 169.627 2261 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.92 % Allowed : 17.49 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.19), residues: 1866 helix: 0.44 (0.21), residues: 662 sheet: -2.06 (0.32), residues: 222 loop : -2.70 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1415 HIS 0.014 0.001 HIS A1261 PHE 0.015 0.001 PHE A 864 TYR 0.019 0.001 TYR A 926 ARG 0.004 0.000 ARG A 568 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 165 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 LYS cc_start: 0.7905 (mmtp) cc_final: 0.7658 (ptmt) REVERT: A 726 LEU cc_start: 0.8472 (mm) cc_final: 0.8138 (mm) REVERT: A 771 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7345 (tm-30) REVERT: A 940 ARG cc_start: 0.7871 (ptm160) cc_final: 0.7322 (ttm-80) REVERT: A 1136 GLN cc_start: 0.7886 (tp40) cc_final: 0.7642 (tp40) REVERT: A 1401 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7646 (m-10) REVERT: A 1493 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7785 (pp) outliers start: 47 outliers final: 27 residues processed: 199 average time/residue: 0.2699 time to fit residues: 80.8274 Evaluate side-chains 178 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 149 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1261 HIS Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1401 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1722 VAL Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 2059 PHE Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2213 THR Chi-restraints excluded: chain A residue 2285 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 19 optimal weight: 0.0770 chunk 82 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 163 optimal weight: 0.4980 chunk 49 optimal weight: 10.0000 overall best weight: 1.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 HIS ** A1818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1966 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15580 Z= 0.193 Angle : 0.562 8.058 21174 Z= 0.285 Chirality : 0.040 0.166 2356 Planarity : 0.004 0.057 2682 Dihedral : 11.653 175.980 2261 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 3.55 % Allowed : 19.04 % Favored : 77.41 % 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: -1.83 (0.19), residues: 1866 helix: 0.71 (0.21), residues: 664 sheet: -1.76 (0.32), residues: 241 loop : -2.58 (0.18), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A1227 HIS 0.006 0.001 HIS A1261 PHE 0.017 0.001 PHE A 864 TYR 0.018 0.001 TYR A 926 ARG 0.003 0.000 ARG A 568 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 156 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8485 (mmp) cc_final: 0.8068 (mmm) REVERT: A 490 LYS cc_start: 0.7921 (mmtp) cc_final: 0.7678 (ptmt) REVERT: A 771 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7348 (tm-30) REVERT: A 940 ARG cc_start: 0.7923 (ptm160) cc_final: 0.7296 (ttm-80) REVERT: A 1401 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7698 (m-10) REVERT: A 1735 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8764 (tt) REVERT: A 2096 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8879 (tt) outliers start: 57 outliers final: 31 residues processed: 199 average time/residue: 0.2593 time to fit residues: 79.2922 Evaluate side-chains 173 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1261 HIS Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1401 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1722 VAL Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2096 LEU Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2213 THR Chi-restraints excluded: chain A residue 2285 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 75 optimal weight: 0.0870 chunk 155 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 GLN A1261 HIS ** A1818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1966 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15580 Z= 0.187 Angle : 0.574 12.150 21174 Z= 0.285 Chirality : 0.040 0.160 2356 Planarity : 0.004 0.057 2682 Dihedral : 11.444 163.830 2261 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.55 % Allowed : 20.04 % Favored : 76.42 % 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: -1.62 (0.19), residues: 1866 helix: 0.86 (0.21), residues: 669 sheet: -1.78 (0.33), residues: 228 loop : -2.41 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A1227 HIS 0.008 0.001 HIS A1261 PHE 0.015 0.001 PHE A 864 TYR 0.018 0.001 TYR A 926 ARG 0.007 0.000 ARG A1338 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 145 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8479 (mmp) cc_final: 0.8129 (mmm) REVERT: A 490 LYS cc_start: 0.7918 (mmtp) cc_final: 0.7677 (ptmt) REVERT: A 726 LEU cc_start: 0.8327 (mm) cc_final: 0.8071 (mm) REVERT: A 771 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7440 (tm-30) REVERT: A 809 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8939 (tt) REVERT: A 940 ARG cc_start: 0.7885 (ptm160) cc_final: 0.7275 (ttm-80) REVERT: A 1401 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7732 (m-10) REVERT: A 1735 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8764 (tt) outliers start: 57 outliers final: 36 residues processed: 191 average time/residue: 0.2901 time to fit residues: 83.7277 Evaluate side-chains 177 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 138 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 930 GLN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1401 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1722 VAL Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 2059 PHE Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2285 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 0.0570 chunk 164 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 182 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1818 GLN A1822 ASN A1922 GLN ** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15580 Z= 0.289 Angle : 0.619 11.585 21174 Z= 0.310 Chirality : 0.042 0.174 2356 Planarity : 0.005 0.057 2682 Dihedral : 11.471 157.342 2261 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 3.80 % Allowed : 20.66 % Favored : 75.54 % 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: -1.64 (0.19), residues: 1866 helix: 0.76 (0.21), residues: 672 sheet: -1.63 (0.32), residues: 246 loop : -2.41 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A1227 HIS 0.007 0.001 HIS A2240 PHE 0.017 0.002 PHE A1089 TYR 0.022 0.002 TYR A 522 ARG 0.010 0.000 ARG A1338 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 143 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8545 (mmp) cc_final: 0.8151 (mmm) REVERT: A 490 LYS cc_start: 0.7965 (mmtp) cc_final: 0.7690 (ptmt) REVERT: A 726 LEU cc_start: 0.8395 (mm) cc_final: 0.8116 (mm) REVERT: A 771 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7363 (tm-30) REVERT: A 809 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8978 (tt) REVERT: A 930 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7194 (pp30) REVERT: A 940 ARG cc_start: 0.7903 (ptm160) cc_final: 0.7291 (ttm-80) REVERT: A 1401 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7726 (m-10) REVERT: A 1735 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8787 (tt) REVERT: A 2011 PRO cc_start: 0.7762 (Cg_endo) cc_final: 0.7495 (Cg_exo) outliers start: 61 outliers final: 41 residues processed: 194 average time/residue: 0.2685 time to fit residues: 79.9904 Evaluate side-chains 181 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 136 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 930 GLN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1197 THR Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1401 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1500 LEU Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1722 VAL Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1832 ILE Chi-restraints excluded: chain A residue 1895 THR Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2285 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 153 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 182 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 GLN A1922 GLN ** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15580 Z= 0.184 Angle : 0.573 11.083 21174 Z= 0.285 Chirality : 0.040 0.161 2356 Planarity : 0.004 0.055 2682 Dihedral : 11.299 152.156 2261 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.99 % Allowed : 21.47 % Favored : 75.54 % 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: -1.40 (0.19), residues: 1866 helix: 0.91 (0.21), residues: 681 sheet: -1.55 (0.32), residues: 251 loop : -2.24 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A1227 HIS 0.005 0.001 HIS A2240 PHE 0.014 0.001 PHE A 864 TYR 0.018 0.001 TYR A 926 ARG 0.010 0.000 ARG A1338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 147 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8502 (mmp) cc_final: 0.8161 (mmm) REVERT: A 490 LYS cc_start: 0.7920 (mmtp) cc_final: 0.7677 (ptmt) REVERT: A 771 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7427 (tm-30) REVERT: A 940 ARG cc_start: 0.7849 (ptm160) cc_final: 0.7176 (ttm-80) REVERT: A 1401 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7682 (m-10) REVERT: A 1735 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8775 (tt) outliers start: 48 outliers final: 38 residues processed: 187 average time/residue: 0.2831 time to fit residues: 79.9725 Evaluate side-chains 178 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 138 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 902 ASN Chi-restraints excluded: chain A residue 930 GLN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1401 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1722 VAL Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1922 GLN Chi-restraints excluded: chain A residue 2083 HIS Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2102 VAL Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2285 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 54 optimal weight: 0.2980 chunk 35 optimal weight: 6.9990 chunk 115 optimal weight: 0.2980 chunk 124 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 165 optimal weight: 0.0050 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 GLN ** A1922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1986 HIS ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15580 Z= 0.158 Angle : 0.572 10.685 21174 Z= 0.281 Chirality : 0.040 0.178 2356 Planarity : 0.004 0.054 2682 Dihedral : 11.147 147.473 2261 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.36 % Allowed : 21.53 % Favored : 75.11 % 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: -1.22 (0.20), residues: 1866 helix: 1.06 (0.21), residues: 680 sheet: -1.52 (0.33), residues: 233 loop : -2.11 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A1227 HIS 0.004 0.001 HIS A2240 PHE 0.014 0.001 PHE A 864 TYR 0.018 0.001 TYR A 926 ARG 0.011 0.000 ARG A1582 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 152 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 ASP cc_start: 0.5426 (m-30) cc_final: 0.5147 (p0) REVERT: A 490 LYS cc_start: 0.7904 (mmtp) cc_final: 0.7574 (ptmt) REVERT: A 726 LEU cc_start: 0.8319 (mm) cc_final: 0.8055 (mm) REVERT: A 771 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7409 (tm-30) REVERT: A 940 ARG cc_start: 0.7852 (ptm160) cc_final: 0.7139 (ttm-80) REVERT: A 1401 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7675 (m-10) REVERT: A 1735 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8772 (tt) REVERT: A 1901 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8756 (mm) outliers start: 54 outliers final: 34 residues processed: 196 average time/residue: 0.2664 time to fit residues: 79.7551 Evaluate side-chains 176 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 139 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 930 GLN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1401 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1832 ILE Chi-restraints excluded: chain A residue 1901 LEU Chi-restraints excluded: chain A residue 2031 VAL Chi-restraints excluded: chain A residue 2059 PHE Chi-restraints excluded: chain A residue 2083 HIS Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2102 VAL Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2213 THR Chi-restraints excluded: chain A residue 2285 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 169 optimal weight: 10.0000 chunk 102 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 chunk 133 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 160 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 179 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 ASN A1922 GLN ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15580 Z= 0.150 Angle : 0.571 10.549 21174 Z= 0.281 Chirality : 0.040 0.172 2356 Planarity : 0.004 0.053 2682 Dihedral : 11.027 143.206 2261 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.80 % Allowed : 22.28 % Favored : 74.92 % 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: -1.08 (0.20), residues: 1866 helix: 1.22 (0.21), residues: 680 sheet: -1.43 (0.33), residues: 234 loop : -2.06 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP A1227 HIS 0.004 0.001 HIS A2240 PHE 0.015 0.001 PHE A 864 TYR 0.019 0.001 TYR A 926 ARG 0.007 0.000 ARG A1582 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 159 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.7880 (mmm) cc_final: 0.7650 (mmm) REVERT: A 365 MET cc_start: 0.7974 (mtm) cc_final: 0.7746 (mtm) REVERT: A 452 ASP cc_start: 0.5360 (m-30) cc_final: 0.5132 (p0) REVERT: A 490 LYS cc_start: 0.7922 (mmtp) cc_final: 0.7603 (ptmt) REVERT: A 771 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7390 (tm-30) REVERT: A 940 ARG cc_start: 0.7749 (ptm160) cc_final: 0.6993 (ttm-80) REVERT: A 1328 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6384 (pp) REVERT: A 1338 ARG cc_start: 0.6828 (ptt180) cc_final: 0.6342 (mmt90) REVERT: A 1401 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7669 (m-10) REVERT: A 1735 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8718 (tt) REVERT: A 1901 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8724 (mm) outliers start: 45 outliers final: 32 residues processed: 199 average time/residue: 0.2617 time to fit residues: 78.5032 Evaluate side-chains 174 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1401 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1901 LEU Chi-restraints excluded: chain A residue 1922 GLN Chi-restraints excluded: chain A residue 2059 PHE Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2213 THR Chi-restraints excluded: chain A residue 2285 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 149 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 115 optimal weight: 0.4980 chunk 91 optimal weight: 0.3980 chunk 119 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 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 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 ASN A1922 GLN ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15580 Z= 0.187 Angle : 0.595 10.394 21174 Z= 0.291 Chirality : 0.041 0.219 2356 Planarity : 0.004 0.054 2682 Dihedral : 11.035 143.557 2261 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.68 % Allowed : 22.46 % Favored : 74.86 % 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: -1.00 (0.20), residues: 1866 helix: 1.19 (0.21), residues: 681 sheet: -1.31 (0.34), residues: 233 loop : -1.96 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP A1227 HIS 0.005 0.001 HIS A2240 PHE 0.020 0.001 PHE A1798 TYR 0.018 0.001 TYR A 926 ARG 0.012 0.000 ARG A 941 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 146 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 MET cc_start: 0.7994 (mtm) cc_final: 0.7757 (mtm) REVERT: A 452 ASP cc_start: 0.5407 (m-30) cc_final: 0.5094 (p0) REVERT: A 490 LYS cc_start: 0.7918 (mmtp) cc_final: 0.7582 (ptmt) REVERT: A 940 ARG cc_start: 0.7830 (ptm160) cc_final: 0.7062 (ttm-80) REVERT: A 1328 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6471 (pp) REVERT: A 1401 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7739 (m-10) REVERT: A 1735 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8768 (tt) REVERT: A 1901 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8713 (mm) REVERT: A 2027 LYS cc_start: 0.6820 (mmmt) cc_final: 0.6586 (mmtm) outliers start: 43 outliers final: 35 residues processed: 185 average time/residue: 0.2587 time to fit residues: 73.9418 Evaluate side-chains 179 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 140 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 902 ASN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 HIS Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1401 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain A residue 1461 ILE Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1832 ILE Chi-restraints excluded: chain A residue 1901 LEU Chi-restraints excluded: chain A residue 1922 GLN Chi-restraints excluded: chain A residue 2031 VAL Chi-restraints excluded: chain A residue 2059 PHE Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2102 VAL Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2213 THR Chi-restraints excluded: chain A residue 2285 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.0030 chunk 150 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 154 optimal weight: 0.0070 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 0.0040 chunk 131 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1922 GLN ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.132618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.112909 restraints weight = 27784.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114158 restraints weight = 19867.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.115153 restraints weight = 15684.605| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15580 Z= 0.155 Angle : 0.581 10.455 21174 Z= 0.283 Chirality : 0.040 0.213 2356 Planarity : 0.004 0.053 2682 Dihedral : 10.952 140.623 2261 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.43 % Allowed : 22.96 % Favored : 74.61 % 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: -0.91 (0.20), residues: 1866 helix: 1.26 (0.21), residues: 677 sheet: -1.14 (0.33), residues: 252 loop : -1.93 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 590 HIS 0.004 0.001 HIS A2240 PHE 0.023 0.001 PHE A1798 TYR 0.019 0.001 TYR A 926 ARG 0.012 0.000 ARG A 941 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2796.48 seconds wall clock time: 52 minutes 8.60 seconds (3128.60 seconds total)