Starting phenix.real_space_refine on Thu Mar 5 01:27:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v86_21096/03_2026/6v86_21096.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v86_21096/03_2026/6v86_21096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6v86_21096/03_2026/6v86_21096.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v86_21096/03_2026/6v86_21096.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v86_21096/03_2026/6v86_21096.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v86_21096/03_2026/6v86_21096.map" } resolution = 4.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 97 5.16 5 C 11364 2.51 5 N 3027 2.21 5 O 3291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17781 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 15103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1890, 15103 Classifications: {'peptide': 1890} Link IDs: {'PTRANS': 84, 'TRANS': 1805} Chain breaks: 28 Chain: "B" Number of atoms: 569 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 72, 545 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Conformer: "B" Number of residues, atoms: 72, 545 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} bond proxies already assigned to first conformer: 517 Chain: "C" Number of atoms: 582 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 74, 559 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Conformer: "B" Number of residues, atoms: 74, 559 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} bond proxies already assigned to first conformer: 532 Chain: "D" Number of atoms: 569 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 72, 545 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Conformer: "B" Number of residues, atoms: 72, 545 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} bond proxies already assigned to first conformer: 517 Chain: "E" Number of atoms: 582 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 74, 559 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Conformer: "B" Number of residues, atoms: 74, 559 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} bond proxies already assigned to first conformer: 532 Chain: "F" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 374 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9936 SG CYS A1373 115.412 56.251 104.943 1.00123.58 S ATOM 9942 SG CYS A1374 112.735 58.424 105.844 1.00114.32 S ATOM 8621 SG CYS A1184 109.520 46.468 88.283 1.00 30.00 S Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N ASER B 211 " occ=0.48 ... (10 atoms not shown) pdb=" OG BSER B 211 " occ=0.52 residue: pdb=" N GLU B 221 " occ=0.84 ... (7 atoms not shown) pdb=" OE2 GLU B 221 " occ=0.84 residue: pdb=" N AASN B 228 " occ=0.42 ... (14 atoms not shown) pdb=" ND2BASN B 228 " occ=0.58 residue: pdb=" N AASN C 220 " occ=0.37 ... (14 atoms not shown) pdb=" ND2BASN C 220 " occ=0.63 residue: pdb=" N ASER C 231 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER C 231 " occ=0.40 residue: pdb=" N ASER D 211 " occ=0.48 ... (10 atoms not shown) pdb=" OG BSER D 211 " occ=0.52 residue: pdb=" N GLU D 221 " occ=0.84 ... (7 atoms not shown) pdb=" OE2 GLU D 221 " occ=0.84 residue: pdb=" N AASN D 228 " occ=0.42 ... (14 atoms not shown) pdb=" ND2BASN D 228 " occ=0.58 residue: pdb=" N AASN E 220 " occ=0.37 ... (14 atoms not shown) pdb=" ND2BASN E 220 " occ=0.63 residue: pdb=" N ASER E 231 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER E 231 " occ=0.40 Time building chain proxies: 3.85, per 1000 atoms: 0.22 Number of scatterers: 17781 At special positions: 0 Unit cell: (184.8, 144.48, 138.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 97 16.00 O 3291 8.00 N 3027 7.00 C 11364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 934.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1374 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1373 " pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" SG CYS A1184 " pdb="ZN ZN A2302 " - pdb=" NE2 HIS A1368 " pdb="ZN ZN A2302 " - pdb=" ND1 HIS A1366 " 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4274 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 7 sheets defined 61.6% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 49 through 55 Processing helix chain 'A' and resid 58 through 74 Processing helix chain 'A' and resid 93 through 98 Processing helix chain 'A' and resid 107 through 140 removed outlier: 3.758A pdb=" N LYS A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N GLY A 127 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 170 Processing helix chain 'A' and resid 173 through 197 Processing helix chain 'A' and resid 235 through 257 removed outlier: 3.935A pdb=" N VAL A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 261 through 282 removed outlier: 3.787A pdb=" N LYS A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 302 removed outlier: 4.311A pdb=" N TYR A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 328 removed outlier: 4.174A pdb=" N ALA A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 346 Processing helix chain 'A' and resid 352 through 364 removed outlier: 3.612A pdb=" N THR A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 removed outlier: 4.185A pdb=" N ALA A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 413 Processing helix chain 'A' and resid 427 through 436 Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.775A pdb=" N LYS A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 490 Processing helix chain 'A' and resid 513 through 520 removed outlier: 3.529A pdb=" N ASN A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 566 through 584 Processing helix chain 'A' and resid 597 through 611 Processing helix chain 'A' and resid 672 through 675 Processing helix chain 'A' and resid 676 through 687 Processing helix chain 'A' and resid 694 through 700 Processing helix chain 'A' and resid 743 through 762 removed outlier: 3.514A pdb=" N TRP A 747 " --> pdb=" O CYS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 815 removed outlier: 3.754A pdb=" N LYS A 792 " --> pdb=" O PRO A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 821 No H-bonds generated for 'chain 'A' and resid 819 through 821' Processing helix chain 'A' and resid 846 through 852 Processing helix chain 'A' and resid 863 through 881 removed outlier: 3.663A pdb=" N SER A 867 " --> pdb=" O CYS A 863 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN A 881 " --> pdb=" O ARG A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 905 removed outlier: 3.625A pdb=" N CYS A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 922 Processing helix chain 'A' and resid 923 through 932 removed outlier: 4.380A pdb=" N VAL A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 938 Processing helix chain 'A' and resid 945 through 950 Processing helix chain 'A' and resid 955 through 971 removed outlier: 3.727A pdb=" N SER A 959 " --> pdb=" O ASP A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 983 removed outlier: 4.457A pdb=" N TYR A 979 " --> pdb=" O TYR A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 996 Processing helix chain 'A' and resid 1008 through 1024 removed outlier: 3.695A pdb=" N ALA A1012 " --> pdb=" O PRO A1008 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1032 removed outlier: 3.744A pdb=" N GLY A1032 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1051 removed outlier: 3.510A pdb=" N ASP A1051 " --> pdb=" O ARG A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1067 removed outlier: 3.800A pdb=" N ALA A1060 " --> pdb=" O PHE A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1078 removed outlier: 3.608A pdb=" N ARG A1071 " --> pdb=" O THR A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1091 Processing helix chain 'A' and resid 1097 through 1105 removed outlier: 3.954A pdb=" N ASP A1105 " --> pdb=" O ASN A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1117 removed outlier: 3.612A pdb=" N ASN A1109 " --> pdb=" O ASP A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1132 Processing helix chain 'A' and resid 1136 through 1154 Proline residue: A1151 - end of helix Processing helix chain 'A' and resid 1165 through 1170 Processing helix chain 'A' and resid 1238 through 1251 removed outlier: 3.985A pdb=" N TRP A1251 " --> pdb=" O GLY A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1271 removed outlier: 3.543A pdb=" N TRP A1260 " --> pdb=" O THR A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1352 Processing helix chain 'A' and resid 1437 through 1453 removed outlier: 4.116A pdb=" N SER A1441 " --> pdb=" O LEU A1437 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A1451 " --> pdb=" O GLN A1447 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A1452 " --> pdb=" O ILE A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1504 removed outlier: 3.872A pdb=" N TYR A1504 " --> pdb=" O SER A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1511 through 1523 Processing helix chain 'A' and resid 1525 through 1537 removed outlier: 4.054A pdb=" N ALA A1529 " --> pdb=" O ILE A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1549 removed outlier: 4.172A pdb=" N ARG A1544 " --> pdb=" O PRO A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1586 Processing helix chain 'A' and resid 1605 through 1624 Processing helix chain 'A' and resid 1636 through 1650 Processing helix chain 'A' and resid 1656 through 1663 removed outlier: 4.241A pdb=" N LEU A1660 " --> pdb=" O SER A1656 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1688 Processing helix chain 'A' and resid 1695 through 1701 removed outlier: 3.654A pdb=" N ALA A1699 " --> pdb=" O GLY A1696 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A1700 " --> pdb=" O GLN A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1768 through 1775 removed outlier: 4.176A pdb=" N HIS A1771 " --> pdb=" O ALA A1768 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS A1772 " --> pdb=" O PRO A1769 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A1775 " --> pdb=" O HIS A1772 " (cutoff:3.500A) Processing helix chain 'A' and resid 1784 through 1796 Processing helix chain 'A' and resid 1815 through 1822 removed outlier: 3.709A pdb=" N GLU A1819 " --> pdb=" O MET A1815 " (cutoff:3.500A) Processing helix chain 'A' and resid 1849 through 1855 Processing helix chain 'A' and resid 1855 through 1861 Processing helix chain 'A' and resid 1891 through 1899 Processing helix chain 'A' and resid 1923 through 1935 Processing helix chain 'A' and resid 1952 through 1964 Processing helix chain 'A' and resid 2001 through 2012 removed outlier: 3.626A pdb=" N GLY A2005 " --> pdb=" O SER A2001 " (cutoff:3.500A) Processing helix chain 'A' and resid 2021 through 2046 removed outlier: 4.359A pdb=" N GLN A2025 " --> pdb=" O GLU A2021 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A2046 " --> pdb=" O ASP A2042 " (cutoff:3.500A) Processing helix chain 'A' and resid 2053 through 2059 Processing helix chain 'A' and resid 2083 through 2104 Processing helix chain 'A' and resid 2126 through 2144 Processing helix chain 'A' and resid 2149 through 2161 Processing helix chain 'A' and resid 2171 through 2175 removed outlier: 3.642A pdb=" N ARG A2175 " --> pdb=" O ASN A2172 " (cutoff:3.500A) Processing helix chain 'A' and resid 2187 through 2191 Processing helix chain 'A' and resid 2194 through 2200 Processing helix chain 'A' and resid 2208 through 2226 removed outlier: 3.668A pdb=" N HIS A2226 " --> pdb=" O VAL A2222 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 247 Processing helix chain 'B' and resid 248 through 269 Processing helix chain 'C' and resid 202 through 269 Processing helix chain 'D' and resid 204 through 247 removed outlier: 4.340A pdb=" N LEU D 208 " --> pdb=" O ASP D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 270 removed outlier: 4.128A pdb=" N MET D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 270 removed outlier: 4.107A pdb=" N LEU E 205 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER E 248 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU E 249 " --> pdb=" O SER E 245 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N MET E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 356 Processing helix chain 'F' and resid 360 through 374 removed outlier: 3.656A pdb=" N GLN F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 390 Processing sheet with id=AA1, first strand: chain 'A' and resid 204 through 208 removed outlier: 3.928A pdb=" N ASN A 208 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 211 " --> pdb=" O ASN A 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 222 Processing sheet with id=AA3, first strand: chain 'A' and resid 765 through 771 Processing sheet with id=AA4, first strand: chain 'A' and resid 704 through 705 Processing sheet with id=AA5, first strand: chain 'A' and resid 829 through 832 Processing sheet with id=AA6, first strand: chain 'A' and resid 1173 through 1176 removed outlier: 4.160A pdb=" N THR A1192 " --> pdb=" O LEU A1367 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1828 through 1829 removed outlier: 7.058A pdb=" N LEU A1805 " --> pdb=" O HIS A1909 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N ASP A1911 " --> pdb=" O LEU A1805 " (cutoff:3.500A) 1016 hydrogen bonds defined for protein. 2977 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: 3.31 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5702 1.34 - 1.46: 2644 1.46 - 1.58: 9609 1.58 - 1.69: 0 1.69 - 1.81: 154 Bond restraints: 18109 Sorted by residual: bond pdb=" N ILE A1737 " pdb=" CA ILE A1737 " ideal model delta sigma weight residual 1.460 1.493 -0.033 8.60e-03 1.35e+04 1.49e+01 bond pdb=" N ILE A1740 " pdb=" CA ILE A1740 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.11e-02 8.12e+03 1.28e+01 bond pdb=" N ILE A1739 " pdb=" CA ILE A1739 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" N ILE A1970 " pdb=" CA ILE A1970 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.22e-02 6.72e+03 8.87e+00 bond pdb=" N PHE A1967 " pdb=" CA PHE A1967 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.23e-02 6.61e+03 8.54e+00 ... (remaining 18104 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 23736 2.02 - 4.05: 711 4.05 - 6.07: 93 6.07 - 8.09: 18 8.09 - 10.12: 3 Bond angle restraints: 24561 Sorted by residual: angle pdb=" N ILE A1737 " pdb=" CA ILE A1737 " pdb=" C ILE A1737 " ideal model delta sigma weight residual 113.71 108.17 5.54 9.50e-01 1.11e+00 3.40e+01 angle pdb=" C ILE A1736 " pdb=" N ILE A1737 " pdb=" CA ILE A1737 " ideal model delta sigma weight residual 121.53 128.87 -7.34 1.40e+00 5.10e-01 2.75e+01 angle pdb=" C SER A 304 " pdb=" N ASP A 305 " pdb=" CA ASP A 305 " ideal model delta sigma weight residual 120.58 127.24 -6.66 1.32e+00 5.74e-01 2.54e+01 angle pdb=" N VAL A 12 " pdb=" CA VAL A 12 " pdb=" C VAL A 12 " ideal model delta sigma weight residual 113.20 108.48 4.72 9.60e-01 1.09e+00 2.41e+01 angle pdb=" CA ILE A1736 " pdb=" C ILE A1736 " pdb=" N ILE A1737 " ideal model delta sigma weight residual 116.60 109.89 6.71 1.45e+00 4.76e-01 2.14e+01 ... (remaining 24556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 9795 17.88 - 35.76: 1020 35.76 - 53.64: 131 53.64 - 71.52: 41 71.52 - 89.40: 14 Dihedral angle restraints: 11001 sinusoidal: 4427 harmonic: 6574 Sorted by residual: dihedral pdb=" CA ASN A1763 " pdb=" C ASN A1763 " pdb=" N PHE A1764 " pdb=" CA PHE A1764 " ideal model delta harmonic sigma weight residual 180.00 151.09 28.91 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA PRO A 714 " pdb=" C PRO A 714 " pdb=" N ALA A 715 " pdb=" CA ALA A 715 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA VAL A1855 " pdb=" C VAL A1855 " pdb=" N PRO A1856 " pdb=" CA PRO A1856 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 10998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2328 0.053 - 0.106: 479 0.106 - 0.159: 76 0.159 - 0.213: 12 0.213 - 0.266: 3 Chirality restraints: 2898 Sorted by residual: chirality pdb=" CB ILE A1740 " pdb=" CA ILE A1740 " pdb=" CG1 ILE A1740 " pdb=" CG2 ILE A1740 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ILE A1970 " pdb=" N ILE A1970 " pdb=" C ILE A1970 " pdb=" CB ILE A1970 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA LEU A1746 " pdb=" N LEU A1746 " pdb=" C LEU A1746 " pdb=" CB LEU A1746 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 2895 not shown) Planarity restraints: 3087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A1736 " -0.028 2.00e-02 2.50e+03 5.92e-02 3.51e+01 pdb=" C ILE A1736 " 0.102 2.00e-02 2.50e+03 pdb=" O ILE A1736 " -0.041 2.00e-02 2.50e+03 pdb=" N ILE A1737 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A1738 " 0.021 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C TRP A1738 " -0.077 2.00e-02 2.50e+03 pdb=" O TRP A1738 " 0.030 2.00e-02 2.50e+03 pdb=" N ILE A1739 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1925 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.98e+00 pdb=" N PRO A1926 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A1926 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1926 " -0.037 5.00e-02 4.00e+02 ... (remaining 3084 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 17 2.16 - 2.84: 6151 2.84 - 3.53: 28068 3.53 - 4.21: 39656 4.21 - 4.90: 65684 Nonbonded interactions: 139576 Sorted by model distance: nonbonded pdb=" O ILE A1739 " pdb=" NH2 ARG A2022 " model vdw 1.470 3.120 nonbonded pdb=" O LEU A1746 " pdb=" NZ LYS A1748 " model vdw 1.484 3.120 nonbonded pdb=" O ILE A1739 " pdb=" NH1 ARG A2022 " model vdw 1.668 3.120 nonbonded pdb=" O ILE A1739 " pdb=" CZ ARG A2022 " model vdw 1.735 3.270 nonbonded pdb=" O ALA A1744 " pdb=" NE1 TRP A1964 " model vdw 1.889 3.120 ... (remaining 139571 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 199 through 210 or resid 212 through 216 or resid 218 thro \ ugh 219 or resid 221 through 227 or resid 229 through 230 or resid 232 through 2 \ 34 or resid 236 through 270)) selection = (chain 'C' and (resid 199 through 210 or resid 212 through 216 or resid 218 thro \ ugh 219 or resid 221 through 227 or resid 229 through 230 or resid 232 through 2 \ 34 or resid 236 through 270)) selection = (chain 'D' and (resid 199 through 210 or resid 212 through 216 or resid 218 thro \ ugh 219 or resid 221 through 227 or resid 229 through 230 or resid 232 through 2 \ 34 or resid 236 through 270)) selection = (chain 'E' and (resid 199 through 210 or resid 212 through 216 or resid 218 thro \ ugh 219 or resid 221 through 227 or resid 229 through 230 or resid 232 through 2 \ 34 or resid 236 through 270)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.080 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 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 : 0.007 0.608 18114 Z= 0.305 Angle : 0.832 10.119 24561 Z= 0.490 Chirality : 0.045 0.266 2898 Planarity : 0.005 0.066 3087 Dihedral : 14.791 89.398 6727 Min Nonbonded Distance : 1.470 Molprobity Statistics. All-atom Clashscore : 23.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.14 % Favored : 86.63 % Rotamer: Outliers : 0.70 % Allowed : 7.11 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.51 (0.14), residues: 2193 helix: -1.80 (0.12), residues: 1287 sheet: -3.13 (0.53), residues: 69 loop : -4.95 (0.15), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1974 TYR 0.020 0.002 TYR A 85 PHE 0.018 0.002 PHE A 562 TRP 0.041 0.002 TRP A1950 HIS 0.006 0.001 HIS A1392 Details of bonding type rmsd covalent geometry : bond 0.00391 (18109) covalent geometry : angle 0.83162 (24561) hydrogen bonds : bond 0.12990 ( 1016) hydrogen bonds : angle 6.42430 ( 2977) metal coordination : bond 0.38083 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 281 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.9207 (mt) cc_final: 0.8731 (tt) REVERT: A 365 LEU cc_start: 0.8021 (pt) cc_final: 0.7804 (pt) REVERT: A 384 MET cc_start: 0.6840 (tpp) cc_final: 0.6135 (tpt) REVERT: A 435 MET cc_start: 0.8807 (mmm) cc_final: 0.8403 (tmm) REVERT: A 569 MET cc_start: 0.8020 (tpt) cc_final: 0.7727 (tpt) REVERT: A 577 GLU cc_start: 0.7246 (tp30) cc_final: 0.7045 (tp30) REVERT: A 1129 LYS cc_start: 0.9210 (tmmt) cc_final: 0.8811 (mttm) REVERT: A 1447 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8172 (mm-40) REVERT: A 1489 MET cc_start: 0.8182 (ttp) cc_final: 0.7903 (ttp) REVERT: A 1761 PHE cc_start: 0.7982 (t80) cc_final: 0.7538 (t80) REVERT: A 1815 MET cc_start: 0.9101 (pmm) cc_final: 0.8872 (pmm) REVERT: A 1920 GLN cc_start: 0.8359 (tm-30) cc_final: 0.8007 (tm-30) REVERT: A 1923 LEU cc_start: 0.8780 (pt) cc_final: 0.8295 (pp) REVERT: B 233 MET cc_start: 0.8091 (mtt) cc_final: 0.7866 (mtt) REVERT: B 237 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8799 (mt-10) REVERT: C 270 MET cc_start: 0.8669 (mtm) cc_final: 0.7943 (pmm) REVERT: F 348 ILE cc_start: 0.8782 (mm) cc_final: 0.8554 (mp) outliers start: 7 outliers final: 0 residues processed: 285 average time/residue: 0.1280 time to fit residues: 56.1050 Evaluate side-chains 183 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 0.5980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 134 ASN A 315 HIS A 368 HIS A 582 ASN A 609 GLN A 670 GLN A 771 GLN ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 ASN A 892 ASN A 925 HIS ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1107 ASN ** A1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1289 ASN A1327 ASN A1352 ASN A1447 GLN ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1679 ASN A1733 ASN ** A1771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1909 HIS A2030 HIS B 202 GLN B 206 ASN B 220 ASN A C 202 GLN C 247 GLN C 251 GLN D 202 GLN D 251 GLN E 220 ASN B E 235 GLN B E 255 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.072039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.056532 restraints weight = 570196.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.059905 restraints weight = 243848.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.060780 restraints weight = 120333.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.060968 restraints weight = 85062.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.061682 restraints weight = 75237.951| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 18114 Z= 0.202 Angle : 0.791 10.378 24561 Z= 0.408 Chirality : 0.046 0.340 2898 Planarity : 0.006 0.065 3087 Dihedral : 6.530 69.820 2409 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.73 % Favored : 87.23 % Rotamer: Outliers : 0.75 % Allowed : 8.51 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.16), residues: 2193 helix: -0.47 (0.13), residues: 1312 sheet: -2.96 (0.53), residues: 74 loop : -4.73 (0.16), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 984 TYR 0.022 0.002 TYR A 85 PHE 0.019 0.002 PHE A2052 TRP 0.040 0.002 TRP A1738 HIS 0.008 0.002 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00439 (18109) covalent geometry : angle 0.79092 (24561) hydrogen bonds : bond 0.05249 ( 1016) hydrogen bonds : angle 5.44998 ( 2977) metal coordination : bond 0.01585 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 239 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.9467 (mt) cc_final: 0.8938 (tt) REVERT: A 236 GLU cc_start: 0.8721 (mp0) cc_final: 0.8438 (mp0) REVERT: A 370 MET cc_start: 0.7486 (ptm) cc_final: 0.7087 (ptm) REVERT: A 384 MET cc_start: 0.7186 (tpp) cc_final: 0.6664 (tpt) REVERT: A 435 MET cc_start: 0.8782 (mmm) cc_final: 0.8397 (tmm) REVERT: A 569 MET cc_start: 0.7983 (tpt) cc_final: 0.7602 (tpt) REVERT: A 670 GLN cc_start: 0.8791 (mm110) cc_final: 0.8498 (mm110) REVERT: A 771 GLN cc_start: 0.6185 (OUTLIER) cc_final: 0.5828 (mm-40) REVERT: A 1129 LYS cc_start: 0.9250 (tmmt) cc_final: 0.8683 (mttp) REVERT: A 1447 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8163 (mm-40) REVERT: A 1489 MET cc_start: 0.8305 (ttp) cc_final: 0.8089 (ttp) REVERT: A 1815 MET cc_start: 0.9034 (pmm) cc_final: 0.8349 (pmm) REVERT: A 1923 LEU cc_start: 0.8747 (pt) cc_final: 0.8336 (pp) REVERT: A 2162 PHE cc_start: 0.8289 (m-80) cc_final: 0.7592 (m-80) REVERT: B 237 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8601 (mt-10) REVERT: B 264 MET cc_start: 0.8456 (mtt) cc_final: 0.8061 (mtt) REVERT: C 242 ARG cc_start: 0.9102 (tpp80) cc_final: 0.8781 (tpt170) REVERT: C 270 MET cc_start: 0.8730 (mtm) cc_final: 0.8097 (pmm) REVERT: F 350 LEU cc_start: 0.8873 (mt) cc_final: 0.8292 (tt) outliers start: 8 outliers final: 0 residues processed: 243 average time/residue: 0.1238 time to fit residues: 46.6461 Evaluate side-chains 176 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 193 optimal weight: 9.9990 chunk 195 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 133 optimal weight: 0.0000 chunk 151 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 161 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 123 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 ASN ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1027 ASN ** A1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1771 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.073820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.057418 restraints weight = 618538.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.061312 restraints weight = 250377.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.063655 restraints weight = 111538.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.063481 restraints weight = 73956.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.063838 restraints weight = 66988.322| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18114 Z= 0.157 Angle : 0.727 10.077 24561 Z= 0.374 Chirality : 0.044 0.167 2898 Planarity : 0.005 0.058 3087 Dihedral : 6.192 69.178 2409 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.15 % Favored : 88.80 % Rotamer: Outliers : 0.40 % Allowed : 6.27 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.17), residues: 2193 helix: 0.12 (0.14), residues: 1321 sheet: -2.96 (0.56), residues: 64 loop : -4.48 (0.17), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 188 TYR 0.021 0.002 TYR A1113 PHE 0.022 0.002 PHE A2052 TRP 0.045 0.002 TRP A1738 HIS 0.005 0.001 HIS A 816 Details of bonding type rmsd covalent geometry : bond 0.00343 (18109) covalent geometry : angle 0.72716 (24561) hydrogen bonds : bond 0.04727 ( 1016) hydrogen bonds : angle 5.13854 ( 2977) metal coordination : bond 0.00316 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.9394 (mt) cc_final: 0.8898 (tt) REVERT: A 240 MET cc_start: 0.8063 (ttp) cc_final: 0.7367 (ttt) REVERT: A 244 MET cc_start: 0.8646 (mtp) cc_final: 0.7870 (mtp) REVERT: A 370 MET cc_start: 0.7548 (ptm) cc_final: 0.7266 (ptm) REVERT: A 384 MET cc_start: 0.7086 (tpp) cc_final: 0.6774 (tpt) REVERT: A 435 MET cc_start: 0.8754 (mmm) cc_final: 0.8285 (tmm) REVERT: A 569 MET cc_start: 0.7879 (tpt) cc_final: 0.7503 (tpt) REVERT: A 670 GLN cc_start: 0.9015 (mm110) cc_final: 0.8573 (mm110) REVERT: A 693 PHE cc_start: 0.8301 (m-80) cc_final: 0.8059 (m-10) REVERT: A 812 PHE cc_start: 0.8888 (t80) cc_final: 0.8643 (t80) REVERT: A 1033 ILE cc_start: 0.8247 (mp) cc_final: 0.8015 (mm) REVERT: A 1489 MET cc_start: 0.8268 (ttp) cc_final: 0.8050 (ttp) REVERT: A 1520 MET cc_start: 0.7967 (tpp) cc_final: 0.7685 (tpp) REVERT: A 1920 GLN cc_start: 0.8013 (tm-30) cc_final: 0.7462 (tm-30) REVERT: A 1923 LEU cc_start: 0.8659 (pt) cc_final: 0.8197 (pp) REVERT: B 233 MET cc_start: 0.7913 (mtm) cc_final: 0.7356 (ppp) REVERT: B 237 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8226 (mt-10) REVERT: B 264 MET cc_start: 0.8511 (mtt) cc_final: 0.8213 (mtt) REVERT: C 238 THR cc_start: 0.7931 (p) cc_final: 0.7554 (p) REVERT: C 242 ARG cc_start: 0.9081 (tpp80) cc_final: 0.8765 (tpt170) REVERT: C 270 MET cc_start: 0.8709 (mtm) cc_final: 0.8030 (pmm) outliers start: 1 outliers final: 0 residues processed: 241 average time/residue: 0.1279 time to fit residues: 47.7795 Evaluate side-chains 176 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 8 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 2 optimal weight: 0.0870 chunk 64 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 ASN ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN B ** 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 = 0.3586 r_free = 0.3586 target = 0.073992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.058365 restraints weight = 463245.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.061580 restraints weight = 207531.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.062674 restraints weight = 111798.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.064379 restraints weight = 69303.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.064305 restraints weight = 50122.755| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18114 Z= 0.150 Angle : 0.719 9.909 24561 Z= 0.366 Chirality : 0.043 0.226 2898 Planarity : 0.005 0.068 3087 Dihedral : 6.058 69.140 2409 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 0.35 % Allowed : 5.77 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.18), residues: 2193 helix: 0.38 (0.14), residues: 1325 sheet: -2.70 (0.57), residues: 68 loop : -4.34 (0.18), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 685 TYR 0.024 0.002 TYR F 367 PHE 0.018 0.001 PHE A2052 TRP 0.032 0.002 TRP A1950 HIS 0.004 0.001 HIS A1804 Details of bonding type rmsd covalent geometry : bond 0.00327 (18109) covalent geometry : angle 0.71901 (24561) hydrogen bonds : bond 0.04555 ( 1016) hydrogen bonds : angle 4.98778 ( 2977) metal coordination : bond 0.00271 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7920 (pt0) cc_final: 0.7422 (pm20) REVERT: A 187 MET cc_start: 0.8163 (ttt) cc_final: 0.7737 (ttt) REVERT: A 240 MET cc_start: 0.7993 (ttp) cc_final: 0.7278 (ttt) REVERT: A 244 MET cc_start: 0.8657 (mtp) cc_final: 0.7837 (mtp) REVERT: A 384 MET cc_start: 0.7075 (tpp) cc_final: 0.6805 (tpt) REVERT: A 435 MET cc_start: 0.8673 (mmm) cc_final: 0.8253 (tmm) REVERT: A 569 MET cc_start: 0.8028 (tpt) cc_final: 0.7767 (mmm) REVERT: A 670 GLN cc_start: 0.8896 (mm110) cc_final: 0.8629 (mm110) REVERT: A 812 PHE cc_start: 0.8895 (t80) cc_final: 0.8631 (t80) REVERT: A 1447 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8035 (tm-30) REVERT: A 1483 LYS cc_start: 0.6478 (pptt) cc_final: 0.5976 (pptt) REVERT: A 1489 MET cc_start: 0.8266 (ttp) cc_final: 0.8039 (ttp) REVERT: A 1520 MET cc_start: 0.8102 (tpp) cc_final: 0.7848 (tpp) REVERT: A 1923 LEU cc_start: 0.8659 (pt) cc_final: 0.8142 (pp) REVERT: A 1973 LEU cc_start: 0.8436 (tt) cc_final: 0.7707 (mp) REVERT: B 237 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8453 (mt-10) REVERT: C 242 ARG cc_start: 0.9166 (tpp80) cc_final: 0.8897 (tpt170) REVERT: C 270 MET cc_start: 0.8630 (mtm) cc_final: 0.8034 (pmm) REVERT: F 350 LEU cc_start: 0.8915 (mm) cc_final: 0.8560 (tt) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1238 time to fit residues: 46.3107 Evaluate side-chains 172 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 179 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 176 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 ASN ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN D 228 ASN B E 247 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.072536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.055896 restraints weight = 575149.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.060268 restraints weight = 234003.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.061889 restraints weight = 99569.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.061775 restraints weight = 76336.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.062471 restraints weight = 61560.757| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18114 Z= 0.191 Angle : 0.780 16.941 24561 Z= 0.394 Chirality : 0.045 0.245 2898 Planarity : 0.006 0.059 3087 Dihedral : 6.233 69.502 2409 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.49 % Favored : 87.46 % Rotamer: Outliers : 0.40 % Allowed : 4.53 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.17), residues: 2193 helix: 0.29 (0.14), residues: 1323 sheet: -2.83 (0.60), residues: 58 loop : -4.34 (0.17), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 685 TYR 0.020 0.002 TYR A 85 PHE 0.020 0.002 PHE A2052 TRP 0.041 0.002 TRP A 113 HIS 0.006 0.001 HIS A1804 Details of bonding type rmsd covalent geometry : bond 0.00414 (18109) covalent geometry : angle 0.78012 (24561) hydrogen bonds : bond 0.04834 ( 1016) hydrogen bonds : angle 5.12378 ( 2977) metal coordination : bond 0.00403 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.7998 (ttp) cc_final: 0.7517 (ttt) REVERT: A 244 MET cc_start: 0.8473 (mtp) cc_final: 0.7913 (mtp) REVERT: A 384 MET cc_start: 0.7016 (tpp) cc_final: 0.6602 (tpt) REVERT: A 435 MET cc_start: 0.8672 (mmm) cc_final: 0.8308 (tmm) REVERT: A 569 MET cc_start: 0.8100 (tpt) cc_final: 0.7891 (mmm) REVERT: A 670 GLN cc_start: 0.8998 (mm110) cc_final: 0.8687 (mm-40) REVERT: A 812 PHE cc_start: 0.8880 (t80) cc_final: 0.8649 (t80) REVERT: A 1244 ARG cc_start: 0.8099 (mpt180) cc_final: 0.7864 (mmt90) REVERT: A 1447 GLN cc_start: 0.8615 (mm-40) cc_final: 0.7986 (tm-30) REVERT: A 1483 LYS cc_start: 0.6654 (pptt) cc_final: 0.6185 (pptt) REVERT: A 1489 MET cc_start: 0.8279 (ttp) cc_final: 0.8064 (ttp) REVERT: A 1520 MET cc_start: 0.8131 (tpp) cc_final: 0.7872 (tpp) REVERT: A 1607 MET cc_start: 0.7582 (mpp) cc_final: 0.7339 (mpp) REVERT: A 1613 LYS cc_start: 0.9297 (tttt) cc_final: 0.9057 (tptt) REVERT: A 1815 MET cc_start: 0.8952 (pmm) cc_final: 0.8437 (pmm) REVERT: A 2006 MET cc_start: 0.8135 (ttp) cc_final: 0.7894 (ttp) REVERT: A 2091 MET cc_start: 0.7838 (mtt) cc_final: 0.7552 (tpp) REVERT: B 237 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8403 (mt-10) REVERT: C 241 ASP cc_start: 0.7985 (m-30) cc_final: 0.7658 (m-30) REVERT: C 242 ARG cc_start: 0.9167 (tpp80) cc_final: 0.8812 (tpt170) REVERT: C 270 MET cc_start: 0.8705 (mtm) cc_final: 0.8093 (pmm) REVERT: D 237 GLU cc_start: 0.8613 (pp20) cc_final: 0.8327 (pp20) REVERT: D 264 MET cc_start: 0.7290 (tpp) cc_final: 0.6755 (tpp) REVERT: F 350 LEU cc_start: 0.9021 (mm) cc_final: 0.8629 (tt) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1176 time to fit residues: 41.9551 Evaluate side-chains 175 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 203 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 182 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 219 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 155 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 ASN ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1143 ASN A1447 GLN ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.072880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.056020 restraints weight = 617119.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.060593 restraints weight = 249255.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.062588 restraints weight = 100127.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.062313 restraints weight = 73216.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.062838 restraints weight = 61462.786| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18114 Z= 0.191 Angle : 0.778 14.447 24561 Z= 0.392 Chirality : 0.045 0.208 2898 Planarity : 0.005 0.055 3087 Dihedral : 6.240 69.370 2409 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.82 % Favored : 87.18 % Rotamer: Outliers : 0.40 % Allowed : 4.23 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.17), residues: 2193 helix: 0.32 (0.14), residues: 1322 sheet: -2.79 (0.61), residues: 56 loop : -4.26 (0.18), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 685 TYR 0.021 0.002 TYR A 85 PHE 0.020 0.002 PHE A2052 TRP 0.041 0.002 TRP A1950 HIS 0.008 0.001 HIS A1539 Details of bonding type rmsd covalent geometry : bond 0.00414 (18109) covalent geometry : angle 0.77840 (24561) hydrogen bonds : bond 0.04842 ( 1016) hydrogen bonds : angle 5.12494 ( 2977) metal coordination : bond 0.00372 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7937 (pt0) cc_final: 0.7358 (pm20) REVERT: A 187 MET cc_start: 0.8216 (ttt) cc_final: 0.7886 (ttt) REVERT: A 240 MET cc_start: 0.8026 (ttp) cc_final: 0.7554 (ttt) REVERT: A 244 MET cc_start: 0.8563 (mtp) cc_final: 0.8006 (mtp) REVERT: A 384 MET cc_start: 0.6697 (tpp) cc_final: 0.6299 (tpt) REVERT: A 435 MET cc_start: 0.8659 (mmm) cc_final: 0.8306 (tmm) REVERT: A 569 MET cc_start: 0.8068 (tpt) cc_final: 0.7771 (tpt) REVERT: A 670 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8716 (mm-40) REVERT: A 812 PHE cc_start: 0.8925 (t80) cc_final: 0.8718 (t80) REVERT: A 1139 ASP cc_start: 0.8662 (m-30) cc_final: 0.8438 (m-30) REVERT: A 1447 GLN cc_start: 0.8674 (mm110) cc_final: 0.8195 (tm-30) REVERT: A 1483 LYS cc_start: 0.6631 (pptt) cc_final: 0.6181 (pptt) REVERT: A 1517 TYR cc_start: 0.8278 (t80) cc_final: 0.8071 (t80) REVERT: A 1520 MET cc_start: 0.8071 (tpp) cc_final: 0.7845 (tpp) REVERT: A 1607 MET cc_start: 0.7577 (mpp) cc_final: 0.7322 (mpp) REVERT: A 1684 ARG cc_start: 0.6553 (mtm180) cc_final: 0.6255 (mtt180) REVERT: A 1815 MET cc_start: 0.8947 (pmm) cc_final: 0.8446 (pmm) REVERT: A 2006 MET cc_start: 0.8145 (ttp) cc_final: 0.7938 (ttp) REVERT: A 2091 MET cc_start: 0.7817 (mtt) cc_final: 0.7534 (tpp) REVERT: C 242 ARG cc_start: 0.9205 (tpp80) cc_final: 0.8846 (tpt170) REVERT: C 270 MET cc_start: 0.8704 (mtm) cc_final: 0.8117 (pmm) REVERT: D 237 GLU cc_start: 0.8635 (pp20) cc_final: 0.8366 (pp20) REVERT: F 350 LEU cc_start: 0.8990 (mm) cc_final: 0.8633 (tt) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1224 time to fit residues: 42.1772 Evaluate side-chains 176 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 109 optimal weight: 0.0050 chunk 126 optimal weight: 0.0030 chunk 162 optimal weight: 0.9990 chunk 104 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 136 optimal weight: 0.0270 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 overall best weight: 0.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1772 HIS B 202 GLN ** D 228 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.077166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.060011 restraints weight = 570225.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.064381 restraints weight = 229310.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.066163 restraints weight = 97892.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.066084 restraints weight = 70056.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.066783 restraints weight = 62833.093| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18114 Z= 0.135 Angle : 0.737 13.406 24561 Z= 0.362 Chirality : 0.043 0.275 2898 Planarity : 0.005 0.069 3087 Dihedral : 5.751 69.228 2409 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 0.40 % Allowed : 1.89 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.18), residues: 2193 helix: 0.79 (0.15), residues: 1311 sheet: -2.53 (0.54), residues: 72 loop : -3.94 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 232 TYR 0.015 0.001 TYR A1517 PHE 0.018 0.001 PHE A 829 TRP 0.035 0.002 TRP A1738 HIS 0.005 0.001 HIS A1762 Details of bonding type rmsd covalent geometry : bond 0.00283 (18109) covalent geometry : angle 0.73691 (24561) hydrogen bonds : bond 0.04203 ( 1016) hydrogen bonds : angle 4.73427 ( 2977) metal coordination : bond 0.00050 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.7961 (tp) cc_final: 0.7421 (pp) REVERT: A 11 GLU cc_start: 0.7982 (pt0) cc_final: 0.7534 (pm20) REVERT: A 29 LEU cc_start: 0.9288 (tt) cc_final: 0.9053 (pp) REVERT: A 64 VAL cc_start: 0.9230 (p) cc_final: 0.8990 (m) REVERT: A 121 CYS cc_start: 0.8430 (t) cc_final: 0.8228 (t) REVERT: A 187 MET cc_start: 0.8170 (ttt) cc_final: 0.7805 (ttt) REVERT: A 259 THR cc_start: 0.7255 (p) cc_final: 0.6305 (p) REVERT: A 363 MET cc_start: 0.7154 (mtt) cc_final: 0.5981 (ptm) REVERT: A 384 MET cc_start: 0.6713 (tpp) cc_final: 0.6475 (tpt) REVERT: A 435 MET cc_start: 0.8605 (mmm) cc_final: 0.8182 (tmm) REVERT: A 569 MET cc_start: 0.8038 (tpt) cc_final: 0.7790 (mmm) REVERT: A 670 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8695 (mm-40) REVERT: A 677 ILE cc_start: 0.8674 (tp) cc_final: 0.8368 (tp) REVERT: A 760 THR cc_start: 0.8579 (m) cc_final: 0.8290 (p) REVERT: A 767 MET cc_start: 0.8416 (ttp) cc_final: 0.7932 (tmm) REVERT: A 812 PHE cc_start: 0.8545 (t80) cc_final: 0.8314 (t80) REVERT: A 1165 ASP cc_start: 0.8570 (t0) cc_final: 0.8032 (m-30) REVERT: A 1447 GLN cc_start: 0.8689 (mm110) cc_final: 0.8090 (tm-30) REVERT: A 1520 MET cc_start: 0.7899 (tpp) cc_final: 0.7690 (tpp) REVERT: A 1607 MET cc_start: 0.7429 (mpp) cc_final: 0.7104 (mpp) REVERT: A 1815 MET cc_start: 0.8871 (pmm) cc_final: 0.8494 (pmm) REVERT: A 1973 LEU cc_start: 0.8382 (tt) cc_final: 0.7602 (mp) REVERT: A 2006 MET cc_start: 0.8074 (ttp) cc_final: 0.7837 (ttp) REVERT: A 2189 GLN cc_start: 0.8382 (tm-30) cc_final: 0.7559 (pm20) REVERT: C 236 LEU cc_start: 0.7856 (mt) cc_final: 0.7638 (mt) REVERT: C 242 ARG cc_start: 0.9225 (tpp80) cc_final: 0.8904 (tpt170) REVERT: C 270 MET cc_start: 0.8585 (mtm) cc_final: 0.8128 (pmm) REVERT: F 350 LEU cc_start: 0.8988 (mm) cc_final: 0.8704 (tt) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1196 time to fit residues: 52.4264 Evaluate side-chains 192 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 125 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 50 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 136 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 GLN A 892 ASN ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1143 ASN ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.075982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.059600 restraints weight = 565908.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.063530 restraints weight = 236019.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.064571 restraints weight = 109620.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.064975 restraints weight = 73046.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.065585 restraints weight = 62181.644| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18114 Z= 0.136 Angle : 0.731 12.678 24561 Z= 0.360 Chirality : 0.043 0.252 2898 Planarity : 0.005 0.053 3087 Dihedral : 5.649 69.538 2409 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 0.40 % Allowed : 1.94 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.18), residues: 2193 helix: 0.78 (0.14), residues: 1334 sheet: -2.39 (0.57), residues: 70 loop : -3.94 (0.19), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1647 TYR 0.018 0.001 TYR A2194 PHE 0.018 0.001 PHE A2052 TRP 0.033 0.002 TRP A1738 HIS 0.005 0.001 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00297 (18109) covalent geometry : angle 0.73074 (24561) hydrogen bonds : bond 0.04278 ( 1016) hydrogen bonds : angle 4.69049 ( 2977) metal coordination : bond 0.00122 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.7961 (tp) cc_final: 0.7337 (pp) REVERT: A 11 GLU cc_start: 0.7968 (pt0) cc_final: 0.7507 (pm20) REVERT: A 64 VAL cc_start: 0.9194 (p) cc_final: 0.8966 (m) REVERT: A 187 MET cc_start: 0.8182 (ttt) cc_final: 0.7883 (ttt) REVERT: A 240 MET cc_start: 0.8675 (ttt) cc_final: 0.8160 (tpp) REVERT: A 259 THR cc_start: 0.7313 (p) cc_final: 0.6353 (p) REVERT: A 384 MET cc_start: 0.6810 (tpp) cc_final: 0.6598 (tpt) REVERT: A 396 MET cc_start: 0.6495 (ppp) cc_final: 0.6293 (ppp) REVERT: A 435 MET cc_start: 0.8612 (mmm) cc_final: 0.8218 (tmm) REVERT: A 569 MET cc_start: 0.8040 (tpt) cc_final: 0.7802 (mmm) REVERT: A 670 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8715 (mm-40) REVERT: A 677 ILE cc_start: 0.8671 (tp) cc_final: 0.8367 (tp) REVERT: A 760 THR cc_start: 0.8571 (m) cc_final: 0.8256 (p) REVERT: A 767 MET cc_start: 0.8463 (ttp) cc_final: 0.8000 (tmm) REVERT: A 812 PHE cc_start: 0.8623 (t80) cc_final: 0.8393 (t80) REVERT: A 1447 GLN cc_start: 0.8706 (mm110) cc_final: 0.8089 (tm-30) REVERT: A 1607 MET cc_start: 0.7490 (mpp) cc_final: 0.7125 (mpp) REVERT: A 1613 LYS cc_start: 0.9237 (tttt) cc_final: 0.8908 (tptt) REVERT: A 1815 MET cc_start: 0.8925 (pmm) cc_final: 0.8493 (pmm) REVERT: A 1973 LEU cc_start: 0.8360 (tt) cc_final: 0.7587 (mp) REVERT: A 2006 MET cc_start: 0.8045 (ttp) cc_final: 0.7743 (ttp) REVERT: A 2189 GLN cc_start: 0.8479 (tm-30) cc_final: 0.7575 (pm20) REVERT: C 232 ARG cc_start: 0.6915 (tpm170) cc_final: 0.6439 (tmm-80) REVERT: C 242 ARG cc_start: 0.9232 (tpp80) cc_final: 0.8911 (tpt170) REVERT: C 270 MET cc_start: 0.8639 (mtm) cc_final: 0.8158 (pmm) REVERT: E 232 ARG cc_start: 0.7371 (mmm160) cc_final: 0.7133 (mmt-90) REVERT: F 350 LEU cc_start: 0.9007 (mm) cc_final: 0.8668 (tt) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.1220 time to fit residues: 46.9463 Evaluate side-chains 192 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 2 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 140 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 GLN A 403 HIS ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 ASN ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 HIS ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.072546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.056783 restraints weight = 539571.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.060558 restraints weight = 226334.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.061417 restraints weight = 107504.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.061839 restraints weight = 72057.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.062305 restraints weight = 63990.802| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 18114 Z= 0.218 Angle : 0.819 13.663 24561 Z= 0.412 Chirality : 0.047 0.234 2898 Planarity : 0.006 0.057 3087 Dihedral : 6.157 69.690 2409 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.40 % Favored : 87.55 % Rotamer: Outliers : 0.40 % Allowed : 1.39 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.18), residues: 2193 helix: 0.54 (0.14), residues: 1329 sheet: -2.75 (0.54), residues: 69 loop : -4.07 (0.18), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1899 TYR 0.022 0.002 TYR A 999 PHE 0.020 0.002 PHE A2052 TRP 0.047 0.003 TRP A 113 HIS 0.008 0.002 HIS A1804 Details of bonding type rmsd covalent geometry : bond 0.00475 (18109) covalent geometry : angle 0.81852 (24561) hydrogen bonds : bond 0.04903 ( 1016) hydrogen bonds : angle 5.02418 ( 2977) metal coordination : bond 0.00414 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8206 (tp) cc_final: 0.7458 (pp) REVERT: A 11 GLU cc_start: 0.7845 (pt0) cc_final: 0.7434 (pm20) REVERT: A 187 MET cc_start: 0.8483 (ttp) cc_final: 0.7855 (ttt) REVERT: A 240 MET cc_start: 0.8842 (ttt) cc_final: 0.7947 (tpp) REVERT: A 244 MET cc_start: 0.8846 (mtm) cc_final: 0.8619 (mtm) REVERT: A 384 MET cc_start: 0.6602 (tpp) cc_final: 0.6321 (tpt) REVERT: A 435 MET cc_start: 0.8654 (mmm) cc_final: 0.8305 (tmm) REVERT: A 569 MET cc_start: 0.8124 (tpt) cc_final: 0.7856 (mmm) REVERT: A 670 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8780 (mm-40) REVERT: A 812 PHE cc_start: 0.8866 (t80) cc_final: 0.8630 (t80) REVERT: A 1447 GLN cc_start: 0.8580 (mm110) cc_final: 0.8173 (tm-30) REVERT: A 1483 LYS cc_start: 0.6651 (pptt) cc_final: 0.6306 (pptt) REVERT: A 1607 MET cc_start: 0.7460 (mpp) cc_final: 0.7085 (mpp) REVERT: A 1815 MET cc_start: 0.8966 (pmm) cc_final: 0.8585 (pmm) REVERT: C 242 ARG cc_start: 0.9164 (tpp80) cc_final: 0.8893 (tpt170) REVERT: C 270 MET cc_start: 0.8764 (mtm) cc_final: 0.8110 (pmm) REVERT: F 350 LEU cc_start: 0.9018 (mm) cc_final: 0.8700 (tt) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1247 time to fit residues: 43.4116 Evaluate side-chains 170 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 49 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 146 optimal weight: 0.4980 chunk 144 optimal weight: 0.8980 chunk 199 optimal weight: 0.9980 chunk 112 optimal weight: 0.0770 chunk 214 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.075514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.058931 restraints weight = 524228.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.063497 restraints weight = 224072.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.064258 restraints weight = 101336.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.065276 restraints weight = 63910.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.065325 restraints weight = 53822.435| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18114 Z= 0.142 Angle : 0.775 13.803 24561 Z= 0.381 Chirality : 0.044 0.367 2898 Planarity : 0.006 0.158 3087 Dihedral : 5.845 69.199 2409 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 0.40 % Allowed : 0.65 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.18), residues: 2193 helix: 0.75 (0.15), residues: 1321 sheet: -2.65 (0.52), residues: 72 loop : -3.84 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 232 TYR 0.013 0.001 TYR A 838 PHE 0.021 0.001 PHE A2015 TRP 0.040 0.002 TRP A1738 HIS 0.007 0.001 HIS A1804 Details of bonding type rmsd covalent geometry : bond 0.00311 (18109) covalent geometry : angle 0.77451 (24561) hydrogen bonds : bond 0.04419 ( 1016) hydrogen bonds : angle 4.80843 ( 2977) metal coordination : bond 0.00090 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8015 (tp) cc_final: 0.7334 (pp) REVERT: A 11 GLU cc_start: 0.7882 (pt0) cc_final: 0.7492 (pm20) REVERT: A 187 MET cc_start: 0.8582 (ttp) cc_final: 0.8171 (ttt) REVERT: A 240 MET cc_start: 0.8684 (ttt) cc_final: 0.8108 (tpp) REVERT: A 244 MET cc_start: 0.8670 (mtm) cc_final: 0.8172 (mtp) REVERT: A 259 THR cc_start: 0.7231 (p) cc_final: 0.6440 (p) REVERT: A 363 MET cc_start: 0.7510 (mtt) cc_final: 0.6363 (ptm) REVERT: A 396 MET cc_start: 0.6521 (ppp) cc_final: 0.6251 (ppp) REVERT: A 435 MET cc_start: 0.8623 (mmm) cc_final: 0.8226 (tmm) REVERT: A 569 MET cc_start: 0.8061 (tpt) cc_final: 0.7827 (mmm) REVERT: A 670 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8684 (mm-40) REVERT: A 749 MET cc_start: 0.8707 (tpp) cc_final: 0.8304 (mmt) REVERT: A 760 THR cc_start: 0.8577 (m) cc_final: 0.8291 (p) REVERT: A 767 MET cc_start: 0.8532 (ttp) cc_final: 0.7934 (tmm) REVERT: A 812 PHE cc_start: 0.8662 (t80) cc_final: 0.8419 (t80) REVERT: A 1165 ASP cc_start: 0.8716 (t0) cc_final: 0.8469 (m-30) REVERT: A 1447 GLN cc_start: 0.8681 (mm110) cc_final: 0.8169 (tm-30) REVERT: A 1607 MET cc_start: 0.7367 (mpp) cc_final: 0.7010 (mpp) REVERT: A 1815 MET cc_start: 0.8937 (pmm) cc_final: 0.8564 (pmm) REVERT: A 1923 LEU cc_start: 0.8603 (pt) cc_final: 0.8188 (pp) REVERT: A 2148 LEU cc_start: 0.8726 (mt) cc_final: 0.7913 (pp) REVERT: A 2189 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7338 (pm20) REVERT: B 237 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8527 (mm-30) REVERT: C 236 LEU cc_start: 0.7825 (mt) cc_final: 0.7444 (mt) REVERT: C 242 ARG cc_start: 0.9156 (tpp80) cc_final: 0.8916 (tpt170) REVERT: C 270 MET cc_start: 0.8732 (mtm) cc_final: 0.8161 (pmm) REVERT: F 350 LEU cc_start: 0.8970 (mm) cc_final: 0.8655 (tt) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1299 time to fit residues: 48.1994 Evaluate side-chains 188 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 2 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 92 optimal weight: 0.0670 chunk 43 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 168 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 overall best weight: 1.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 ASN ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1622 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.074219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.057395 restraints weight = 617295.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.061755 restraints weight = 250491.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.063584 restraints weight = 104176.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.063559 restraints weight = 73065.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.064086 restraints weight = 63729.375| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 18114 Z= 0.160 Angle : 0.767 13.556 24561 Z= 0.382 Chirality : 0.044 0.240 2898 Planarity : 0.006 0.159 3087 Dihedral : 5.873 69.596 2409 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 0.40 % Allowed : 0.35 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.18), residues: 2193 helix: 0.73 (0.14), residues: 1323 sheet: -2.71 (0.52), residues: 72 loop : -3.88 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 232 TYR 0.021 0.002 TYR A2194 PHE 0.019 0.002 PHE A 562 TRP 0.036 0.002 TRP A1738 HIS 0.007 0.001 HIS A1804 Details of bonding type rmsd covalent geometry : bond 0.00358 (18109) covalent geometry : angle 0.76675 (24561) hydrogen bonds : bond 0.04506 ( 1016) hydrogen bonds : angle 4.84055 ( 2977) metal coordination : bond 0.00253 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2760.08 seconds wall clock time: 48 minutes 54.53 seconds (2934.53 seconds total)