Starting phenix.real_space_refine on Fri Feb 16 17:14:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mex_23806/02_2024/7mex_23806.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mex_23806/02_2024/7mex_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mex_23806/02_2024/7mex_23806.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mex_23806/02_2024/7mex_23806.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mex_23806/02_2024/7mex_23806.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mex_23806/02_2024/7mex_23806.pdb" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Residue "C GLU 24": "OE1" <-> "OE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B ASP 132": "OD1" <-> "OD2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 916": "OD1" <-> "OD2" Residue "A GLU 996": "OE1" <-> "OE2" Residue "A TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1728": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15941 Number of models: 1 Model: "" Number of chains: 4 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: 14094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1744, 14094 Unusual residues: {' ZN': 7} Classifications: {'peptide': 1737, 'undetermined': 7} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 61, 'TRANS': 1675, None: 7} Not linked: pdbres="ILE A1812 " pdbres=" ZN A2001 " Not linked: pdbres=" ZN A2001 " pdbres=" ZN A2002 " Not linked: pdbres=" ZN A2002 " pdbres=" ZN A2003 " Not linked: pdbres=" ZN A2003 " pdbres=" ZN A2004 " Not linked: pdbres=" ZN A2004 " pdbres=" ZN A2005 " ... (remaining 2 not shown) 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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 5, 'ASP:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 66 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: 8.40, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.93 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 1.99 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: 6.30 Time building geometry restraints manager: 6.44 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: 99.21 - 106.18: 385 106.18 - 113.15: 8813 113.15 - 120.12: 5775 120.12 - 127.08: 6882 127.08 - 134.05: 171 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: 1.56 - 2.23: 8 2.23 - 2.90: 6110 2.90 - 3.56: 23334 3.56 - 4.23: 36995 4.23 - 4.90: 64678 Nonbonded interactions: 131125 Sorted by model distance: nonbonded pdb=" C CYS C 76 " pdb=" NZ LYS D 17 " model vdw 1.562 3.350 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 2.440 nonbonded pdb=" OH TYR A 824 " pdb=" OD2 ASP A 836 " model vdw 2.180 2.440 nonbonded pdb=" O ILE A1665 " pdb=" OH TYR A1784 " model vdw 2.192 2.440 ... (remaining 131120 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.950 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 46.370 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.610 ------------------------------------------------------------------------------- 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 : 0.003 0.038 16279 Z= 0.176 Angle : 0.519 9.009 22026 Z= 0.285 Chirality : 0.040 0.186 2468 Planarity : 0.003 0.044 2818 Dihedral : 14.137 89.113 6078 Min Nonbonded Distance : 1.562 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (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 TRP 0.011 0.001 TRP B 149 HIS 0.003 0.001 HIS A 150 PHE 0.014 0.001 PHE A 758 TYR 0.016 0.001 TYR A 49 ARG 0.004 0.000 ARG A 755 *********************** 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 fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.735 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: 0.3739 time to fit residues: 63.5241 Evaluate side-chains 81 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 177 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 876 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16279 Z= 0.343 Angle : 0.583 9.631 22026 Z= 0.300 Chirality : 0.042 0.152 2468 Planarity : 0.004 0.043 2818 Dihedral : 4.101 26.854 2126 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.11 % Allowed : 6.12 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.20), residues: 1948 helix: 1.51 (0.17), residues: 998 sheet: -0.18 (0.49), residues: 112 loop : -0.19 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1259 HIS 0.006 0.001 HIS A 161 PHE 0.015 0.001 PHE B 72 TYR 0.013 0.001 TYR A1784 ARG 0.007 0.001 ARG A1768 *********************** 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 79 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 79 average time/residue: 0.3377 time to fit residues: 40.3358 Evaluate side-chains 69 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 1.998 ------------------------------------------------------------------------------- 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: 196 random chunks: chunk 98 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 121 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16279 Z= 0.373 Angle : 0.578 10.357 22026 Z= 0.298 Chirality : 0.042 0.136 2468 Planarity : 0.004 0.050 2818 Dihedral : 4.209 27.669 2126 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.50 % Allowed : 9.08 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.20), residues: 1948 helix: 1.64 (0.17), residues: 996 sheet: -0.32 (0.50), residues: 112 loop : -0.31 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1259 HIS 0.006 0.001 HIS A 472 PHE 0.012 0.001 PHE A1505 TYR 0.011 0.001 TYR A1784 ARG 0.011 0.001 ARG A1169 *********************** 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 84 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 82 average time/residue: 0.2837 time to fit residues: 36.9776 Evaluate side-chains 68 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 2.070 ------------------------------------------------------------------------------- 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 108 ASP Chi-restraints excluded: chain A residue 354 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 85 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 189 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 169 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16279 Z= 0.244 Angle : 0.528 11.074 22026 Z= 0.268 Chirality : 0.040 0.135 2468 Planarity : 0.003 0.045 2818 Dihedral : 4.095 27.797 2126 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.50 % Allowed : 10.63 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 1948 helix: 1.78 (0.17), residues: 998 sheet: -0.33 (0.50), residues: 112 loop : -0.27 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1259 HIS 0.004 0.001 HIS B 133 PHE 0.009 0.001 PHE A1043 TYR 0.010 0.001 TYR A1565 ARG 0.004 0.000 ARG C 74 *********************** 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 80 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7436 (tmm) outliers start: 9 outliers final: 3 residues processed: 77 average time/residue: 0.2781 time to fit residues: 34.3126 Evaluate side-chains 70 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 1.883 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 575 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 141 optimal weight: 0.0370 chunk 78 optimal weight: 0.7980 chunk 161 optimal weight: 0.0770 chunk 130 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16279 Z= 0.136 Angle : 0.483 12.703 22026 Z= 0.244 Chirality : 0.039 0.143 2468 Planarity : 0.003 0.047 2818 Dihedral : 3.863 27.489 2126 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.78 % Allowed : 10.86 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.20), residues: 1948 helix: 1.95 (0.17), residues: 996 sheet: -0.26 (0.51), residues: 112 loop : -0.16 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 594 HIS 0.003 0.001 HIS A1745 PHE 0.010 0.001 PHE A1043 TYR 0.008 0.001 TYR A 895 ARG 0.004 0.000 ARG C 74 *********************** 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 93 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 89 average time/residue: 0.2776 time to fit residues: 39.8188 Evaluate side-chains 71 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 575 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.4980 chunk 170 optimal weight: 8.9990 chunk 37 optimal weight: 0.0470 chunk 111 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 189 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16279 Z= 0.148 Angle : 0.494 12.671 22026 Z= 0.246 Chirality : 0.039 0.167 2468 Planarity : 0.003 0.046 2818 Dihedral : 3.762 27.262 2126 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.45 % Allowed : 12.03 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.20), residues: 1948 helix: 2.01 (0.17), residues: 995 sheet: -0.29 (0.51), residues: 112 loop : -0.10 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 594 HIS 0.002 0.000 HIS A1745 PHE 0.011 0.001 PHE C 45 TYR 0.012 0.001 TYR A1656 ARG 0.005 0.000 ARG A 37 *********************** 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 84 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1771 MET cc_start: 0.6819 (tpt) cc_final: 0.6595 (tpt) outliers start: 8 outliers final: 5 residues processed: 82 average time/residue: 0.2919 time to fit residues: 38.2631 Evaluate side-chains 75 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 1.807 ------------------------------------------------------------------------------- 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 575 THR Chi-restraints excluded: chain A residue 1151 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 108 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 188 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16279 Z= 0.141 Angle : 0.485 11.784 22026 Z= 0.242 Chirality : 0.039 0.168 2468 Planarity : 0.003 0.046 2818 Dihedral : 3.693 27.119 2126 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.61 % Allowed : 12.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.20), residues: 1948 helix: 2.06 (0.17), residues: 996 sheet: -0.19 (0.52), residues: 111 loop : -0.08 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 594 HIS 0.003 0.000 HIS A1745 PHE 0.008 0.001 PHE A 238 TYR 0.008 0.001 TYR A1656 ARG 0.003 0.000 ARG C 74 *********************** 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 86 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 83 average time/residue: 0.2639 time to fit residues: 35.6223 Evaluate side-chains 76 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 1151 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** A1745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16279 Z= 0.362 Angle : 0.589 11.628 22026 Z= 0.296 Chirality : 0.041 0.185 2468 Planarity : 0.003 0.044 2818 Dihedral : 3.942 27.334 2126 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.72 % Allowed : 12.86 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.20), residues: 1948 helix: 2.07 (0.17), residues: 998 sheet: -0.36 (0.52), residues: 112 loop : -0.15 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1259 HIS 0.005 0.001 HIS A1722 PHE 0.013 0.001 PHE A 414 TYR 0.010 0.001 TYR A 903 ARG 0.005 0.000 ARG C 74 *********************** 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 fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 81 average time/residue: 0.2930 time to fit residues: 37.8640 Evaluate side-chains 76 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 1131 ASN Chi-restraints excluded: chain A residue 1151 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16279 Z= 0.169 Angle : 0.519 12.030 22026 Z= 0.258 Chirality : 0.039 0.197 2468 Planarity : 0.003 0.046 2818 Dihedral : 3.825 27.420 2126 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.39 % Allowed : 12.97 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.20), residues: 1948 helix: 2.18 (0.17), residues: 992 sheet: -0.27 (0.52), residues: 112 loop : -0.08 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 594 HIS 0.003 0.001 HIS B 133 PHE 0.009 0.001 PHE C 45 TYR 0.008 0.001 TYR A1656 ARG 0.008 0.000 ARG C 74 *********************** 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 79 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 77 average time/residue: 0.2669 time to fit residues: 33.1609 Evaluate side-chains 75 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 1.968 ------------------------------------------------------------------------------- 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 108 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 1151 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.8980 chunk 186 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 195 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16279 Z= 0.333 Angle : 0.603 11.937 22026 Z= 0.299 Chirality : 0.041 0.188 2468 Planarity : 0.003 0.050 2818 Dihedral : 3.991 27.338 2126 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.50 % Allowed : 13.20 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.20), residues: 1948 helix: 2.06 (0.17), residues: 998 sheet: -0.51 (0.51), residues: 114 loop : -0.15 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1259 HIS 0.005 0.001 HIS A1722 PHE 0.012 0.001 PHE A1505 TYR 0.009 0.001 TYR A1565 ARG 0.010 0.000 ARG C 74 ********************** 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 fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 74 average time/residue: 0.2836 time to fit residues: 33.6978 Evaluate side-chains 75 residues out of total 1817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 2.041 ------------------------------------------------------------------------------- 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 108 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1640 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.0070 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.046842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.034783 restraints weight = 78317.217| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 4.03 r_work: 0.2593 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16279 Z= 0.163 Angle : 0.530 12.363 22026 Z= 0.261 Chirality : 0.039 0.186 2468 Planarity : 0.003 0.046 2818 Dihedral : 3.850 27.381 2126 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.50 % Allowed : 13.20 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.20), residues: 1948 helix: 2.19 (0.17), residues: 992 sheet: -0.34 (0.52), residues: 112 loop : -0.09 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 594 HIS 0.003 0.001 HIS B 133 PHE 0.009 0.001 PHE A1043 TYR 0.007 0.001 TYR A 895 ARG 0.010 0.000 ARG C 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2570.74 seconds wall clock time: 48 minutes 32.18 seconds (2912.18 seconds total)