Starting phenix.real_space_refine on Fri Feb 16 12:57:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbw_25800/02_2024/7tbw_25800_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbw_25800/02_2024/7tbw_25800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbw_25800/02_2024/7tbw_25800.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbw_25800/02_2024/7tbw_25800.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbw_25800/02_2024/7tbw_25800_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbw_25800/02_2024/7tbw_25800_updated.pdb" } resolution = 3.1 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 90 5.16 5 C 9895 2.51 5 N 2563 2.21 5 O 2782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A ASP 411": "OD1" <-> "OD2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A ASP 434": "OD1" <-> "OD2" Residue "A ASP 441": "OD1" <-> "OD2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A ASP 462": "OD1" <-> "OD2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 815": "OE1" <-> "OE2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A PHE 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 891": "OE1" <-> "OE2" Residue "A ASP 917": "OD1" <-> "OD2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1079": "NH1" <-> "NH2" Residue "A ARG 1082": "NH1" <-> "NH2" Residue "A ARG 1100": "NH1" <-> "NH2" Residue "A TYR 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1198": "OE1" <-> "OE2" Residue "A ASP 1199": "OD1" <-> "OD2" Residue "A TYR 1206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1246": "OE1" <-> "OE2" Residue "A GLU 1253": "OE1" <-> "OE2" Residue "A ARG 1336": "NH1" <-> "NH2" Residue "A GLU 1386": "OE1" <-> "OE2" Residue "A GLU 1403": "OE1" <-> "OE2" Residue "A ASP 1411": "OD1" <-> "OD2" Residue "A GLU 1420": "OE1" <-> "OE2" Residue "A ASP 1426": "OD1" <-> "OD2" Residue "A GLU 1435": "OE1" <-> "OE2" Residue "A ARG 1503": "NH1" <-> "NH2" Residue "A ASP 1567": "OD1" <-> "OD2" Residue "A ASP 1571": "OD1" <-> "OD2" Residue "A GLU 1622": "OE1" <-> "OE2" Residue "A ASP 1654": "OD1" <-> "OD2" Residue "A ARG 1680": "NH1" <-> "NH2" Residue "A GLU 1789": "OE1" <-> "OE2" Residue "A ASP 1801": "OD1" <-> "OD2" Residue "A ASP 1847": "OD1" <-> "OD2" Residue "A GLU 1893": "OE1" <-> "OE2" Residue "A ASP 1904": "OD1" <-> "OD2" Residue "A ARG 2004": "NH1" <-> "NH2" Residue "A GLU 2005": "OE1" <-> "OE2" Residue "A PHE 2010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2039": "OE1" <-> "OE2" Residue "A ARG 2051": "NH1" <-> "NH2" Residue "A ARG 2081": "NH1" <-> "NH2" Residue "A ARG 2095": "NH1" <-> "NH2" Residue "A GLU 2108": "OE1" <-> "OE2" Residue "A ARG 2113": "NH1" <-> "NH2" Residue "A ARG 2123": "NH1" <-> "NH2" Residue "A ASP 2151": "OD1" <-> "OD2" Residue "A PHE 2159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2170": "OE1" <-> "OE2" Residue "A ASP 2205": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15338 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 15129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1928, 15129 Classifications: {'peptide': 1928} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 2, 'PTRANS': 91, 'TRANS': 1834} Chain breaks: 14 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 120 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 1, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.46, per 1000 atoms: 0.55 Number of scatterers: 15338 At special positions: 0 Unit cell: (105.5, 91.152, 207.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 90 16.00 P 6 15.00 Mg 2 11.99 O 2782 8.00 N 2563 7.00 C 9895 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 626 " - pdb=" SG CYS A1465 " distance=2.03 Simple disulfide: pdb=" SG CYS A1418 " - pdb=" SG CYS A1429 " distance=2.03 Simple disulfide: pdb=" SG CYS A1463 " - pdb=" SG CYS A1477 " distance=2.04 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=1, symmetry=0 Links applied BETA1-3 " BMA C 3 " - " BMA C 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " BETA1-6 " BMA C 3 " - " BMA C 5 " NAG-ASN " NAG A2506 " - " ASN A 98 " " NAG A2507 " - " ASN A1637 " " NAG B 1 " - " ASN A 400 " " NAG C 1 " - " ASN A1504 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.62 Conformation dependent library (CDL) restraints added in 3.0 seconds 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3606 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 9 sheets defined 52.1% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.83 Creating SS restraints... Processing helix chain 'A' and resid 4 through 20 Processing helix chain 'A' and resid 22 through 44 Proline residue: A 32 - end of helix removed outlier: 4.163A pdb=" N ILE A 35 " --> pdb=" O TRP A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 66 through 75 Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 101 through 117 Processing helix chain 'A' and resid 121 through 135 Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.571A pdb=" N LEU A 206 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 226 removed outlier: 3.973A pdb=" N GLU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 239 removed outlier: 4.273A pdb=" N MET A 233 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASP A 234 " --> pdb=" O SER A 231 " (cutoff:3.500A) Proline residue: A 238 - end of helix Processing helix chain 'A' and resid 247 through 250 No H-bonds generated for 'chain 'A' and resid 247 through 250' Processing helix chain 'A' and resid 253 through 274 Processing helix chain 'A' and resid 278 through 288 Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 369 through 379 Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 390 through 409 removed outlier: 4.424A pdb=" N LEU A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA A 407 " --> pdb=" O PHE A 403 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N PHE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 416 Processing helix chain 'A' and resid 419 through 426 Processing helix chain 'A' and resid 431 through 440 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 460 through 467 Processing helix chain 'A' and resid 484 through 501 Processing helix chain 'A' and resid 516 through 528 Processing helix chain 'A' and resid 587 through 590 No H-bonds generated for 'chain 'A' and resid 587 through 590' Processing helix chain 'A' and resid 593 through 608 Processing helix chain 'A' and resid 631 through 664 Proline residue: A 641 - end of helix removed outlier: 4.325A pdb=" N THR A 645 " --> pdb=" O PRO A 641 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TRP A 648 " --> pdb=" O MET A 644 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 674 Processing helix chain 'A' and resid 678 through 706 Proline residue: A 692 - end of helix Processing helix chain 'A' and resid 715 through 739 removed outlier: 3.749A pdb=" N LEU A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 756 removed outlier: 3.934A pdb=" N ALA A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLY A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 767 Processing helix chain 'A' and resid 773 through 779 Processing helix chain 'A' and resid 785 through 799 Processing helix chain 'A' and resid 821 through 845 Processing helix chain 'A' and resid 940 through 946 Processing helix chain 'A' and resid 968 through 974 removed outlier: 4.059A pdb=" N ASN A 974 " --> pdb=" O THR A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1001 removed outlier: 4.543A pdb=" N LYS A1001 " --> pdb=" O TYR A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1019 Processing helix chain 'A' and resid 1030 through 1032 No H-bonds generated for 'chain 'A' and resid 1030 through 1032' Processing helix chain 'A' and resid 1035 through 1046 Processing helix chain 'A' and resid 1065 through 1077 removed outlier: 3.553A pdb=" N ARG A1069 " --> pdb=" O PRO A1065 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A1070 " --> pdb=" O TYR A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1096 Processing helix chain 'A' and resid 1115 through 1121 Processing helix chain 'A' and resid 1182 through 1190 removed outlier: 3.636A pdb=" N HIS A1190 " --> pdb=" O LEU A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1227 Processing helix chain 'A' and resid 1244 through 1253 Processing helix chain 'A' and resid 1322 through 1341 Processing helix chain 'A' and resid 1344 through 1350 Processing helix chain 'A' and resid 1352 through 1366 Processing helix chain 'A' and resid 1402 through 1408 Processing helix chain 'A' and resid 1446 through 1449 No H-bonds generated for 'chain 'A' and resid 1446 through 1449' Processing helix chain 'A' and resid 1505 through 1522 Processing helix chain 'A' and resid 1548 through 1560 Processing helix chain 'A' and resid 1571 through 1583 Processing helix chain 'A' and resid 1601 through 1617 Processing helix chain 'A' and resid 1644 through 1680 removed outlier: 3.968A pdb=" N THR A1651 " --> pdb=" O ALA A1647 " (cutoff:3.500A) Proline residue: A1669 - end of helix removed outlier: 4.249A pdb=" N PHE A1672 " --> pdb=" O VAL A1668 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL A1673 " --> pdb=" O PRO A1669 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL A1674 " --> pdb=" O ALA A1670 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE A1675 " --> pdb=" O SER A1671 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A1676 " --> pdb=" O PHE A1672 " (cutoff:3.500A) Processing helix chain 'A' and resid 1684 through 1690 Processing helix chain 'A' and resid 1695 through 1724 Proline residue: A1713 - end of helix Processing helix chain 'A' and resid 1735 through 1754 Proline residue: A1751 - end of helix Processing helix chain 'A' and resid 1763 through 1789 Processing helix chain 'A' and resid 1795 through 1809 Processing helix chain 'A' and resid 1811 through 1833 Processing helix chain 'A' and resid 1849 through 1871 Processing helix chain 'A' and resid 1893 through 1904 Processing helix chain 'A' and resid 1952 through 1960 Processing helix chain 'A' and resid 1981 through 1987 removed outlier: 3.803A pdb=" N ASN A1987 " --> pdb=" O GLU A1983 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2014 Processing helix chain 'A' and resid 2018 through 2032 removed outlier: 3.611A pdb=" N VAL A2021 " --> pdb=" O GLU A2018 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLY A2022 " --> pdb=" O LYS A2019 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A2023 " --> pdb=" O GLU A2020 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A2031 " --> pdb=" O ALA A2028 " (cutoff:3.500A) Processing helix chain 'A' and resid 2042 through 2044 No H-bonds generated for 'chain 'A' and resid 2042 through 2044' Processing helix chain 'A' and resid 2047 through 2058 removed outlier: 4.171A pdb=" N ARG A2051 " --> pdb=" O GLY A2047 " (cutoff:3.500A) Processing helix chain 'A' and resid 2077 through 2092 Processing helix chain 'A' and resid 2104 through 2110 Processing helix chain 'A' and resid 2128 through 2134 Processing helix chain 'A' and resid 2153 through 2162 Processing helix chain 'A' and resid 2187 through 2196 Processing helix chain 'A' and resid 2213 through 2223 Processing sheet with id= A, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.181A pdb=" N TYR A1388 " --> pdb=" O GLY A1533 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N PHE A1535 " --> pdb=" O TYR A1388 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE A1390 " --> pdb=" O PHE A1535 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU A1537 " --> pdb=" O PHE A1390 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER A1392 " --> pdb=" O LEU A1537 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N VAL A1539 " --> pdb=" O SER A1392 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE A1496 " --> pdb=" O THR A1389 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL A1391 " --> pdb=" O ILE A1496 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLN A1498 " --> pdb=" O VAL A1391 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ASN A1393 " --> pdb=" O GLN A1498 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 535 through 537 removed outlier: 7.178A pdb=" N GLY A1628 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N TYR A 554 " --> pdb=" O GLY A1628 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR A1630 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE A 556 " --> pdb=" O THR A1630 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE A1632 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 899 through 902 Processing sheet with id= D, first strand: chain 'A' and resid 931 through 933 removed outlier: 6.306A pdb=" N ALA A1102 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER A1105 " --> pdb=" O LEU A1109 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU A1109 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 975 through 978 removed outlier: 6.275A pdb=" N VAL A1053 " --> pdb=" O GLY A 976 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N CYS A 978 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE A1055 " --> pdb=" O CYS A 978 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1239 through 1241 removed outlier: 3.847A pdb=" N GLU A1198 " --> pdb=" O THR A1205 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL A1207 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU A1196 " --> pdb=" O VAL A1207 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1934 through 1936 removed outlier: 3.655A pdb=" N LEU A1912 " --> pdb=" O ILE A1936 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 2113 through 2117 removed outlier: 5.775A pdb=" N VAL A2097 " --> pdb=" O PHE A1942 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU A1944 " --> pdb=" O VAL A2097 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A2099 " --> pdb=" O LEU A1944 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLY A1946 " --> pdb=" O LEU A2099 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY A1989 " --> pdb=" O PHE A2067 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASP A2069 " --> pdb=" O GLY A1989 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS A1991 " --> pdb=" O ASP A2069 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 2175 through 2179 710 hydrogen bonds defined for protein. 2025 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: 6.85 Time building geometry restraints manager: 7.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4830 1.34 - 1.46: 3558 1.46 - 1.58: 7146 1.58 - 1.70: 10 1.70 - 1.81: 146 Bond restraints: 15690 Sorted by residual: bond pdb=" C4 ATP A2503 " pdb=" C5 ATP A2503 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.93e+01 bond pdb=" C4 ATP A2502 " pdb=" C5 ATP A2502 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.71e+01 bond pdb=" C5 ATP A2502 " pdb=" C6 ATP A2502 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.00e-02 1.00e+04 5.42e+01 bond pdb=" C5 ATP A2503 " pdb=" C6 ATP A2503 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" C8 ATP A2502 " pdb=" N7 ATP A2502 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.34e+01 ... (remaining 15685 not shown) Histogram of bond angle deviations from ideal: 100.60 - 107.72: 674 107.72 - 114.85: 9327 114.85 - 121.97: 8319 121.97 - 129.10: 2852 129.10 - 136.22: 129 Bond angle restraints: 21301 Sorted by residual: angle pdb=" PB ATP A2503 " pdb=" O3B ATP A2503 " pdb=" PG ATP A2503 " ideal model delta sigma weight residual 139.87 120.48 19.39 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PB ATP A2502 " pdb=" O3B ATP A2502 " pdb=" PG ATP A2502 " ideal model delta sigma weight residual 139.87 121.15 18.72 1.00e+00 1.00e+00 3.50e+02 angle pdb=" PA ATP A2502 " pdb=" O3A ATP A2502 " pdb=" PB ATP A2502 " ideal model delta sigma weight residual 136.83 121.34 15.49 1.00e+00 1.00e+00 2.40e+02 angle pdb=" PA ATP A2503 " pdb=" O3A ATP A2503 " pdb=" PB ATP A2503 " ideal model delta sigma weight residual 136.83 122.51 14.32 1.00e+00 1.00e+00 2.05e+02 angle pdb=" C5 ATP A2503 " pdb=" C4 ATP A2503 " pdb=" N3 ATP A2503 " ideal model delta sigma weight residual 126.80 118.68 8.12 1.00e+00 1.00e+00 6.60e+01 ... (remaining 21296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.46: 9038 23.46 - 46.93: 402 46.93 - 70.39: 51 70.39 - 93.85: 33 93.85 - 117.32: 18 Dihedral angle restraints: 9542 sinusoidal: 3963 harmonic: 5579 Sorted by residual: dihedral pdb=" CB CYS A1463 " pdb=" SG CYS A1463 " pdb=" SG CYS A1477 " pdb=" CB CYS A1477 " ideal model delta sinusoidal sigma weight residual -86.00 -150.28 64.28 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CA SER A 783 " pdb=" C SER A 783 " pdb=" N PRO A 784 " pdb=" CA PRO A 784 " ideal model delta harmonic sigma weight residual 180.00 147.82 32.18 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA LEU A2180 " pdb=" C LEU A2180 " pdb=" N PRO A2181 " pdb=" CA PRO A2181 " ideal model delta harmonic sigma weight residual -180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 9539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2244 0.071 - 0.142: 190 0.142 - 0.212: 1 0.212 - 0.283: 4 0.283 - 0.354: 2 Chirality restraints: 2441 Sorted by residual: chirality pdb=" C14 CLR A2501 " pdb=" C13 CLR A2501 " pdb=" C15 CLR A2501 " pdb=" C8 CLR A2501 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C5 BMA C 4 " pdb=" C4 BMA C 4 " pdb=" C6 BMA C 4 " pdb=" O5 BMA C 4 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 2438 not shown) Planarity restraints: 2663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 783 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO A 784 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 784 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 784 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 386 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.19e+00 pdb=" N PRO A 387 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 387 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 387 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 759 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO A 760 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " -0.023 5.00e-02 4.00e+02 ... (remaining 2660 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 199 2.66 - 3.22: 14690 3.22 - 3.78: 24394 3.78 - 4.34: 32717 4.34 - 4.90: 52874 Nonbonded interactions: 124874 Sorted by model distance: nonbonded pdb=" O2B ATP A2503 " pdb="MG MG A2504 " model vdw 2.101 2.170 nonbonded pdb=" OG SER A1953 " pdb="MG MG A2504 " model vdw 2.149 2.170 nonbonded pdb=" O2G ATP A2503 " pdb="MG MG A2504 " model vdw 2.204 2.170 nonbonded pdb=" OE1 GLN A1993 " pdb="MG MG A2504 " model vdw 2.209 2.170 nonbonded pdb=" OD1 ASN A 820 " pdb=" OG1 THR A 822 " model vdw 2.254 2.440 ... (remaining 124869 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 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: 7.630 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 46.140 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 0.083 15690 Z= 0.193 Angle : 0.625 19.392 21301 Z= 0.393 Chirality : 0.041 0.354 2441 Planarity : 0.003 0.066 2659 Dihedral : 14.879 117.319 5918 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.23 % Allowed : 7.24 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.18), residues: 1898 helix: -0.18 (0.15), residues: 1070 sheet: -1.14 (0.40), residues: 154 loop : -3.31 (0.20), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1334 HIS 0.002 0.000 HIS A1626 PHE 0.009 0.001 PHE A1663 TYR 0.006 0.001 TYR A1698 ARG 0.002 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 334 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 ASP cc_start: 0.7278 (p0) cc_final: 0.6916 (p0) REVERT: A 601 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6701 (mm-30) REVERT: A 815 GLU cc_start: 0.5963 (mm-30) cc_final: 0.5509 (mm-30) REVERT: A 827 MET cc_start: 0.7791 (tpp) cc_final: 0.7489 (tpt) REVERT: A 831 ASP cc_start: 0.6880 (m-30) cc_final: 0.6565 (m-30) REVERT: A 984 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7622 (pp) REVERT: A 1430 GLN cc_start: 0.6846 (mp10) cc_final: 0.6071 (tm-30) REVERT: A 1720 ILE cc_start: 0.7638 (mt) cc_final: 0.7131 (mt) REVERT: A 1799 ILE cc_start: 0.5837 (mp) cc_final: 0.5529 (mt) REVERT: A 1802 ILE cc_start: 0.7494 (mp) cc_final: 0.7245 (mt) REVERT: A 1861 VAL cc_start: 0.8118 (t) cc_final: 0.7869 (t) REVERT: A 2180 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.5640 (mm) outliers start: 20 outliers final: 11 residues processed: 351 average time/residue: 0.3120 time to fit residues: 155.3203 Evaluate side-chains 216 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 203 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2110 LEU Chi-restraints excluded: chain A residue 2180 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 7.9990 chunk 145 optimal weight: 0.0170 chunk 80 optimal weight: 0.2980 chunk 49 optimal weight: 0.5980 chunk 98 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 302 GLN A 356 ASN A 508 ASN A 551 HIS A 621 GLN A 732 GLN A 744 ASN ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 GLN A 980 GLN A1038 GLN A1185 ASN A1326 GLN A1393 ASN A1610 ASN ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1678 GLN A1702 ASN A1871 GLN A1948 ASN A2049 ASN A2172 HIS A2177 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15690 Z= 0.153 Angle : 0.561 10.047 21301 Z= 0.260 Chirality : 0.041 0.235 2441 Planarity : 0.004 0.088 2659 Dihedral : 10.714 92.675 2398 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.39 % Allowed : 11.42 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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: -0.85 (0.19), residues: 1898 helix: 0.79 (0.16), residues: 1086 sheet: -0.77 (0.40), residues: 160 loop : -2.93 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 278 HIS 0.005 0.001 HIS A 551 PHE 0.018 0.001 PHE A1786 TYR 0.014 0.001 TYR A 115 ARG 0.006 0.000 ARG A2030 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 220 time to evaluate : 1.813 Fit side-chains revert: symmetry clash REVERT: A 575 ASP cc_start: 0.7281 (p0) cc_final: 0.6961 (p0) REVERT: A 601 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6699 (mm-30) REVERT: A 640 MET cc_start: 0.8127 (tpp) cc_final: 0.7690 (tpp) REVERT: A 815 GLU cc_start: 0.6220 (mm-30) cc_final: 0.5971 (mm-30) REVERT: A 984 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7705 (pp) REVERT: A 1078 TYR cc_start: 0.8610 (m-10) cc_final: 0.8206 (m-10) REVERT: A 1126 TYR cc_start: 0.6685 (m-80) cc_final: 0.6445 (m-80) REVERT: A 1190 HIS cc_start: 0.5297 (m-70) cc_final: 0.4353 (m170) REVERT: A 1245 GLU cc_start: 0.7857 (tt0) cc_final: 0.7626 (tt0) REVERT: A 1430 GLN cc_start: 0.6818 (mp10) cc_final: 0.6010 (tm-30) REVERT: A 1802 ILE cc_start: 0.7445 (mp) cc_final: 0.7187 (mt) REVERT: A 1813 PHE cc_start: 0.7946 (t80) cc_final: 0.7671 (t80) REVERT: A 2000 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8235 (mt) outliers start: 39 outliers final: 22 residues processed: 250 average time/residue: 0.2896 time to fit residues: 107.1416 Evaluate side-chains 217 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 193 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1798 ASN Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1833 GLU Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2110 LEU Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2180 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 118 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 188 optimal weight: 0.4980 chunk 155 optimal weight: 0.7980 chunk 173 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 140 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1595 ASN ** A1600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1688 GLN A1800 ASN A1986 GLN A2179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15690 Z= 0.163 Angle : 0.565 11.037 21301 Z= 0.266 Chirality : 0.041 0.198 2441 Planarity : 0.004 0.090 2659 Dihedral : 8.526 82.748 2392 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.89 % Allowed : 12.83 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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: -0.27 (0.20), residues: 1898 helix: 1.23 (0.16), residues: 1083 sheet: -0.55 (0.40), residues: 169 loop : -2.61 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 484 HIS 0.003 0.001 HIS A1223 PHE 0.012 0.001 PHE A 36 TYR 0.020 0.001 TYR A1698 ARG 0.010 0.000 ARG A2030 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 203 time to evaluate : 1.784 Fit side-chains revert: symmetry clash REVERT: A 302 GLN cc_start: 0.7145 (tp40) cc_final: 0.6897 (mp10) REVERT: A 358 LEU cc_start: 0.8409 (tt) cc_final: 0.8096 (mt) REVERT: A 438 MET cc_start: 0.7609 (ttm) cc_final: 0.6864 (tmm) REVERT: A 601 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6680 (mm-30) REVERT: A 640 MET cc_start: 0.8288 (tpt) cc_final: 0.7813 (tpp) REVERT: A 815 GLU cc_start: 0.6160 (mm-30) cc_final: 0.5893 (mm-30) REVERT: A 984 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7858 (pp) REVERT: A 1078 TYR cc_start: 0.8635 (m-10) cc_final: 0.8230 (m-10) REVERT: A 1126 TYR cc_start: 0.6804 (m-80) cc_final: 0.6568 (m-80) REVERT: A 1430 GLN cc_start: 0.6881 (mp10) cc_final: 0.5956 (tm-30) REVERT: A 1720 ILE cc_start: 0.7919 (mt) cc_final: 0.7616 (mt) REVERT: A 1802 ILE cc_start: 0.7535 (mp) cc_final: 0.7207 (mp) REVERT: A 2000 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8624 (mt) REVERT: A 2130 HIS cc_start: 0.7987 (t70) cc_final: 0.7630 (t70) outliers start: 47 outliers final: 33 residues processed: 240 average time/residue: 0.2770 time to fit residues: 100.3298 Evaluate side-chains 219 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1595 ASN Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1798 ASN Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2110 LEU Chi-restraints excluded: chain A residue 2125 LEU Chi-restraints excluded: chain A residue 2139 TYR Chi-restraints excluded: chain A residue 2140 THR Chi-restraints excluded: chain A residue 2167 VAL Chi-restraints excluded: chain A residue 2176 LEU Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2203 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 744 ASN A 935 ASN A 980 GLN A1058 GLN A1393 ASN A1498 GLN ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1600 HIS ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1826 GLN A1986 GLN A2179 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 15690 Z= 0.318 Angle : 0.659 9.066 21301 Z= 0.325 Chirality : 0.045 0.213 2441 Planarity : 0.005 0.108 2659 Dihedral : 8.285 78.662 2392 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.05 % Allowed : 13.93 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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: -0.21 (0.20), residues: 1898 helix: 1.19 (0.16), residues: 1072 sheet: -0.28 (0.40), residues: 168 loop : -2.42 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 484 HIS 0.007 0.001 HIS A2006 PHE 0.031 0.002 PHE A1535 TYR 0.015 0.002 TYR A 924 ARG 0.009 0.001 ARG A1572 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 175 time to evaluate : 1.862 Fit side-chains revert: symmetry clash REVERT: A 302 GLN cc_start: 0.7148 (tp40) cc_final: 0.6888 (mp10) REVERT: A 438 MET cc_start: 0.7546 (ttm) cc_final: 0.6875 (tmm) REVERT: A 518 TRP cc_start: 0.6971 (m100) cc_final: 0.6554 (m-10) REVERT: A 640 MET cc_start: 0.8403 (tpt) cc_final: 0.8142 (tpp) REVERT: A 742 ARG cc_start: 0.5753 (mtt90) cc_final: 0.4927 (mtt90) REVERT: A 815 GLU cc_start: 0.6315 (mm-30) cc_final: 0.6081 (mm-30) REVERT: A 984 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8109 (pp) REVERT: A 1078 TYR cc_start: 0.8736 (m-10) cc_final: 0.8353 (m-10) REVERT: A 1190 HIS cc_start: 0.5326 (m-70) cc_final: 0.4395 (m170) REVERT: A 1402 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8541 (tt) REVERT: A 1427 THR cc_start: 0.7491 (OUTLIER) cc_final: 0.7264 (m) REVERT: A 1802 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7386 (mt) outliers start: 66 outliers final: 43 residues processed: 225 average time/residue: 0.2801 time to fit residues: 95.7245 Evaluate side-chains 206 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 159 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1798 ASN Chi-restraints excluded: chain A residue 1802 ILE Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1833 GLU Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1903 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2110 LEU Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2139 TYR Chi-restraints excluded: chain A residue 2167 VAL Chi-restraints excluded: chain A residue 2176 LEU Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2203 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1498 GLN A1610 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1780 ASN ** A1800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1986 GLN A2179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15690 Z= 0.228 Angle : 0.593 8.954 21301 Z= 0.291 Chirality : 0.042 0.180 2441 Planarity : 0.004 0.099 2659 Dihedral : 8.126 84.008 2392 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.38 % Allowed : 14.73 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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: -0.09 (0.20), residues: 1898 helix: 1.27 (0.16), residues: 1079 sheet: -0.30 (0.40), residues: 162 loop : -2.32 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 484 HIS 0.005 0.001 HIS A 551 PHE 0.021 0.001 PHE A 36 TYR 0.016 0.001 TYR A 115 ARG 0.005 0.000 ARG A1344 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 167 time to evaluate : 1.726 Fit side-chains revert: symmetry clash REVERT: A 302 GLN cc_start: 0.7144 (tp40) cc_final: 0.6927 (mp10) REVERT: A 424 TRP cc_start: 0.8440 (t-100) cc_final: 0.8179 (t60) REVERT: A 427 MET cc_start: 0.8543 (tmm) cc_final: 0.8183 (tmm) REVERT: A 438 MET cc_start: 0.7564 (ttm) cc_final: 0.6862 (tmm) REVERT: A 518 TRP cc_start: 0.7091 (m100) cc_final: 0.6632 (m-10) REVERT: A 640 MET cc_start: 0.8377 (tpt) cc_final: 0.8066 (tpp) REVERT: A 742 ARG cc_start: 0.6013 (mtt90) cc_final: 0.4867 (mtt90) REVERT: A 917 ASP cc_start: 0.7610 (m-30) cc_final: 0.7373 (m-30) REVERT: A 984 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8114 (pp) REVERT: A 1078 TYR cc_start: 0.8722 (m-10) cc_final: 0.8448 (m-10) REVERT: A 1190 HIS cc_start: 0.5351 (m-70) cc_final: 0.4476 (m-70) REVERT: A 1430 GLN cc_start: 0.7474 (mp10) cc_final: 0.5902 (tm-30) REVERT: A 1802 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7399 (mt) outliers start: 55 outliers final: 39 residues processed: 210 average time/residue: 0.2596 time to fit residues: 83.3495 Evaluate side-chains 194 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 153 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1498 GLN Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1798 ASN Chi-restraints excluded: chain A residue 1802 ILE Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1833 GLU Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1869 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2125 LEU Chi-restraints excluded: chain A residue 2139 TYR Chi-restraints excluded: chain A residue 2140 THR Chi-restraints excluded: chain A residue 2167 VAL Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2203 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 185 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 97 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1318 GLN ** A1617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1986 GLN A2179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15690 Z= 0.252 Angle : 0.602 9.349 21301 Z= 0.295 Chirality : 0.043 0.183 2441 Planarity : 0.004 0.096 2659 Dihedral : 8.087 85.667 2388 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.56 % Allowed : 15.65 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.11 % 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: 0.01 (0.20), residues: 1898 helix: 1.36 (0.16), residues: 1070 sheet: -0.46 (0.39), residues: 172 loop : -2.21 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 484 HIS 0.005 0.001 HIS A1634 PHE 0.023 0.001 PHE A 36 TYR 0.014 0.001 TYR A1388 ARG 0.007 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 154 time to evaluate : 1.932 Fit side-chains revert: symmetry clash REVERT: A 302 GLN cc_start: 0.7223 (tp40) cc_final: 0.7001 (mp10) REVERT: A 424 TRP cc_start: 0.8476 (t-100) cc_final: 0.8213 (t60) REVERT: A 427 MET cc_start: 0.8595 (tmm) cc_final: 0.8387 (tmm) REVERT: A 438 MET cc_start: 0.7579 (ttm) cc_final: 0.6880 (tmm) REVERT: A 518 TRP cc_start: 0.7233 (m100) cc_final: 0.6710 (m-10) REVERT: A 640 MET cc_start: 0.8414 (tpt) cc_final: 0.8085 (tpp) REVERT: A 742 ARG cc_start: 0.6113 (OUTLIER) cc_final: 0.4696 (mtt90) REVERT: A 917 ASP cc_start: 0.7633 (m-30) cc_final: 0.7427 (m-30) REVERT: A 984 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8167 (pp) REVERT: A 1078 TYR cc_start: 0.8737 (m-10) cc_final: 0.8459 (m-10) REVERT: A 1190 HIS cc_start: 0.5373 (m-70) cc_final: 0.4478 (m-70) REVERT: A 1802 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7443 (mt) REVERT: A 2057 MET cc_start: 0.9143 (mtm) cc_final: 0.8872 (mtm) outliers start: 58 outliers final: 43 residues processed: 199 average time/residue: 0.2642 time to fit residues: 80.9278 Evaluate side-chains 197 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 151 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 742 ARG Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1798 ASN Chi-restraints excluded: chain A residue 1802 ILE Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1869 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2140 THR Chi-restraints excluded: chain A residue 2167 VAL Chi-restraints excluded: chain A residue 2176 LEU Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2203 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 105 optimal weight: 0.0980 chunk 135 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1986 GLN A2179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15690 Z= 0.176 Angle : 0.575 10.642 21301 Z= 0.279 Chirality : 0.041 0.173 2441 Planarity : 0.004 0.091 2659 Dihedral : 7.770 87.181 2386 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.56 % Allowed : 15.59 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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: 0.11 (0.20), residues: 1898 helix: 1.45 (0.16), residues: 1071 sheet: -0.43 (0.38), residues: 174 loop : -2.21 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 484 HIS 0.003 0.001 HIS A 551 PHE 0.018 0.001 PHE A1971 TYR 0.013 0.001 TYR A1698 ARG 0.006 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 161 time to evaluate : 1.867 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8207 (mt) cc_final: 0.7686 (mt) REVERT: A 302 GLN cc_start: 0.7152 (tp40) cc_final: 0.6921 (mp10) REVERT: A 424 TRP cc_start: 0.8483 (t-100) cc_final: 0.8259 (t60) REVERT: A 438 MET cc_start: 0.7577 (ttm) cc_final: 0.6865 (tmm) REVERT: A 518 TRP cc_start: 0.7275 (m100) cc_final: 0.6734 (m-10) REVERT: A 640 MET cc_start: 0.8414 (tpt) cc_final: 0.8083 (tpp) REVERT: A 742 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.4858 (mtt90) REVERT: A 984 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8069 (pp) REVERT: A 1078 TYR cc_start: 0.8734 (m-10) cc_final: 0.8499 (m-10) REVERT: A 1190 HIS cc_start: 0.5387 (m-70) cc_final: 0.4512 (m-70) REVERT: A 1430 GLN cc_start: 0.7492 (mp10) cc_final: 0.5807 (tm-30) REVERT: A 1477 CYS cc_start: 0.2919 (OUTLIER) cc_final: 0.2305 (t) REVERT: A 1802 ILE cc_start: 0.7655 (mp) cc_final: 0.7429 (mt) REVERT: A 1865 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8693 (mt) outliers start: 58 outliers final: 34 residues processed: 205 average time/residue: 0.2701 time to fit residues: 85.0697 Evaluate side-chains 189 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 151 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 742 ARG Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1477 CYS Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1798 ASN Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1869 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2125 LEU Chi-restraints excluded: chain A residue 2167 VAL Chi-restraints excluded: chain A residue 2176 LEU Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2203 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 55 optimal weight: 0.0980 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 126 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 chunk 168 optimal weight: 0.4980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1633 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1986 GLN A2179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15690 Z= 0.169 Angle : 0.584 10.885 21301 Z= 0.282 Chirality : 0.041 0.171 2441 Planarity : 0.004 0.090 2659 Dihedral : 7.713 89.587 2385 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.07 % Allowed : 16.33 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.05 % 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: 0.21 (0.20), residues: 1898 helix: 1.52 (0.16), residues: 1070 sheet: -0.31 (0.39), residues: 165 loop : -2.13 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 590 HIS 0.004 0.000 HIS A 551 PHE 0.015 0.001 PHE A 36 TYR 0.014 0.001 TYR A 115 ARG 0.005 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 154 time to evaluate : 1.855 Fit side-chains revert: symmetry clash REVERT: A 302 GLN cc_start: 0.7184 (tp40) cc_final: 0.6970 (mp10) REVERT: A 424 TRP cc_start: 0.8457 (t-100) cc_final: 0.8155 (t60) REVERT: A 438 MET cc_start: 0.7575 (ttm) cc_final: 0.6870 (tmm) REVERT: A 518 TRP cc_start: 0.7266 (m100) cc_final: 0.6722 (m-10) REVERT: A 640 MET cc_start: 0.8403 (tpt) cc_final: 0.8065 (tpp) REVERT: A 742 ARG cc_start: 0.6421 (OUTLIER) cc_final: 0.4995 (mtt90) REVERT: A 984 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8065 (pp) REVERT: A 1078 TYR cc_start: 0.8733 (m-10) cc_final: 0.8529 (m-10) REVERT: A 1190 HIS cc_start: 0.5360 (m-70) cc_final: 0.4485 (m-70) REVERT: A 1246 GLU cc_start: 0.7560 (pm20) cc_final: 0.7334 (pm20) REVERT: A 1383 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8499 (ptp) REVERT: A 1430 GLN cc_start: 0.7505 (mp10) cc_final: 0.5886 (tm-30) REVERT: A 1477 CYS cc_start: 0.3024 (OUTLIER) cc_final: 0.2404 (t) REVERT: A 1802 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7398 (mt) REVERT: A 1865 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8616 (mt) outliers start: 50 outliers final: 35 residues processed: 190 average time/residue: 0.2760 time to fit residues: 79.5841 Evaluate side-chains 191 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 150 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 742 ARG Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1383 MET Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1477 CYS Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1798 ASN Chi-restraints excluded: chain A residue 1802 ILE Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1988 MET Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2125 LEU Chi-restraints excluded: chain A residue 2140 THR Chi-restraints excluded: chain A residue 2167 VAL Chi-restraints excluded: chain A residue 2176 LEU Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2203 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 172 optimal weight: 0.0570 chunk 103 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 113 optimal weight: 0.2980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1986 GLN A2179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15690 Z= 0.171 Angle : 0.587 11.399 21301 Z= 0.282 Chirality : 0.041 0.173 2441 Planarity : 0.004 0.089 2659 Dihedral : 7.707 87.768 2385 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.01 % Allowed : 16.39 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.05 % 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: 0.27 (0.20), residues: 1898 helix: 1.55 (0.17), residues: 1070 sheet: -0.21 (0.39), residues: 165 loop : -2.11 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 484 HIS 0.004 0.001 HIS A 551 PHE 0.016 0.001 PHE A 36 TYR 0.013 0.001 TYR A 115 ARG 0.005 0.000 ARG A 530 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 151 time to evaluate : 1.822 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8158 (mt) cc_final: 0.7526 (mt) REVERT: A 302 GLN cc_start: 0.7155 (tp40) cc_final: 0.6937 (mp10) REVERT: A 438 MET cc_start: 0.7549 (ttm) cc_final: 0.6840 (tmm) REVERT: A 518 TRP cc_start: 0.7274 (m100) cc_final: 0.6731 (m-10) REVERT: A 640 MET cc_start: 0.8412 (tpt) cc_final: 0.8067 (tpp) REVERT: A 742 ARG cc_start: 0.6548 (OUTLIER) cc_final: 0.5063 (mtt90) REVERT: A 984 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8050 (pp) REVERT: A 1190 HIS cc_start: 0.5365 (m-70) cc_final: 0.4491 (m-70) REVERT: A 1383 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8496 (ptp) REVERT: A 1430 GLN cc_start: 0.7473 (mp10) cc_final: 0.5908 (tm-30) REVERT: A 1477 CYS cc_start: 0.3162 (OUTLIER) cc_final: 0.2572 (t) REVERT: A 1802 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7424 (mt) REVERT: A 1865 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8583 (mt) outliers start: 49 outliers final: 38 residues processed: 186 average time/residue: 0.2797 time to fit residues: 79.0460 Evaluate side-chains 190 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 146 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 742 ARG Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1101 ILE Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1383 MET Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1477 CYS Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1802 ILE Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1988 MET Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2125 LEU Chi-restraints excluded: chain A residue 2140 THR Chi-restraints excluded: chain A residue 2167 VAL Chi-restraints excluded: chain A residue 2176 LEU Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2203 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.2980 chunk 111 optimal weight: 0.7980 chunk 86 optimal weight: 0.0570 chunk 126 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 120 optimal weight: 0.0070 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1986 GLN A2179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15690 Z= 0.173 Angle : 0.592 10.032 21301 Z= 0.283 Chirality : 0.041 0.228 2441 Planarity : 0.004 0.089 2659 Dihedral : 7.693 89.589 2385 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.70 % Allowed : 16.57 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.05 % 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: 0.28 (0.20), residues: 1898 helix: 1.55 (0.16), residues: 1071 sheet: -0.18 (0.39), residues: 165 loop : -2.08 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 484 HIS 0.005 0.000 HIS A 551 PHE 0.015 0.001 PHE A 36 TYR 0.013 0.001 TYR A 115 ARG 0.004 0.000 ARG A 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 155 time to evaluate : 1.766 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8273 (mt) cc_final: 0.7666 (mt) REVERT: A 302 GLN cc_start: 0.7152 (tp40) cc_final: 0.6943 (mp10) REVERT: A 438 MET cc_start: 0.7577 (ttm) cc_final: 0.6851 (tmm) REVERT: A 518 TRP cc_start: 0.7281 (m100) cc_final: 0.6740 (m-10) REVERT: A 640 MET cc_start: 0.8413 (tpt) cc_final: 0.8065 (tpp) REVERT: A 742 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.5066 (mtt90) REVERT: A 984 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8034 (pp) REVERT: A 1190 HIS cc_start: 0.5368 (m-70) cc_final: 0.4500 (m-70) REVERT: A 1383 MET cc_start: 0.8745 (ptm) cc_final: 0.8478 (ptp) REVERT: A 1430 GLN cc_start: 0.7382 (mp10) cc_final: 0.5924 (tm-30) REVERT: A 1477 CYS cc_start: 0.3110 (OUTLIER) cc_final: 0.2494 (t) REVERT: A 1802 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7419 (mt) outliers start: 44 outliers final: 35 residues processed: 186 average time/residue: 0.2755 time to fit residues: 78.0534 Evaluate side-chains 191 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 152 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 742 ARG Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1101 ILE Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1477 CYS Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1802 ILE Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1988 MET Chi-restraints excluded: chain A residue 2125 LEU Chi-restraints excluded: chain A residue 2140 THR Chi-restraints excluded: chain A residue 2167 VAL Chi-restraints excluded: chain A residue 2176 LEU Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2203 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 140 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 19 optimal weight: 0.0870 chunk 28 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1986 GLN A2179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.137760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.099408 restraints weight = 23830.785| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.14 r_work: 0.3091 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15690 Z= 0.160 Angle : 0.585 9.818 21301 Z= 0.279 Chirality : 0.041 0.209 2441 Planarity : 0.004 0.088 2659 Dihedral : 7.600 85.969 2385 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.82 % Allowed : 16.57 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.05 % 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: 0.33 (0.20), residues: 1898 helix: 1.57 (0.17), residues: 1077 sheet: -0.12 (0.39), residues: 165 loop : -2.08 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 484 HIS 0.005 0.000 HIS A 551 PHE 0.013 0.001 PHE A 36 TYR 0.013 0.001 TYR A 115 ARG 0.004 0.000 ARG A 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3550.99 seconds wall clock time: 65 minutes 21.49 seconds (3921.49 seconds total)