Starting phenix.real_space_refine on Tue Apr 9 20:39:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oro_13044/04_2024/7oro_13044.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oro_13044/04_2024/7oro_13044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oro_13044/04_2024/7oro_13044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oro_13044/04_2024/7oro_13044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oro_13044/04_2024/7oro_13044.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oro_13044/04_2024/7oro_13044.pdb" } resolution = 2.9 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 48 5.49 5 Mg 1 5.21 5 S 108 5.16 5 C 10962 2.51 5 N 2900 2.21 5 O 3396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 24": "OD1" <-> "OD2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 355": "OD1" <-> "OD2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 568": "OE1" <-> "OE2" Residue "A ASP 723": "OD1" <-> "OD2" Residue "A ASP 765": "OD1" <-> "OD2" Residue "A ASP 810": "OD1" <-> "OD2" Residue "A PHE 948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1006": "OE1" <-> "OE2" Residue "A GLU 1212": "OE1" <-> "OE2" Residue "A ASP 1410": "OD1" <-> "OD2" Residue "A GLU 1417": "OE1" <-> "OE2" Residue "A TYR 1442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1564": "OE1" <-> "OE2" Residue "A GLU 1697": "OE1" <-> "OE2" Residue "A ASP 1776": "OD1" <-> "OD2" Residue "A TYR 1989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2006": "OE1" <-> "OE2" Residue "A ASP 2072": "OD1" <-> "OD2" Residue "A GLU 2075": "OE1" <-> "OE2" Residue "A PHE 2136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2190": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 17416 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 299 Classifications: {'RNA': 14} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain: "S" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 297 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain: "T" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "P" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 16394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2010, 16394 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'peptide': 2008, 'undetermined': 2} Link IDs: {'PTRANS': 67, 'TRANS': 1940, None: 2} Not linked: pdbres="PHE A2238 " pdbres=" ZN A2301 " Not linked: pdbres=" ZN A2301 " pdbres=" MG A2302 " Chain breaks: 7 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16062 SG CYS A2064 61.365 30.363 27.421 1.00122.45 S Time building chain proxies: 9.72, per 1000 atoms: 0.56 Number of scatterers: 17416 At special positions: 0 Unit cell: (106.485, 130.53, 139.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 108 16.00 P 48 15.00 Mg 1 11.99 O 3396 8.00 N 2900 7.00 C 10962 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: 8.07 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A2169 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2064 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A2182 " 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3876 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 15 sheets defined 59.4% alpha, 8.9% beta 13 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 7.34 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 Processing helix chain 'A' and resid 18 through 46 removed outlier: 3.865A pdb=" N LYS A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP A 24 " --> pdb=" O CYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 99 through 120 removed outlier: 4.619A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 158 through 172 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 200 through 203 Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 215 through 227 Processing helix chain 'A' and resid 237 through 265 removed outlier: 4.745A pdb=" N LYS A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASP A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 292 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 356 through 373 Processing helix chain 'A' and resid 407 through 418 Processing helix chain 'A' and resid 447 through 466 Processing helix chain 'A' and resid 475 through 489 removed outlier: 5.916A pdb=" N SER A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ARG A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 502 Processing helix chain 'A' and resid 502 through 522 removed outlier: 4.036A pdb=" N GLN A 506 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 620 Proline residue: A 608 - end of helix Processing helix chain 'A' and resid 626 through 639 removed outlier: 4.237A pdb=" N TYR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 650 removed outlier: 3.986A pdb=" N LEU A 646 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 661 removed outlier: 4.249A pdb=" N TYR A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 673 Processing helix chain 'A' and resid 680 through 700 removed outlier: 3.633A pdb=" N PHE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 704 removed outlier: 3.762A pdb=" N VAL A 704 " --> pdb=" O ARG A 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 701 through 704' Processing helix chain 'A' and resid 737 through 747 Processing helix chain 'A' and resid 748 through 752 removed outlier: 3.502A pdb=" N ASN A 752 " --> pdb=" O PHE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 780 Processing helix chain 'A' and resid 795 through 814 removed outlier: 3.647A pdb=" N HIS A 814 " --> pdb=" O ASP A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 830 through 838 removed outlier: 3.511A pdb=" N THR A 833 " --> pdb=" O SER A 830 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 834 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N SER A 835 " --> pdb=" O THR A 832 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A 836 " --> pdb=" O THR A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 Processing helix chain 'A' and resid 894 through 900 Processing helix chain 'A' and resid 911 through 921 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.637A pdb=" N GLN A 932 " --> pdb=" O PRO A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 985 removed outlier: 4.097A pdb=" N LEU A 984 " --> pdb=" O GLU A 980 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN A 985 " --> pdb=" O ARG A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1020 removed outlier: 4.396A pdb=" N LYS A 999 " --> pdb=" O ASP A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1028 Processing helix chain 'A' and resid 1043 through 1049 Processing helix chain 'A' and resid 1071 through 1079 removed outlier: 3.869A pdb=" N TRP A1075 " --> pdb=" O TYR A1071 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A1076 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1099 Processing helix chain 'A' and resid 1106 through 1115 Processing helix chain 'A' and resid 1123 through 1129 Processing helix chain 'A' and resid 1148 through 1174 Processing helix chain 'A' and resid 1201 through 1220 removed outlier: 3.781A pdb=" N ILE A1205 " --> pdb=" O GLU A1201 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1258 Processing helix chain 'A' and resid 1259 through 1261 No H-bonds generated for 'chain 'A' and resid 1259 through 1261' Processing helix chain 'A' and resid 1267 through 1285 removed outlier: 3.522A pdb=" N SER A1274 " --> pdb=" O GLU A1270 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A1275 " --> pdb=" O ASP A1271 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A1278 " --> pdb=" O SER A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1307 Processing helix chain 'A' and resid 1340 through 1347 Processing helix chain 'A' and resid 1350 through 1365 Processing helix chain 'A' and resid 1366 through 1370 Processing helix chain 'A' and resid 1373 through 1380 Processing helix chain 'A' and resid 1381 through 1384 Processing helix chain 'A' and resid 1385 through 1389 Processing helix chain 'A' and resid 1390 through 1403 Processing helix chain 'A' and resid 1418 through 1422 Processing helix chain 'A' and resid 1441 through 1453 Processing helix chain 'A' and resid 1455 through 1467 removed outlier: 3.963A pdb=" N GLU A1459 " --> pdb=" O GLY A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1472 Processing helix chain 'A' and resid 1477 through 1489 removed outlier: 3.946A pdb=" N TYR A1489 " --> pdb=" O VAL A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1499 removed outlier: 3.648A pdb=" N LYS A1495 " --> pdb=" O SER A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1513 Processing helix chain 'A' and resid 1520 through 1526 removed outlier: 3.906A pdb=" N ILE A1524 " --> pdb=" O ASP A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1548 through 1563 removed outlier: 3.738A pdb=" N SER A1562 " --> pdb=" O ARG A1558 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A1563 " --> pdb=" O ASP A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1578 Processing helix chain 'A' and resid 1581 through 1593 Processing helix chain 'A' and resid 1622 through 1632 Processing helix chain 'A' and resid 1641 through 1660 removed outlier: 3.638A pdb=" N ALA A1646 " --> pdb=" O PRO A1642 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG A1647 " --> pdb=" O THR A1643 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP A1648 " --> pdb=" O GLU A1644 " (cutoff:3.500A) Processing helix chain 'A' and resid 1660 through 1677 Processing helix chain 'A' and resid 1680 through 1700 Processing helix chain 'A' and resid 1717 through 1729 Processing helix chain 'A' and resid 1760 through 1779 Processing helix chain 'A' and resid 1782 through 1795 removed outlier: 4.683A pdb=" N ALA A1786 " --> pdb=" O LEU A1782 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1811 Processing helix chain 'A' and resid 1818 through 1825 removed outlier: 3.532A pdb=" N THR A1825 " --> pdb=" O LEU A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1830 through 1840 Processing helix chain 'A' and resid 1983 through 1991 Processing helix chain 'A' and resid 2014 through 2019 removed outlier: 3.980A pdb=" N VAL A2019 " --> pdb=" O SER A2016 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2039 Processing helix chain 'A' and resid 2046 through 2052 Processing helix chain 'A' and resid 2054 through 2059 Processing helix chain 'A' and resid 2060 through 2062 No H-bonds generated for 'chain 'A' and resid 2060 through 2062' Processing helix chain 'A' and resid 2069 through 2074 Processing helix chain 'A' and resid 2109 through 2129 Processing helix chain 'A' and resid 2138 through 2155 Processing helix chain 'A' and resid 2158 through 2176 Processing helix chain 'A' and resid 2177 through 2183 Processing helix chain 'A' and resid 2200 through 2210 Processing helix chain 'A' and resid 2216 through 2238 removed outlier: 4.340A pdb=" N VAL A2221 " --> pdb=" O PRO A2217 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET A2222 " --> pdb=" O PRO A2218 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A2238 " --> pdb=" O ILE A2234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.583A pdb=" N LEU A 138 " --> pdb=" O LYS A1617 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 295 removed outlier: 5.869A pdb=" N GLU A 293 " --> pdb=" O ILE A 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 386 through 388 removed outlier: 5.672A pdb=" N LEU A 392 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE A 561 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 586 " --> pdb=" O CYS A 583 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 388 removed outlier: 5.672A pdb=" N LEU A 392 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 663 through 664 Processing sheet with id=AA6, first strand: chain 'A' and resid 716 through 717 removed outlier: 6.616A pdb=" N ILE A 709 " --> pdb=" O TYR A2099 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N SER A2101 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N LEU A 711 " --> pdb=" O SER A2101 " (cutoff:3.500A) removed outlier: 11.236A pdb=" N ARG A2103 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 727 through 728 Processing sheet with id=AA8, first strand: chain 'A' and resid 842 through 846 Processing sheet with id=AA9, first strand: chain 'A' and resid 959 through 963 removed outlier: 6.450A pdb=" N PHE A 945 " --> pdb=" O ILE A1104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1236 through 1237 Processing sheet with id=AB2, first strand: chain 'A' and resid 1594 through 1596 Processing sheet with id=AB3, first strand: chain 'A' and resid 1606 through 1609 Processing sheet with id=AB4, first strand: chain 'A' and resid 1800 through 1801 Processing sheet with id=AB5, first strand: chain 'A' and resid 1999 through 2000 Processing sheet with id=AB6, first strand: chain 'A' and resid 2027 through 2028 902 hydrogen bonds defined for protein. 2598 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 10.40 Time building geometry restraints manager: 8.21 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: 3408 1.33 - 1.45: 4392 1.45 - 1.57: 9798 1.57 - 1.69: 92 1.69 - 1.81: 179 Bond restraints: 17869 Sorted by residual: bond pdb=" CA SER A 664 " pdb=" CB SER A 664 " ideal model delta sigma weight residual 1.533 1.478 0.055 1.66e-02 3.63e+03 1.10e+01 bond pdb=" N LEU A1828 " pdb=" CA LEU A1828 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.03e+01 bond pdb=" CA SER A1192 " pdb=" CB SER A1192 " ideal model delta sigma weight residual 1.531 1.486 0.045 1.52e-02 4.33e+03 8.65e+00 bond pdb=" N ILE A 656 " pdb=" CA ILE A 656 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.55e+00 bond pdb=" N ILE A 938 " pdb=" CA ILE A 938 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.21e-02 6.83e+03 7.89e+00 ... (remaining 17864 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.26: 644 106.26 - 113.23: 9731 113.23 - 120.20: 6570 120.20 - 127.17: 7138 127.17 - 134.14: 241 Bond angle restraints: 24324 Sorted by residual: angle pdb=" N GLU A1350 " pdb=" CA GLU A1350 " pdb=" C GLU A1350 " ideal model delta sigma weight residual 113.38 100.72 12.66 1.23e+00 6.61e-01 1.06e+02 angle pdb=" N PRO A2217 " pdb=" CA PRO A2217 " pdb=" C PRO A2217 " ideal model delta sigma weight residual 110.70 121.42 -10.72 1.22e+00 6.72e-01 7.72e+01 angle pdb=" CA GLY A1436 " pdb=" C GLY A1436 " pdb=" O GLY A1436 " ideal model delta sigma weight residual 122.01 117.57 4.44 9.70e-01 1.06e+00 2.09e+01 angle pdb=" CA PRO A2217 " pdb=" C PRO A2217 " pdb=" N PRO A2218 " ideal model delta sigma weight residual 117.93 123.29 -5.36 1.20e+00 6.94e-01 1.99e+01 angle pdb=" CA ASP A 35 " pdb=" CB ASP A 35 " pdb=" CG ASP A 35 " ideal model delta sigma weight residual 112.60 116.65 -4.05 1.00e+00 1.00e+00 1.64e+01 ... (remaining 24319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.44: 9971 18.44 - 36.89: 731 36.89 - 55.33: 153 55.33 - 73.78: 74 73.78 - 92.22: 7 Dihedral angle restraints: 10936 sinusoidal: 4970 harmonic: 5966 Sorted by residual: dihedral pdb=" O4' G S 16 " pdb=" C1' G S 16 " pdb=" N9 G S 16 " pdb=" C4 G S 16 " ideal model delta sinusoidal sigma weight residual 70.00 -9.60 79.60 1 2.00e+01 2.50e-03 1.97e+01 dihedral pdb=" CA THR A2093 " pdb=" C THR A2093 " pdb=" N PRO A2094 " pdb=" CA PRO A2094 " ideal model delta harmonic sigma weight residual 180.00 158.34 21.66 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA TRP A1143 " pdb=" C TRP A1143 " pdb=" N LEU A1144 " pdb=" CA LEU A1144 " ideal model delta harmonic sigma weight residual -180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 10933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2352 0.062 - 0.124: 336 0.124 - 0.185: 43 0.185 - 0.247: 9 0.247 - 0.309: 5 Chirality restraints: 2745 Sorted by residual: chirality pdb=" CA ILE A 388 " pdb=" N ILE A 388 " pdb=" C ILE A 388 " pdb=" CB ILE A 388 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA PRO A2217 " pdb=" N PRO A2217 " pdb=" C PRO A2217 " pdb=" CB PRO A2217 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA ILE A2216 " pdb=" N ILE A2216 " pdb=" C ILE A2216 " pdb=" CB ILE A2216 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 2742 not shown) Planarity restraints: 2903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1641 " 0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO A1642 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A1642 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A1642 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1349 " -0.015 2.00e-02 2.50e+03 3.14e-02 9.88e+00 pdb=" C LEU A1349 " 0.054 2.00e-02 2.50e+03 pdb=" O LEU A1349 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A1350 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1826 " -0.013 2.00e-02 2.50e+03 2.72e-02 7.38e+00 pdb=" C GLY A1826 " 0.047 2.00e-02 2.50e+03 pdb=" O GLY A1826 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A1827 " -0.016 2.00e-02 2.50e+03 ... (remaining 2900 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 90 2.59 - 3.17: 14878 3.17 - 3.75: 28058 3.75 - 4.32: 40336 4.32 - 4.90: 65601 Nonbonded interactions: 148963 Sorted by model distance: nonbonded pdb=" OD1 ASP A1188 " pdb="MG MG A2302 " model vdw 2.015 2.170 nonbonded pdb=" O ILE A2118 " pdb=" OG1 THR A2122 " model vdw 2.210 2.440 nonbonded pdb=" OG SER A1443 " pdb=" OH TYR A1489 " model vdw 2.277 2.440 nonbonded pdb=" OD2 ASP A1413 " pdb=" OH TYR A1576 " model vdw 2.330 2.440 nonbonded pdb=" OG1 THR A2122 " pdb=" NZ LYS A2174 " model vdw 2.340 2.520 ... (remaining 148958 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.730 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 61.780 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.005 0.058 17869 Z= 0.291 Angle : 0.677 12.658 24324 Z= 0.442 Chirality : 0.047 0.309 2745 Planarity : 0.004 0.081 2903 Dihedral : 14.187 92.223 7060 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.22 % Allowed : 0.92 % Favored : 98.87 % 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: 1.47 (0.19), residues: 1992 helix: 2.03 (0.16), residues: 1080 sheet: 0.71 (0.41), residues: 151 loop : -0.50 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2160 HIS 0.004 0.001 HIS A 760 PHE 0.024 0.001 PHE A1768 TYR 0.016 0.001 TYR A2181 ARG 0.006 0.001 ARG A1690 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 176 time to evaluate : 2.241 Fit side-chains REVERT: A 763 MET cc_start: 0.9065 (mmt) cc_final: 0.8857 (mmp) REVERT: A 2070 ILE cc_start: 0.7895 (pt) cc_final: 0.7659 (mt) outliers start: 4 outliers final: 0 residues processed: 178 average time/residue: 1.6068 time to fit residues: 316.6815 Evaluate side-chains 125 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 185 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 397 GLN A 760 HIS A 985 ASN A1007 GLN A1181 ASN A1448 GLN A2040 GLN ** A2049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2141 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17869 Z= 0.186 Angle : 0.495 9.086 24324 Z= 0.265 Chirality : 0.039 0.179 2745 Planarity : 0.004 0.052 2903 Dihedral : 12.619 99.067 2898 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.56 % Favored : 97.39 % Rotamer: Outliers : 0.92 % Allowed : 7.29 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.19), residues: 1992 helix: 2.06 (0.16), residues: 1090 sheet: 0.78 (0.43), residues: 137 loop : -0.37 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1143 HIS 0.006 0.001 HIS A2169 PHE 0.020 0.001 PHE A 210 TYR 0.014 0.001 TYR A1989 ARG 0.008 0.000 ARG A1829 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 2.118 Fit side-chains REVERT: A 1671 MET cc_start: 0.7058 (ttt) cc_final: 0.6771 (ttm) REVERT: A 2204 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.5885 (t80) outliers start: 17 outliers final: 8 residues processed: 146 average time/residue: 1.4785 time to fit residues: 241.7656 Evaluate side-chains 130 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1685 LEU Chi-restraints excluded: chain A residue 1987 LEU Chi-restraints excluded: chain A residue 2204 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 154 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 185 optimal weight: 0.6980 chunk 200 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 332 GLN A2040 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17869 Z= 0.167 Angle : 0.465 8.029 24324 Z= 0.249 Chirality : 0.039 0.180 2745 Planarity : 0.003 0.043 2903 Dihedral : 12.505 97.556 2898 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.31 % Favored : 97.64 % Rotamer: Outliers : 1.40 % Allowed : 8.74 % Favored : 89.85 % 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: 1.65 (0.19), residues: 1992 helix: 2.14 (0.16), residues: 1090 sheet: 0.81 (0.43), residues: 137 loop : -0.37 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1143 HIS 0.005 0.001 HIS A 760 PHE 0.018 0.001 PHE A1768 TYR 0.011 0.001 TYR A 669 ARG 0.013 0.000 ARG A1439 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 2.115 Fit side-chains REVERT: A 231 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.6971 (t80) REVERT: A 534 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8285 (mtm) REVERT: A 718 GLN cc_start: 0.7235 (tt0) cc_final: 0.6808 (tm-30) REVERT: A 732 PHE cc_start: 0.9545 (OUTLIER) cc_final: 0.8344 (p90) REVERT: A 1671 MET cc_start: 0.7050 (ttt) cc_final: 0.6766 (ttm) REVERT: A 1690 ARG cc_start: 0.7820 (mtp180) cc_final: 0.7532 (ttm-80) REVERT: A 1817 ASP cc_start: 0.8158 (m-30) cc_final: 0.7851 (OUTLIER) REVERT: A 2203 MET cc_start: 0.5373 (tmm) cc_final: 0.4563 (ttt) outliers start: 26 outliers final: 9 residues processed: 146 average time/residue: 1.4972 time to fit residues: 244.3619 Evaluate side-chains 134 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1685 LEU Chi-restraints excluded: chain A residue 1987 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 96 optimal weight: 0.0570 chunk 20 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 319 ASN ** A1658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17869 Z= 0.246 Angle : 0.491 8.153 24324 Z= 0.262 Chirality : 0.040 0.179 2745 Planarity : 0.004 0.040 2903 Dihedral : 12.548 98.595 2898 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 1.67 % Allowed : 10.04 % Favored : 88.29 % 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: 1.54 (0.19), residues: 1992 helix: 2.07 (0.16), residues: 1090 sheet: 0.79 (0.44), residues: 132 loop : -0.47 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1143 HIS 0.006 0.001 HIS A 760 PHE 0.022 0.001 PHE A1768 TYR 0.014 0.001 TYR A 504 ARG 0.015 0.001 ARG A1439 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 1.940 Fit side-chains REVERT: A 143 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7699 (p0) REVERT: A 231 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.7053 (t80) REVERT: A 412 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8532 (mp) REVERT: A 424 HIS cc_start: 0.5936 (OUTLIER) cc_final: 0.5365 (m-70) REVERT: A 534 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8334 (mtp) REVERT: A 732 PHE cc_start: 0.9573 (OUTLIER) cc_final: 0.8250 (p90) REVERT: A 971 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8467 (mtm) REVERT: A 1671 MET cc_start: 0.7063 (ttt) cc_final: 0.6774 (ttm) REVERT: A 1690 ARG cc_start: 0.7814 (mtp180) cc_final: 0.7577 (ttm-80) REVERT: A 1817 ASP cc_start: 0.8360 (m-30) cc_final: 0.8017 (p0) REVERT: A 2130 THR cc_start: 0.6430 (p) cc_final: 0.6028 (p) outliers start: 31 outliers final: 10 residues processed: 142 average time/residue: 1.4291 time to fit residues: 228.5808 Evaluate side-chains 135 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1685 LEU Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1987 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 176 optimal weight: 0.0980 chunk 49 optimal weight: 8.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17869 Z= 0.184 Angle : 0.464 9.262 24324 Z= 0.247 Chirality : 0.038 0.178 2745 Planarity : 0.003 0.045 2903 Dihedral : 12.481 98.609 2898 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.31 % Favored : 97.64 % Rotamer: Outliers : 1.67 % Allowed : 10.90 % Favored : 87.43 % 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: 1.61 (0.19), residues: 1992 helix: 2.17 (0.16), residues: 1089 sheet: 0.75 (0.44), residues: 132 loop : -0.48 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1143 HIS 0.006 0.001 HIS A 760 PHE 0.028 0.001 PHE A2207 TYR 0.012 0.001 TYR A 504 ARG 0.017 0.000 ARG A1439 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 2.005 Fit side-chains REVERT: A 143 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7652 (p0) REVERT: A 231 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.7095 (t80) REVERT: A 412 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8527 (mp) REVERT: A 424 HIS cc_start: 0.5891 (OUTLIER) cc_final: 0.5334 (m-70) REVERT: A 534 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8279 (mtm) REVERT: A 686 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7859 (mtt) REVERT: A 718 GLN cc_start: 0.7170 (tt0) cc_final: 0.6667 (tm-30) REVERT: A 732 PHE cc_start: 0.9578 (OUTLIER) cc_final: 0.8295 (p90) REVERT: A 1671 MET cc_start: 0.7097 (ttt) cc_final: 0.6816 (ttm) REVERT: A 1690 ARG cc_start: 0.7826 (mtp180) cc_final: 0.7603 (ttm-80) REVERT: A 1817 ASP cc_start: 0.8320 (m-30) cc_final: 0.8009 (OUTLIER) REVERT: A 1989 TYR cc_start: 0.8020 (t80) cc_final: 0.7783 (t80) REVERT: A 2203 MET cc_start: 0.5243 (tmm) cc_final: 0.4598 (ttp) outliers start: 31 outliers final: 12 residues processed: 145 average time/residue: 1.4168 time to fit residues: 230.5611 Evaluate side-chains 139 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1557 MET Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1987 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.0970 chunk 177 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17869 Z= 0.193 Angle : 0.473 8.266 24324 Z= 0.252 Chirality : 0.039 0.178 2745 Planarity : 0.003 0.060 2903 Dihedral : 12.458 98.423 2898 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.56 % Favored : 97.39 % Rotamer: Outliers : 1.51 % Allowed : 11.71 % Favored : 86.78 % 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 (0.19), residues: 1992 helix: 2.15 (0.16), residues: 1090 sheet: 0.77 (0.45), residues: 132 loop : -0.51 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1143 HIS 0.005 0.001 HIS A 760 PHE 0.023 0.001 PHE A2207 TYR 0.012 0.001 TYR A 504 ARG 0.018 0.000 ARG A1439 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 2.020 Fit side-chains REVERT: A 143 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7629 (p0) REVERT: A 231 TYR cc_start: 0.7478 (OUTLIER) cc_final: 0.7122 (t80) REVERT: A 412 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8518 (mp) REVERT: A 424 HIS cc_start: 0.5937 (OUTLIER) cc_final: 0.5405 (m-70) REVERT: A 686 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7810 (mtt) REVERT: A 718 GLN cc_start: 0.7143 (tt0) cc_final: 0.6578 (tm-30) REVERT: A 732 PHE cc_start: 0.9570 (OUTLIER) cc_final: 0.8316 (p90) REVERT: A 971 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8445 (mtm) REVERT: A 1056 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7545 (mm-30) REVERT: A 1671 MET cc_start: 0.7097 (ttt) cc_final: 0.6813 (ttm) REVERT: A 1817 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.8016 (OUTLIER) REVERT: A 1989 TYR cc_start: 0.8126 (t80) cc_final: 0.7872 (t80) REVERT: A 2203 MET cc_start: 0.5231 (tmm) cc_final: 0.4380 (ttt) outliers start: 28 outliers final: 12 residues processed: 145 average time/residue: 1.4540 time to fit residues: 236.0214 Evaluate side-chains 143 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1817 ASP Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1987 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 112 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 166 optimal weight: 0.0570 chunk 110 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17869 Z= 0.156 Angle : 0.473 15.746 24324 Z= 0.249 Chirality : 0.038 0.178 2745 Planarity : 0.003 0.063 2903 Dihedral : 12.389 98.121 2898 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.46 % Favored : 97.49 % Rotamer: Outliers : 1.57 % Allowed : 12.03 % Favored : 86.40 % 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: 1.66 (0.19), residues: 1992 helix: 2.21 (0.16), residues: 1089 sheet: 0.84 (0.43), residues: 145 loop : -0.49 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1143 HIS 0.005 0.001 HIS A 760 PHE 0.032 0.001 PHE A2207 TYR 0.010 0.001 TYR A 504 ARG 0.017 0.000 ARG A1439 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 2.148 Fit side-chains revert: symmetry clash REVERT: A 143 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7607 (p0) REVERT: A 231 TYR cc_start: 0.7474 (OUTLIER) cc_final: 0.7182 (t80) REVERT: A 412 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8511 (mp) REVERT: A 424 HIS cc_start: 0.5963 (OUTLIER) cc_final: 0.5382 (m-70) REVERT: A 686 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.7903 (mtt) REVERT: A 718 GLN cc_start: 0.7127 (tt0) cc_final: 0.6746 (tm-30) REVERT: A 732 PHE cc_start: 0.9556 (OUTLIER) cc_final: 0.8352 (p90) REVERT: A 765 ASP cc_start: 0.7540 (m-30) cc_final: 0.7230 (m-30) REVERT: A 1056 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7531 (mm-30) REVERT: A 1671 MET cc_start: 0.7087 (ttt) cc_final: 0.6804 (ttm) REVERT: A 1813 TYR cc_start: 0.8527 (m-80) cc_final: 0.8110 (m-80) REVERT: A 1817 ASP cc_start: 0.8164 (m-30) cc_final: 0.7906 (OUTLIER) REVERT: A 1989 TYR cc_start: 0.8034 (t80) cc_final: 0.7769 (t80) outliers start: 29 outliers final: 11 residues processed: 147 average time/residue: 1.4438 time to fit residues: 238.4742 Evaluate side-chains 140 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1657 GLU Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 2064 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 38 optimal weight: 0.4980 chunk 125 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 chunk 178 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17869 Z= 0.167 Angle : 0.470 9.624 24324 Z= 0.248 Chirality : 0.038 0.178 2745 Planarity : 0.003 0.071 2903 Dihedral : 12.349 97.944 2898 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.56 % Favored : 97.39 % Rotamer: Outliers : 1.62 % Allowed : 12.25 % Favored : 86.13 % 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: 1.69 (0.19), residues: 1992 helix: 2.24 (0.16), residues: 1090 sheet: 0.94 (0.44), residues: 140 loop : -0.51 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1143 HIS 0.005 0.001 HIS A 760 PHE 0.029 0.001 PHE A2207 TYR 0.011 0.001 TYR A 714 ARG 0.019 0.000 ARG A1439 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 2.026 Fit side-chains REVERT: A 231 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.7219 (t80) REVERT: A 412 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8510 (mp) REVERT: A 424 HIS cc_start: 0.5987 (OUTLIER) cc_final: 0.5453 (m-70) REVERT: A 686 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7835 (mtt) REVERT: A 718 GLN cc_start: 0.7141 (tt0) cc_final: 0.6742 (tm-30) REVERT: A 732 PHE cc_start: 0.9554 (OUTLIER) cc_final: 0.8337 (p90) REVERT: A 765 ASP cc_start: 0.7523 (m-30) cc_final: 0.7206 (m-30) REVERT: A 971 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8402 (mtm) REVERT: A 1056 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7566 (mm-30) REVERT: A 1671 MET cc_start: 0.7085 (ttt) cc_final: 0.6802 (ttm) REVERT: A 1813 TYR cc_start: 0.8517 (m-80) cc_final: 0.8095 (m-80) REVERT: A 1817 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7912 (OUTLIER) REVERT: A 1989 TYR cc_start: 0.8061 (t80) cc_final: 0.7843 (t80) REVERT: A 2108 MET cc_start: 0.8211 (ptp) cc_final: 0.7986 (ptm) REVERT: A 2151 LEU cc_start: 0.7762 (tp) cc_final: 0.7522 (tt) REVERT: A 2203 MET cc_start: 0.5365 (tmm) cc_final: 0.4065 (ttt) outliers start: 30 outliers final: 12 residues processed: 147 average time/residue: 1.4296 time to fit residues: 235.5456 Evaluate side-chains 142 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1817 ASP Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 2064 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 79 optimal weight: 0.0060 chunk 143 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 165 optimal weight: 0.5980 chunk 173 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17869 Z= 0.160 Angle : 0.485 10.223 24324 Z= 0.253 Chirality : 0.038 0.177 2745 Planarity : 0.003 0.076 2903 Dihedral : 12.317 97.905 2898 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % Rotamer: Outliers : 1.51 % Allowed : 12.74 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.71 (0.19), residues: 1992 helix: 2.26 (0.16), residues: 1090 sheet: 0.93 (0.44), residues: 140 loop : -0.51 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1143 HIS 0.005 0.001 HIS A 760 PHE 0.037 0.001 PHE A2207 TYR 0.010 0.001 TYR A 677 ARG 0.021 0.000 ARG A1439 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 125 time to evaluate : 2.135 Fit side-chains REVERT: A 231 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.7260 (t80) REVERT: A 412 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8506 (mp) REVERT: A 424 HIS cc_start: 0.5986 (OUTLIER) cc_final: 0.5300 (m-70) REVERT: A 597 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.7009 (p0) REVERT: A 686 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.7904 (mtt) REVERT: A 718 GLN cc_start: 0.7126 (tt0) cc_final: 0.6726 (tm-30) REVERT: A 732 PHE cc_start: 0.9548 (OUTLIER) cc_final: 0.8309 (p90) REVERT: A 971 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8399 (mtm) REVERT: A 1671 MET cc_start: 0.7113 (ttt) cc_final: 0.6829 (ttm) REVERT: A 1706 ILE cc_start: 0.8787 (mt) cc_final: 0.8541 (tp) REVERT: A 1813 TYR cc_start: 0.8490 (m-80) cc_final: 0.8075 (m-80) REVERT: A 1817 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7902 (OUTLIER) REVERT: A 1989 TYR cc_start: 0.8037 (t80) cc_final: 0.7807 (t80) REVERT: A 2108 MET cc_start: 0.8247 (ptp) cc_final: 0.7999 (ptm) REVERT: A 2203 MET cc_start: 0.5358 (tmm) cc_final: 0.4324 (ttt) outliers start: 28 outliers final: 10 residues processed: 142 average time/residue: 1.5112 time to fit residues: 240.3285 Evaluate side-chains 140 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1817 ASP Chi-restraints excluded: chain A residue 2064 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 602 GLN A1515 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17869 Z= 0.180 Angle : 0.491 9.664 24324 Z= 0.257 Chirality : 0.039 0.209 2745 Planarity : 0.004 0.083 2903 Dihedral : 12.317 97.874 2898 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Rotamer: Outliers : 1.13 % Allowed : 13.28 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.19), residues: 1992 helix: 2.23 (0.16), residues: 1090 sheet: 0.90 (0.44), residues: 140 loop : -0.51 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1143 HIS 0.005 0.001 HIS A 760 PHE 0.032 0.001 PHE A2207 TYR 0.011 0.001 TYR A 504 ARG 0.021 0.000 ARG A1439 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 2.302 Fit side-chains REVERT: A 120 LEU cc_start: 0.8727 (mm) cc_final: 0.7984 (tp) REVERT: A 231 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.7298 (t80) REVERT: A 412 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8523 (mp) REVERT: A 424 HIS cc_start: 0.5991 (OUTLIER) cc_final: 0.5270 (m-70) REVERT: A 686 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7828 (mtt) REVERT: A 718 GLN cc_start: 0.7171 (tt0) cc_final: 0.6750 (tm-30) REVERT: A 732 PHE cc_start: 0.9555 (OUTLIER) cc_final: 0.8317 (p90) REVERT: A 971 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8411 (mtm) REVERT: A 1671 MET cc_start: 0.7117 (ttt) cc_final: 0.6830 (ttm) REVERT: A 1706 ILE cc_start: 0.8796 (mt) cc_final: 0.8552 (tp) REVERT: A 1813 TYR cc_start: 0.8515 (m-80) cc_final: 0.8100 (m-80) REVERT: A 1817 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7910 (OUTLIER) REVERT: A 1989 TYR cc_start: 0.8037 (t80) cc_final: 0.7790 (t80) REVERT: A 2108 MET cc_start: 0.8242 (ptp) cc_final: 0.7988 (ptm) REVERT: A 2203 MET cc_start: 0.5389 (tmm) cc_final: 0.4089 (ttt) outliers start: 21 outliers final: 13 residues processed: 135 average time/residue: 1.5136 time to fit residues: 229.7037 Evaluate side-chains 140 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1817 ASP Chi-restraints excluded: chain A residue 2000 ILE Chi-restraints excluded: chain A residue 2064 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 602 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.101156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.074595 restraints weight = 31082.544| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.06 r_work: 0.2883 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17869 Z= 0.235 Angle : 0.527 13.086 24324 Z= 0.274 Chirality : 0.040 0.176 2745 Planarity : 0.004 0.084 2903 Dihedral : 12.371 98.472 2898 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 1.46 % Allowed : 13.22 % Favored : 85.32 % 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: 1.55 (0.19), residues: 1992 helix: 2.13 (0.16), residues: 1090 sheet: 0.84 (0.44), residues: 140 loop : -0.57 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2160 HIS 0.007 0.001 HIS A2182 PHE 0.041 0.001 PHE A2207 TYR 0.013 0.001 TYR A 504 ARG 0.021 0.001 ARG A1439 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5138.81 seconds wall clock time: 94 minutes 15.50 seconds (5655.50 seconds total)