Starting phenix.real_space_refine on Wed Mar 4 19:48:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mex_23806/03_2026/7mex_23806.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mex_23806/03_2026/7mex_23806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mex_23806/03_2026/7mex_23806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mex_23806/03_2026/7mex_23806.map" model { file = "/net/cci-nas-00/data/ceres_data/7mex_23806/03_2026/7mex_23806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mex_23806/03_2026/7mex_23806.cif" } resolution = 3.35 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= 0.003 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 7 6.06 5 S 83 5.16 5 C 10176 2.51 5 N 2686 2.21 5 O 2989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s 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: 15941 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1210 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 15, 'TRANS': 134} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain breaks: 1 Chain: "A" Number of atoms: 14087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1737, 14087 Classifications: {'peptide': 1737} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 61, 'TRANS': 1675} Chain breaks: 5 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 5, 'HIS:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' ZN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2866 SG CYS A 136 53.691 71.975 40.032 1.00 35.95 S ATOM 2891 SG CYS A 139 52.315 73.584 37.001 1.00 43.56 S ATOM 2757 SG CYS A 123 67.826 78.694 33.624 1.00 53.07 S ATOM 2951 SG CYS A 148 67.026 78.353 37.412 1.00 45.26 S ATOM 2975 SG CYS A 151 64.559 79.790 35.029 1.00 53.16 S ATOM 3163 SG CYS A 175 65.362 76.103 34.882 1.00 41.39 S ATOM 2975 SG CYS A 151 64.559 79.790 35.029 1.00 53.16 S ATOM 3177 SG CYS A 177 61.880 79.158 32.585 1.00 50.09 S ATOM 3271 SG CYS A 189 62.283 82.606 34.072 1.00 63.24 S ATOM 15078 SG CYS A1703 68.256 82.236 67.195 1.00 27.27 S ATOM 15099 SG CYS A1706 68.764 85.836 66.463 1.00 25.98 S ATOM 15247 SG CYS A1727 70.393 84.336 69.391 1.00 33.48 S ATOM 11769 SG CYS A1295 62.956 68.517 89.932 1.00 27.11 S ATOM 11988 SG CYS A1320 64.232 64.957 90.207 1.00 32.62 S ATOM 12009 SG CYS A1323 61.650 66.054 87.147 1.00 28.14 S ATOM 11169 SG CYS A1220 64.803 60.667 100.527 1.00 53.65 S ATOM 11188 SG CYS A1223 65.441 57.870 102.848 1.00 67.39 S ATOM 11839 SG CYS A1303 68.297 59.686 101.763 1.00 58.29 S Time building chain proxies: 3.45, per 1000 atoms: 0.22 Number of scatterers: 15941 At special positions: 0 Unit cell: (129.686, 132.875, 126.497, 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 7 29.99 S 83 16.00 O 2989 8.00 N 2686 7.00 C 10176 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 640.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 157 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 160 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 136 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 139 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 151 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 175 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 148 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 123 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" NE2 HIS A 118 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 151 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 177 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 189 " pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" NE2 HIS A1722 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1706 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1727 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1703 " pdb=" ZN A2005 " pdb="ZN ZN A2005 " - pdb=" ND1 HIS A1297 " pdb="ZN ZN A2005 " - pdb=" SG CYS A1295 " pdb="ZN ZN A2005 " - pdb=" SG CYS A1320 " pdb="ZN ZN A2005 " - pdb=" SG CYS A1323 " pdb=" ZN A2006 " pdb="ZN ZN A2006 " - pdb=" ND1 HIS A1300 " pdb="ZN ZN A2006 " - pdb=" SG CYS A1223 " pdb="ZN ZN A2006 " - pdb=" SG CYS A1303 " pdb="ZN ZN A2006 " - pdb=" SG CYS A1220 " pdb=" ZN A2007 " pdb="ZN ZN A2007 " - pdb=" NE2 HIS A1763 " pdb="ZN ZN A2007 " - pdb=" NE2 HIS A 161 " Number of angles added : 20 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3802 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 13 sheets defined 56.9% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'B' and resid 4 through 19 removed outlier: 3.600A pdb=" N GLU B 18 " --> pdb=" O LYS B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 113 removed outlier: 3.671A pdb=" N PHE B 113 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 133 Processing helix chain 'B' and resid 133 through 150 removed outlier: 3.543A pdb=" N GLU B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 21 Processing helix chain 'A' and resid 33 through 57 removed outlier: 3.735A pdb=" N ALA A 38 " --> pdb=" O PRO A 34 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 57 " --> pdb=" O TYR A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 61 Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.901A pdb=" N LEU A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 92 through 98 removed outlier: 4.227A pdb=" N ILE A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 216 through 240 removed outlier: 3.901A pdb=" N GLN A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 262 removed outlier: 4.506A pdb=" N LYS A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASP A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 276 removed outlier: 3.553A pdb=" N GLN A 270 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 334 Processing helix chain 'A' and resid 342 through 349 Processing helix chain 'A' and resid 361 through 369 removed outlier: 4.469A pdb=" N GLY A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLY A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 removed outlier: 4.420A pdb=" N ASN A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 403 removed outlier: 3.547A pdb=" N LEU A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 424 removed outlier: 3.822A pdb=" N THR A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 443 removed outlier: 3.943A pdb=" N VAL A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 447 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.686A pdb=" N THR A 480 " --> pdb=" O GLU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 509 Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 514 through 532 Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 535 through 546 removed outlier: 3.705A pdb=" N ILE A 546 " --> pdb=" O GLN A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 560 through 564 Processing helix chain 'A' and resid 565 through 573 Processing helix chain 'A' and resid 576 through 585 Processing helix chain 'A' and resid 587 through 601 removed outlier: 3.768A pdb=" N ILE A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 642 removed outlier: 3.744A pdb=" N ILE A 627 " --> pdb=" O LYS A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 650 Processing helix chain 'A' and resid 651 through 664 removed outlier: 3.928A pdb=" N LEU A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 710 removed outlier: 4.337A pdb=" N TYR A 689 " --> pdb=" O ASN A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 732 removed outlier: 3.712A pdb=" N PHE A 719 " --> pdb=" O ASP A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 773 removed outlier: 3.613A pdb=" N VAL A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 781 Processing helix chain 'A' and resid 788 through 807 removed outlier: 4.701A pdb=" N PHE A 794 " --> pdb=" O LYS A 790 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER A 795 " --> pdb=" O ILE A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 825 removed outlier: 4.104A pdb=" N LEU A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 846 Processing helix chain 'A' and resid 850 through 862 removed outlier: 3.889A pdb=" N ILE A 854 " --> pdb=" O ASP A 850 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 855 " --> pdb=" O ILE A 851 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 856 " --> pdb=" O PRO A 852 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP A 862 " --> pdb=" O ILE A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 869 Processing helix chain 'A' and resid 873 through 877 removed outlier: 3.657A pdb=" N THR A 877 " --> pdb=" O TYR A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 881 No H-bonds generated for 'chain 'A' and resid 879 through 881' Processing helix chain 'A' and resid 882 through 900 Processing helix chain 'A' and resid 909 through 927 Processing helix chain 'A' and resid 933 through 940 Processing helix chain 'A' and resid 941 through 945 Processing helix chain 'A' and resid 947 through 958 Processing helix chain 'A' and resid 977 through 983 removed outlier: 3.569A pdb=" N TYR A 980 " --> pdb=" O ALA A 977 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA A 981 " --> pdb=" O SER A 978 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 983 " --> pdb=" O TYR A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 991 Processing helix chain 'A' and resid 995 through 1007 Processing helix chain 'A' and resid 1028 through 1034 removed outlier: 3.582A pdb=" N LEU A1032 " --> pdb=" O LYS A1029 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN A1033 " --> pdb=" O ASP A1030 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A1034 " --> pdb=" O ALA A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1040 Processing helix chain 'A' and resid 1040 through 1058 Processing helix chain 'A' and resid 1062 through 1082 Processing helix chain 'A' and resid 1088 through 1093 Processing helix chain 'A' and resid 1094 through 1104 removed outlier: 4.081A pdb=" N LEU A1098 " --> pdb=" O PRO A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1129 removed outlier: 3.800A pdb=" N LYS A1128 " --> pdb=" O LYS A1124 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A1129 " --> pdb=" O MET A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1141 removed outlier: 4.036A pdb=" N SER A1136 " --> pdb=" O GLU A1132 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1153 removed outlier: 4.331A pdb=" N TYR A1145 " --> pdb=" O PHE A1141 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL A1146 " --> pdb=" O GLY A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1194 Processing helix chain 'A' and resid 1251 through 1256 removed outlier: 3.687A pdb=" N PHE A1255 " --> pdb=" O ASN A1251 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A1256 " --> pdb=" O PRO A1252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1251 through 1256' Processing helix chain 'A' and resid 1273 through 1284 removed outlier: 3.578A pdb=" N LEU A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A1284 " --> pdb=" O LEU A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1311 Processing helix chain 'A' and resid 1344 through 1351 Processing helix chain 'A' and resid 1354 through 1359 removed outlier: 3.559A pdb=" N LEU A1358 " --> pdb=" O SER A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1362 No H-bonds generated for 'chain 'A' and resid 1360 through 1362' Processing helix chain 'A' and resid 1366 through 1384 Processing helix chain 'A' and resid 1388 through 1394 Processing helix chain 'A' and resid 1398 through 1400 No H-bonds generated for 'chain 'A' and resid 1398 through 1400' Processing helix chain 'A' and resid 1401 through 1421 removed outlier: 3.959A pdb=" N ILE A1405 " --> pdb=" O ASP A1401 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1424 No H-bonds generated for 'chain 'A' and resid 1422 through 1424' Processing helix chain 'A' and resid 1435 through 1456 Processing helix chain 'A' and resid 1477 through 1489 Processing helix chain 'A' and resid 1493 through 1514 removed outlier: 3.513A pdb=" N THR A1497 " --> pdb=" O SER A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1534 Processing helix chain 'A' and resid 1540 through 1551 Processing helix chain 'A' and resid 1561 through 1594 removed outlier: 3.562A pdb=" N LEU A1577 " --> pdb=" O LEU A1573 " (cutoff:3.500A) Proline residue: A1578 - end of helix Processing helix chain 'A' and resid 1609 through 1614 Processing helix chain 'A' and resid 1619 through 1630 Processing helix chain 'A' and resid 1634 through 1641 removed outlier: 3.735A pdb=" N THR A1641 " --> pdb=" O ASP A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1648 through 1652 Processing helix chain 'A' and resid 1672 through 1677 Processing helix chain 'A' and resid 1693 through 1697 removed outlier: 3.590A pdb=" N ASN A1696 " --> pdb=" O ASN A1693 " (cutoff:3.500A) Processing helix chain 'A' and resid 1715 through 1720 Processing helix chain 'A' and resid 1720 through 1725 Processing helix chain 'A' and resid 1767 through 1772 removed outlier: 4.014A pdb=" N MET A1771 " --> pdb=" O GLY A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1773 through 1775 No H-bonds generated for 'chain 'A' and resid 1773 through 1775' Processing helix chain 'A' and resid 1780 through 1793 removed outlier: 3.693A pdb=" N ASN A1793 " --> pdb=" O ARG A1789 " (cutoff:3.500A) Processing helix chain 'A' and resid 1795 through 1805 Processing helix chain 'A' and resid 1805 through 1812 removed outlier: 3.553A pdb=" N THR A1811 " --> pdb=" O GLU A1807 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 12 through 16 removed outlier: 8.955A pdb=" N LEU C 67 " --> pdb=" O GLN C 2 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE C 4 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU C 69 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS C 6 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N LEU C 71 " --> pdb=" O LYS C 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 24 through 28 removed outlier: 3.589A pdb=" N LYS B 71 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 136 Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 360 removed outlier: 7.102A pdb=" N VAL A 313 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N CYS A 357 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N TYR A 311 " --> pdb=" O CYS A 357 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLN A 359 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU A 309 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER A 377 " --> pdb=" O TYR A 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 605 through 607 removed outlier: 3.534A pdb=" N VAL A 610 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 737 through 738 Processing sheet with id=AA7, first strand: chain 'A' and resid 931 through 932 Processing sheet with id=AA8, first strand: chain 'A' and resid 1232 through 1233 Processing sheet with id=AA9, first strand: chain 'A' and resid 1290 through 1294 removed outlier: 3.548A pdb=" N ASP A1239 " --> pdb=" O VAL A1291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1318 through 1319 Processing sheet with id=AB2, first strand: chain 'A' and resid 1603 through 1604 Processing sheet with id=AB3, first strand: chain 'A' and resid 1709 through 1711 removed outlier: 3.501A pdb=" N GLU A1741 " --> pdb=" O MET A1736 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1759 through 1761 755 hydrogen bonds defined for protein. 2166 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: 3.24 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4476 1.33 - 1.46: 2868 1.46 - 1.58: 8814 1.58 - 1.70: 0 1.70 - 1.82: 121 Bond restraints: 16279 Sorted by residual: bond pdb=" N LYS A1425 " pdb=" CA LYS A1425 " ideal model delta sigma weight residual 1.462 1.492 -0.030 7.70e-03 1.69e+04 1.49e+01 bond pdb=" N VAL A1766 " pdb=" CA VAL A1766 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.19e+01 bond pdb=" N VAL A1109 " pdb=" CA VAL A1109 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.21e-02 6.83e+03 8.32e+00 bond pdb=" N ILE A1429 " pdb=" CA ILE A1429 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.91e+00 bond pdb=" N LYS A1106 " pdb=" CA LYS A1106 " ideal model delta sigma weight residual 1.454 1.490 -0.037 1.34e-02 5.57e+03 7.61e+00 ... (remaining 16274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 21694 1.80 - 3.60: 293 3.60 - 5.41: 31 5.41 - 7.21: 4 7.21 - 9.01: 4 Bond angle restraints: 22026 Sorted by residual: angle pdb=" C LYS A1083 " pdb=" N ASP A1084 " pdb=" CA ASP A1084 " ideal model delta sigma weight residual 122.46 127.22 -4.76 1.41e+00 5.03e-01 1.14e+01 angle pdb=" CA VAL A1766 " pdb=" C VAL A1766 " pdb=" O VAL A1766 " ideal model delta sigma weight residual 121.67 118.33 3.34 1.05e+00 9.07e-01 1.01e+01 angle pdb=" CA PRO A1426 " pdb=" C PRO A1426 " pdb=" O PRO A1426 " ideal model delta sigma weight residual 123.16 118.50 4.66 1.49e+00 4.50e-01 9.77e+00 angle pdb=" CB MET B 34 " pdb=" CG MET B 34 " pdb=" SD MET B 34 " ideal model delta sigma weight residual 112.70 121.71 -9.01 3.00e+00 1.11e-01 9.02e+00 angle pdb=" CA SER A1111 " pdb=" C SER A1111 " pdb=" O SER A1111 " ideal model delta sigma weight residual 121.45 118.27 3.18 1.07e+00 8.73e-01 8.83e+00 ... (remaining 22021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 8889 17.82 - 35.65: 805 35.65 - 53.47: 152 53.47 - 71.29: 18 71.29 - 89.11: 16 Dihedral angle restraints: 9880 sinusoidal: 4043 harmonic: 5837 Sorted by residual: dihedral pdb=" CA GLN A1748 " pdb=" C GLN A1748 " pdb=" N PRO A1749 " pdb=" CA PRO A1749 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA ASP A 793 " pdb=" CB ASP A 793 " pdb=" CG ASP A 793 " pdb=" OD1 ASP A 793 " ideal model delta sinusoidal sigma weight residual -30.00 -89.58 59.58 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ILE A 740 " pdb=" C ILE A 740 " pdb=" N TYR A 741 " pdb=" CA TYR A 741 " ideal model delta harmonic sigma weight residual 180.00 163.03 16.97 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 9877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1730 0.037 - 0.074: 548 0.074 - 0.111: 161 0.111 - 0.148: 26 0.148 - 0.186: 3 Chirality restraints: 2468 Sorted by residual: chirality pdb=" CB ILE A1429 " pdb=" CA ILE A1429 " pdb=" CG1 ILE A1429 " pdb=" CG2 ILE A1429 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CA ILE A1429 " pdb=" N ILE A1429 " pdb=" C ILE A1429 " pdb=" CB ILE A1429 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.26e-01 chirality pdb=" CB ILE A1681 " pdb=" CA ILE A1681 " pdb=" CG1 ILE A1681 " pdb=" CG2 ILE A1681 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.45e-01 ... (remaining 2465 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 851 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO A 852 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 852 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 852 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 46 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO B 47 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 47 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 47 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 102 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO A 103 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " -0.023 5.00e-02 4.00e+02 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 150 2.61 - 3.18: 14167 3.18 - 3.75: 24699 3.75 - 4.33: 34803 4.33 - 4.90: 57302 Nonbonded interactions: 131121 Sorted by model distance: nonbonded pdb=" OD1 ASP A1775 " pdb="ZN ZN A2007 " model vdw 2.037 2.230 nonbonded pdb=" OH TYR A 933 " pdb=" OD1 ASP A 952 " model vdw 2.168 3.040 nonbonded pdb=" OH TYR A 824 " pdb=" OD2 ASP A 836 " model vdw 2.180 3.040 nonbonded pdb=" O ILE A1665 " pdb=" OH TYR A1784 " model vdw 2.192 3.040 nonbonded pdb=" OH TYR A 895 " pdb=" OD2 ASP A 984 " model vdw 2.209 3.040 ... (remaining 131116 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 17.470 Find NCS groups from input model: 0.080 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 0.685 16306 Z= 0.296 Angle : 0.530 9.009 22046 Z= 0.286 Chirality : 0.040 0.186 2468 Planarity : 0.003 0.044 2818 Dihedral : 14.137 89.113 6078 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.06 % Allowed : 0.28 % Favored : 99.67 % 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: 0.70 (0.19), residues: 1948 helix: 1.30 (0.17), residues: 971 sheet: -0.49 (0.49), residues: 115 loop : -0.29 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 755 TYR 0.016 0.001 TYR A 49 PHE 0.014 0.001 PHE A 758 TRP 0.011 0.001 TRP B 149 HIS 0.003 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00275 (16279) covalent geometry : angle 0.51888 (22026) hydrogen bonds : bond 0.15666 ( 755) hydrogen bonds : angle 5.84085 ( 2166) metal coordination : bond 0.17188 ( 26) metal coordination : angle 3.59236 ( 20) Misc. bond : bond 0.13221 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.1692 time to fit residues: 28.6195 Evaluate side-chains 81 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 HIS A 876 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.045910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.033746 restraints weight = 79490.166| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 4.01 r_work: 0.2546 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 16306 Z= 0.328 Angle : 0.676 11.036 22046 Z= 0.343 Chirality : 0.045 0.147 2468 Planarity : 0.004 0.043 2818 Dihedral : 4.289 27.924 2126 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.17 % Allowed : 6.01 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.85 (0.19), residues: 1948 helix: 1.39 (0.17), residues: 992 sheet: -0.42 (0.48), residues: 114 loop : -0.20 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1768 TYR 0.015 0.002 TYR A1784 PHE 0.014 0.002 PHE A 414 TRP 0.020 0.002 TRP A1259 HIS 0.006 0.002 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00737 (16279) covalent geometry : angle 0.65967 (22026) hydrogen bonds : bond 0.04287 ( 755) hydrogen bonds : angle 4.90411 ( 2166) metal coordination : bond 0.02153 ( 26) metal coordination : angle 4.90351 ( 20) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8365 (tm-30) REVERT: C 63 LYS cc_start: 0.9491 (mmtm) cc_final: 0.9131 (mppt) REVERT: A 1347 MET cc_start: 0.8821 (tmm) cc_final: 0.8617 (tmm) REVERT: A 1804 MET cc_start: 0.9311 (mtp) cc_final: 0.8858 (mtp) outliers start: 3 outliers final: 1 residues processed: 80 average time/residue: 0.1451 time to fit residues: 17.5083 Evaluate side-chains 68 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 131 optimal weight: 20.0000 chunk 187 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 0.0870 chunk 53 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.047230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.035157 restraints weight = 78392.180| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 4.02 r_work: 0.2600 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16306 Z= 0.121 Angle : 0.521 10.530 22046 Z= 0.264 Chirality : 0.040 0.142 2468 Planarity : 0.004 0.052 2818 Dihedral : 4.063 28.052 2126 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.22 % Allowed : 7.68 % Favored : 92.09 % 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: 1.09 (0.20), residues: 1948 helix: 1.59 (0.17), residues: 1002 sheet: -0.12 (0.50), residues: 112 loop : -0.15 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1169 TYR 0.009 0.001 TYR A 49 PHE 0.012 0.001 PHE C 45 TRP 0.012 0.001 TRP A 594 HIS 0.003 0.001 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00277 (16279) covalent geometry : angle 0.50795 (22026) hydrogen bonds : bond 0.03654 ( 755) hydrogen bonds : angle 4.37425 ( 2166) metal coordination : bond 0.00840 ( 26) metal coordination : angle 3.91954 ( 20) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7362 (ttp) cc_final: 0.6986 (mtp) REVERT: C 16 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8248 (tm-30) REVERT: C 21 ASP cc_start: 0.8991 (m-30) cc_final: 0.8773 (m-30) REVERT: C 34 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8316 (tm-30) REVERT: C 60 ASN cc_start: 0.9309 (m-40) cc_final: 0.8919 (p0) REVERT: B 142 LYS cc_start: 0.9354 (mmmm) cc_final: 0.9119 (mmtm) REVERT: A 40 MET cc_start: 0.9220 (tmm) cc_final: 0.8908 (tmm) REVERT: A 354 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7827 (tmm) REVERT: A 1347 MET cc_start: 0.8793 (tmm) cc_final: 0.8540 (tmm) REVERT: A 1380 MET cc_start: 0.9345 (tmm) cc_final: 0.9143 (tmm) REVERT: A 1804 MET cc_start: 0.9183 (mtp) cc_final: 0.8674 (mtp) outliers start: 4 outliers final: 1 residues processed: 86 average time/residue: 0.1277 time to fit residues: 17.1447 Evaluate side-chains 71 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain A residue 354 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1745 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 = 0.3170 r_free = 0.3170 target = 0.046747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.034639 restraints weight = 78760.958| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 4.03 r_work: 0.2587 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16306 Z= 0.146 Angle : 0.512 9.352 22046 Z= 0.258 Chirality : 0.040 0.145 2468 Planarity : 0.003 0.055 2818 Dihedral : 3.945 27.995 2126 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.50 % Allowed : 9.41 % Favored : 90.09 % 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: 1.21 (0.20), residues: 1948 helix: 1.73 (0.17), residues: 996 sheet: 0.01 (0.51), residues: 112 loop : -0.15 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 74 TYR 0.008 0.001 TYR A1565 PHE 0.013 0.001 PHE C 45 TRP 0.012 0.001 TRP A1259 HIS 0.003 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00338 (16279) covalent geometry : angle 0.49806 (22026) hydrogen bonds : bond 0.03387 ( 755) hydrogen bonds : angle 4.18974 ( 2166) metal coordination : bond 0.01012 ( 26) metal coordination : angle 3.99532 ( 20) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 16 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8183 (tm-30) REVERT: C 21 ASP cc_start: 0.8955 (m-30) cc_final: 0.8734 (m-30) REVERT: C 34 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8430 (tm-30) REVERT: A 354 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7851 (tmm) REVERT: A 900 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7596 (tm-30) REVERT: A 1347 MET cc_start: 0.8810 (tmm) cc_final: 0.8571 (tmm) REVERT: A 1804 MET cc_start: 0.9171 (mtp) cc_final: 0.8649 (mtm) outliers start: 9 outliers final: 2 residues processed: 82 average time/residue: 0.1293 time to fit residues: 16.8599 Evaluate side-chains 74 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain A residue 354 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 104 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 160 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 389 GLN ** A1745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.044249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.032193 restraints weight = 80574.280| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 3.97 r_work: 0.2501 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 16306 Z= 0.394 Angle : 0.717 11.794 22046 Z= 0.357 Chirality : 0.045 0.146 2468 Planarity : 0.004 0.044 2818 Dihedral : 4.440 28.120 2126 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.45 % Allowed : 11.08 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.81 (0.19), residues: 1948 helix: 1.46 (0.16), residues: 998 sheet: -0.35 (0.50), residues: 114 loop : -0.40 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 74 TYR 0.015 0.002 TYR A 692 PHE 0.019 0.002 PHE A 414 TRP 0.029 0.002 TRP A1259 HIS 0.007 0.002 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00877 (16279) covalent geometry : angle 0.69703 (22026) hydrogen bonds : bond 0.04071 ( 755) hydrogen bonds : angle 4.68525 ( 2166) metal coordination : bond 0.02573 ( 26) metal coordination : angle 5.56783 ( 20) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8576 (tm-30) REVERT: B 34 MET cc_start: 0.9574 (mmm) cc_final: 0.8684 (mmm) REVERT: A 1347 MET cc_start: 0.8998 (tmm) cc_final: 0.8738 (tmm) REVERT: A 1804 MET cc_start: 0.9155 (mtp) cc_final: 0.8689 (mtp) outliers start: 8 outliers final: 3 residues processed: 71 average time/residue: 0.1305 time to fit residues: 14.6562 Evaluate side-chains 67 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain A residue 354 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 140 optimal weight: 0.0050 chunk 154 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1745 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 = 0.3141 r_free = 0.3141 target = 0.045645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.033624 restraints weight = 78507.048| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 3.99 r_work: 0.2553 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16306 Z= 0.158 Angle : 0.539 11.279 22046 Z= 0.269 Chirality : 0.041 0.144 2468 Planarity : 0.003 0.046 2818 Dihedral : 4.157 28.310 2126 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.89 % Allowed : 11.41 % Favored : 87.69 % 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: 1.18 (0.20), residues: 1948 helix: 1.79 (0.17), residues: 998 sheet: -0.16 (0.52), residues: 112 loop : -0.26 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 74 TYR 0.010 0.001 TYR A1656 PHE 0.011 0.001 PHE A1043 TRP 0.013 0.001 TRP A1259 HIS 0.004 0.001 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00364 (16279) covalent geometry : angle 0.52353 (22026) hydrogen bonds : bond 0.03435 ( 755) hydrogen bonds : angle 4.22713 ( 2166) metal coordination : bond 0.01193 ( 26) metal coordination : angle 4.24524 ( 20) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8434 (tm-30) REVERT: B 71 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8701 (ptmm) REVERT: A 354 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7520 (tmm) REVERT: A 1347 MET cc_start: 0.8885 (tmm) cc_final: 0.8673 (tmm) REVERT: A 1804 MET cc_start: 0.9122 (mtp) cc_final: 0.8623 (mtm) outliers start: 16 outliers final: 7 residues processed: 83 average time/residue: 0.1308 time to fit residues: 16.7916 Evaluate side-chains 70 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1771 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 178 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 132 optimal weight: 0.1980 chunk 134 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1745 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 = 0.3151 r_free = 0.3151 target = 0.045929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.033899 restraints weight = 77959.668| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 4.00 r_work: 0.2568 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16306 Z= 0.137 Angle : 0.529 11.552 22046 Z= 0.263 Chirality : 0.040 0.142 2468 Planarity : 0.003 0.054 2818 Dihedral : 3.992 28.037 2126 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.61 % Allowed : 12.03 % Favored : 87.36 % 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: 1.31 (0.20), residues: 1948 helix: 1.88 (0.17), residues: 999 sheet: -0.04 (0.52), residues: 112 loop : -0.19 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 346 TYR 0.009 0.001 TYR A 895 PHE 0.010 0.001 PHE A1043 TRP 0.011 0.001 TRP A 594 HIS 0.004 0.001 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00318 (16279) covalent geometry : angle 0.51507 (22026) hydrogen bonds : bond 0.03270 ( 755) hydrogen bonds : angle 4.11069 ( 2166) metal coordination : bond 0.01015 ( 26) metal coordination : angle 4.08167 ( 20) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8406 (tm-30) REVERT: A 354 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7513 (tmm) REVERT: A 877 THR cc_start: 0.9560 (OUTLIER) cc_final: 0.9314 (p) REVERT: A 1347 MET cc_start: 0.8843 (tmm) cc_final: 0.8619 (tmm) REVERT: A 1804 MET cc_start: 0.9144 (mtp) cc_final: 0.8638 (mtm) outliers start: 11 outliers final: 6 residues processed: 75 average time/residue: 0.1186 time to fit residues: 14.5444 Evaluate side-chains 72 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1698 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 68 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 162 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 182 optimal weight: 0.6980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1745 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 = 0.3141 r_free = 0.3141 target = 0.045564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.033556 restraints weight = 78833.125| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 4.00 r_work: 0.2553 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16306 Z= 0.176 Angle : 0.550 11.451 22046 Z= 0.272 Chirality : 0.040 0.137 2468 Planarity : 0.004 0.056 2818 Dihedral : 3.978 27.825 2126 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.84 % Allowed : 12.08 % Favored : 87.08 % 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: 1.35 (0.20), residues: 1948 helix: 1.91 (0.17), residues: 998 sheet: 0.02 (0.52), residues: 112 loop : -0.18 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 346 TYR 0.009 0.001 TYR A1565 PHE 0.009 0.001 PHE A 414 TRP 0.014 0.001 TRP A1259 HIS 0.003 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00404 (16279) covalent geometry : angle 0.53468 (22026) hydrogen bonds : bond 0.03309 ( 755) hydrogen bonds : angle 4.13842 ( 2166) metal coordination : bond 0.01252 ( 26) metal coordination : angle 4.25045 ( 20) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8404 (tm-30) REVERT: A 354 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7595 (tmm) REVERT: A 1347 MET cc_start: 0.8842 (tmm) cc_final: 0.8610 (tmm) REVERT: A 1804 MET cc_start: 0.9132 (mtp) cc_final: 0.8653 (mtm) outliers start: 15 outliers final: 7 residues processed: 79 average time/residue: 0.1141 time to fit residues: 14.4248 Evaluate side-chains 74 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1698 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 90 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 173 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 123 optimal weight: 0.0270 chunk 133 optimal weight: 20.0000 overall best weight: 2.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1745 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 = 0.3151 r_free = 0.3151 target = 0.045871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.033877 restraints weight = 78046.562| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.99 r_work: 0.2566 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16306 Z= 0.141 Angle : 0.536 11.633 22046 Z= 0.263 Chirality : 0.040 0.139 2468 Planarity : 0.003 0.055 2818 Dihedral : 3.908 27.687 2126 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.45 % Allowed : 12.58 % Favored : 86.97 % 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: 1.40 (0.20), residues: 1948 helix: 1.95 (0.17), residues: 998 sheet: 0.05 (0.53), residues: 112 loop : -0.15 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 346 TYR 0.008 0.001 TYR A 895 PHE 0.009 0.001 PHE A1043 TRP 0.011 0.001 TRP A1259 HIS 0.003 0.001 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00325 (16279) covalent geometry : angle 0.52255 (22026) hydrogen bonds : bond 0.03203 ( 755) hydrogen bonds : angle 4.06080 ( 2166) metal coordination : bond 0.01044 ( 26) metal coordination : angle 4.03147 ( 20) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7611 (mtp) cc_final: 0.7207 (mtt) REVERT: C 34 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8434 (tm-30) REVERT: C 41 GLN cc_start: 0.8702 (mt0) cc_final: 0.8481 (mt0) REVERT: C 52 ASP cc_start: 0.9030 (m-30) cc_final: 0.8691 (m-30) REVERT: A 354 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7570 (tmm) REVERT: A 1347 MET cc_start: 0.8802 (tmm) cc_final: 0.8583 (tmm) REVERT: A 1804 MET cc_start: 0.9131 (mtp) cc_final: 0.8637 (mtp) outliers start: 8 outliers final: 7 residues processed: 72 average time/residue: 0.1261 time to fit residues: 14.6033 Evaluate side-chains 75 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1698 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 16 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 135 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 183 optimal weight: 20.0000 chunk 142 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1745 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 = 0.3149 r_free = 0.3149 target = 0.045810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.033798 restraints weight = 78686.631| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 4.02 r_work: 0.2567 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16306 Z= 0.146 Angle : 0.545 11.948 22046 Z= 0.267 Chirality : 0.040 0.137 2468 Planarity : 0.003 0.055 2818 Dihedral : 3.886 27.636 2126 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.45 % Allowed : 12.75 % Favored : 86.80 % 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: 1.42 (0.20), residues: 1948 helix: 1.96 (0.17), residues: 998 sheet: 0.07 (0.53), residues: 112 loop : -0.12 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 346 TYR 0.008 0.001 TYR A 895 PHE 0.009 0.001 PHE A1043 TRP 0.011 0.001 TRP A1259 HIS 0.003 0.001 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00339 (16279) covalent geometry : angle 0.53184 (22026) hydrogen bonds : bond 0.03176 ( 755) hydrogen bonds : angle 4.05430 ( 2166) metal coordination : bond 0.01061 ( 26) metal coordination : angle 4.03199 ( 20) Misc. bond : bond 0.00011 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7591 (mtp) cc_final: 0.7302 (mtt) REVERT: C 34 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8431 (tm-30) REVERT: A 1347 MET cc_start: 0.8812 (tmm) cc_final: 0.8607 (tmm) REVERT: A 1804 MET cc_start: 0.9137 (mtp) cc_final: 0.8644 (mtp) outliers start: 8 outliers final: 8 residues processed: 73 average time/residue: 0.1079 time to fit residues: 12.9474 Evaluate side-chains 77 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1698 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 157 optimal weight: 0.1980 chunk 81 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 28 optimal weight: 0.0370 chunk 121 optimal weight: 5.9990 chunk 69 optimal weight: 0.0770 overall best weight: 1.4620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN ** A1745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.046292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.034298 restraints weight = 77809.850| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 4.01 r_work: 0.2587 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16306 Z= 0.114 Angle : 0.530 12.188 22046 Z= 0.259 Chirality : 0.040 0.139 2468 Planarity : 0.003 0.054 2818 Dihedral : 3.795 27.523 2126 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.45 % Allowed : 12.75 % Favored : 86.80 % 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: 1.47 (0.20), residues: 1948 helix: 2.01 (0.17), residues: 992 sheet: 0.13 (0.54), residues: 112 loop : -0.10 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 346 TYR 0.008 0.001 TYR A 895 PHE 0.010 0.001 PHE A1043 TRP 0.011 0.001 TRP A 594 HIS 0.003 0.001 HIS A1745 Details of bonding type rmsd covalent geometry : bond 0.00265 (16279) covalent geometry : angle 0.51790 (22026) hydrogen bonds : bond 0.03035 ( 755) hydrogen bonds : angle 3.97047 ( 2166) metal coordination : bond 0.00877 ( 26) metal coordination : angle 3.79872 ( 20) Misc. bond : bond 0.00003 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3101.53 seconds wall clock time: 54 minutes 18.99 seconds (3258.99 seconds total)