Starting phenix.real_space_refine on Sat Mar 16 01:02:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbz_25802/03_2024/7tbz_25802_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbz_25802/03_2024/7tbz_25802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbz_25802/03_2024/7tbz_25802.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbz_25802/03_2024/7tbz_25802.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbz_25802/03_2024/7tbz_25802_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbz_25802/03_2024/7tbz_25802_updated.pdb" } resolution = 4.3 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 8585 2.51 5 N 2233 2.21 5 O 2387 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 8": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 629": "OD1" <-> "OD2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 664": "OE1" <-> "OE2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 799": "OE1" <-> "OE2" Residue "A GLU 843": "OE1" <-> "OE2" Residue "A GLU 992": "OE1" <-> "OE2" Residue "A ASP 1057": "OD1" <-> "OD2" Residue "A ARG 1069": "NH1" <-> "NH2" Residue "A ARG 1082": "NH1" <-> "NH2" Residue "A ASP 1095": "OD1" <-> "OD2" Residue "A ARG 1100": "NH1" <-> "NH2" Residue "A PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1246": "OE1" <-> "OE2" Residue "A PHE 1248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1336": "NH1" <-> "NH2" Residue "A PHE 1348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1420": "OE1" <-> "OE2" Residue "A ASP 1468": "OD1" <-> "OD2" Residue "A ARG 1503": "NH1" <-> "NH2" Residue "A TYR 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1645": "OE1" <-> "OE2" Residue "A ASP 1654": "OD1" <-> "OD2" Residue "A ARG 1680": "NH1" <-> "NH2" Residue "A PHE 1689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1706": "OD1" <-> "OD2" Residue "A PHE 1721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1830": "OD1" <-> "OD2" Residue "A GLU 1833": "OE1" <-> "OE2" Residue "A TYR 1872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2004": "NH1" <-> "NH2" Residue "A ARG 2051": "NH1" <-> "NH2" Residue "A ASP 2069": "OD1" <-> "OD2" Residue "A ARG 2081": "NH1" <-> "NH2" Residue "A ARG 2095": "NH1" <-> "NH2" Residue "A GLU 2106": "OE1" <-> "OE2" Residue "A ARG 2113": "NH1" <-> "NH2" Residue "A PHE 2217": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13275 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1788, 13130 Classifications: {'peptide': 1788} Incomplete info: {'truncation_to_alanine': 343} Link IDs: {'PTRANS': 87, 'TRANS': 1700} Chain breaks: 15 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1118 Unresolved non-hydrogen angles: 1399 Unresolved non-hydrogen dihedrals: 901 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 19, 'ASP:plan': 22, 'TYR:plan': 3, 'ASN:plan1': 13, 'HIS:plan': 12, 'PHE:plan': 9, 'GLU:plan': 29, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 517 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'CLR': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.10, per 1000 atoms: 0.53 Number of scatterers: 13275 At special positions: 0 Unit cell: (81.674, 100.198, 215.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2387 8.00 N 2233 7.00 C 8585 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=2.04 Simple disulfide: pdb=" SG CYS A1418 " - pdb=" SG CYS A1429 " distance=2.03 Simple disulfide: pdb=" SG CYS A1463 " - pdb=" SG CYS A1477 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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 A2601 " - " ASN A1637 " " NAG A2602 " - " ASN A 98 " " NAG B 1 " - " ASN A 400 " " NAG C 1 " - " ASN A1504 " Time building additional restraints: 5.24 Conformation dependent library (CDL) restraints added in 2.7 seconds 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3346 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 9 sheets defined 52.2% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'A' and resid 4 through 21 removed outlier: 3.676A pdb=" N GLN A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 44 Proline residue: A 32 - end of helix 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 74 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 116 Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 253 through 272 Processing helix chain 'A' and resid 278 through 288 Processing helix chain 'A' and resid 297 through 308 Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 353 through 364 Processing helix chain 'A' and resid 371 through 379 Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 390 through 409 removed outlier: 5.123A pdb=" N LEU A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ALA A 407 " --> pdb=" O PHE A 403 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 Proline residue: A 421 - end of helix 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 503 Processing helix chain 'A' and resid 517 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 638 Processing helix chain 'A' and resid 640 through 664 removed outlier: 4.775A pdb=" N ALA A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N TRP A 648 " --> pdb=" O MET A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 673 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: 4.175A pdb=" N THR A 738 " --> pdb=" O PHE A 734 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 764 removed outlier: 4.704A pdb=" N GLY A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Proline residue: A 760 - end of helix Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 773 through 779 Processing helix chain 'A' and resid 783 through 798 Processing helix chain 'A' and resid 821 through 845 removed outlier: 3.994A pdb=" N ALA A 844 " --> pdb=" O TRP A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 946 Processing helix chain 'A' and resid 972 through 974 No H-bonds generated for 'chain 'A' and resid 972 through 974' Processing helix chain 'A' and resid 990 through 1001 Processing helix chain 'A' and resid 1005 through 1019 Processing helix chain 'A' and resid 1024 through 1027 No H-bonds generated for 'chain 'A' and resid 1024 through 1027' Processing helix chain 'A' and resid 1035 through 1047 removed outlier: 3.890A pdb=" N ALA A1046 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE A1047 " --> pdb=" O VAL A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1078 removed outlier: 3.509A pdb=" N TYR A1078 " --> pdb=" O LEU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1097 Processing helix chain 'A' and resid 1115 through 1121 Processing helix chain 'A' and resid 1181 through 1190 Processing helix chain 'A' and resid 1217 through 1227 Processing helix chain 'A' and resid 1244 through 1251 Processing helix chain 'A' and resid 1323 through 1341 Processing helix chain 'A' and resid 1349 through 1365 Proline residue: A1354 - end of helix Processing helix chain 'A' and resid 1381 through 1383 No H-bonds generated for 'chain 'A' and resid 1381 through 1383' Processing helix chain 'A' and resid 1402 through 1409 Processing helix chain 'A' and resid 1445 through 1450 Processing helix chain 'A' and resid 1505 through 1523 removed outlier: 3.940A pdb=" N ASN A1523 " --> pdb=" O LYS A1519 " (cutoff:3.500A) Processing helix chain 'A' and resid 1549 through 1560 Processing helix chain 'A' and resid 1571 through 1581 Processing helix chain 'A' and resid 1602 through 1617 Processing helix chain 'A' and resid 1640 through 1678 removed outlier: 3.533A pdb=" N THR A1650 " --> pdb=" O VAL A1646 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR A1651 " --> pdb=" O ALA A1647 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N SER A1652 " --> pdb=" O LEU A1648 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL A1653 " --> pdb=" O MET A1649 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A1654 " --> pdb=" O THR A1650 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N CYS A1660 " --> pdb=" O LEU A1656 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A1661 " --> pdb=" O VAL A1657 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE A1667 " --> pdb=" O PHE A1663 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL A1668 " --> pdb=" O ALA A1664 " (cutoff:3.500A) Proline residue: A1669 - end of helix removed outlier: 3.903A pdb=" N PHE A1672 " --> pdb=" O VAL A1668 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1690 Processing helix chain 'A' and resid 1695 through 1723 removed outlier: 4.158A pdb=" N VAL A1712 " --> pdb=" O CYS A1708 " (cutoff:3.500A) Proline residue: A1713 - end of helix Processing helix chain 'A' and resid 1727 through 1730 No H-bonds generated for 'chain 'A' and resid 1727 through 1730' Processing helix chain 'A' and resid 1735 through 1749 Processing helix chain 'A' and resid 1755 through 1757 No H-bonds generated for 'chain 'A' and resid 1755 through 1757' Processing helix chain 'A' and resid 1766 through 1785 removed outlier: 3.807A pdb=" N THR A1785 " --> pdb=" O GLY A1781 " (cutoff:3.500A) Processing helix chain 'A' and resid 1800 through 1809 removed outlier: 4.145A pdb=" N LEU A1808 " --> pdb=" O LYS A1804 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE A1809 " --> pdb=" O SER A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1811 through 1835 Processing helix chain 'A' and resid 1851 through 1872 removed outlier: 3.651A pdb=" N GLN A1871 " --> pdb=" O THR A1867 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A1872 " --> pdb=" O VAL A1868 " (cutoff:3.500A) Processing helix chain 'A' and resid 1952 through 1959 Processing helix chain 'A' and resid 2003 through 2014 Processing helix chain 'A' and resid 2021 through 2031 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 2059 removed outlier: 3.760A pdb=" N LEU A2059 " --> pdb=" O THR A2055 " (cutoff:3.500A) Processing helix chain 'A' and resid 2080 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 2200 removed outlier: 4.487A pdb=" N LYS A2199 " --> pdb=" O SER A2195 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG A2200 " --> pdb=" O GLN A2196 " (cutoff:3.500A) Processing helix chain 'A' and resid 2213 through 2222 Processing sheet with id= A, first strand: chain 'A' and resid 383 through 385 removed outlier: 3.543A pdb=" N TYR A 385 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 535 through 537 removed outlier: 6.967A pdb=" N GLY A1628 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N TYR A 554 " --> pdb=" O GLY A1628 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR A1630 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE A 556 " --> pdb=" O THR A1630 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N PHE A1632 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ALA A1631 " --> pdb=" O LEU A1379 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 616 through 621 removed outlier: 4.602A pdb=" N GLY A1533 " --> pdb=" O TYR A1388 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE A1390 " --> pdb=" O GLY A1533 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A1496 " --> pdb=" O THR A1389 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL A1391 " --> pdb=" O ILE A1496 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLN A1498 " --> pdb=" O VAL A1391 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ASN A1393 " --> pdb=" O GLN A1498 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 956 through 959 removed outlier: 3.636A pdb=" N TYR A 958 " --> pdb=" O SER A 900 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 900 " --> pdb=" O TYR A 958 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE A 923 " --> pdb=" O GLY A 898 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1236 through 1240 removed outlier: 3.685A pdb=" N SER A1236 " --> pdb=" O VAL A1131 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A1207 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A1196 " --> pdb=" O VAL A1207 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1944 through 1946 removed outlier: 6.010A pdb=" N ALA A2115 " --> pdb=" O LEU A1945 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1988 through 1990 removed outlier: 7.543A pdb=" N VAL A2065 " --> pdb=" O GLY A1989 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 2205 through 2209 removed outlier: 3.745A pdb=" N GLN A2177 " --> pdb=" O GLU A2170 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU A2170 " --> pdb=" O GLN A2177 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N GLN A2179 " --> pdb=" O LEU A2168 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU A2168 " --> pdb=" O GLN A2179 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1101 through 1105 removed outlier: 5.954A pdb=" N SER A1105 " --> pdb=" O LEU A1109 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU A1109 " --> pdb=" O SER A1105 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1917 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: 5.44 Time building geometry restraints manager: 5.73 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: 4241 1.34 - 1.46: 3198 1.46 - 1.58: 6028 1.58 - 1.70: 0 1.70 - 1.81: 111 Bond restraints: 13578 Sorted by residual: bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C THR A 386 " pdb=" N PRO A 387 " ideal model delta sigma weight residual 1.331 1.360 -0.028 1.21e-02 6.83e+03 5.50e+00 bond pdb=" C1 NAG A2602 " pdb=" O5 NAG A2602 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.43e+00 ... (remaining 13573 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.43: 395 106.43 - 113.33: 7403 113.33 - 120.22: 4770 120.22 - 127.12: 5789 127.12 - 134.01: 161 Bond angle restraints: 18518 Sorted by residual: angle pdb=" N VAL A 380 " pdb=" CA VAL A 380 " pdb=" C VAL A 380 " ideal model delta sigma weight residual 113.53 108.88 4.65 9.80e-01 1.04e+00 2.25e+01 angle pdb=" CA VAL A 380 " pdb=" C VAL A 380 " pdb=" N GLY A 381 " ideal model delta sigma weight residual 119.31 116.53 2.78 1.15e+00 7.56e-01 5.85e+00 angle pdb=" C HIS A 934 " pdb=" N ASN A 935 " pdb=" CA ASN A 935 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.79e+00 angle pdb=" C LYS A 613 " pdb=" N LYS A 614 " pdb=" CA LYS A 614 " ideal model delta sigma weight residual 121.54 125.93 -4.39 1.91e+00 2.74e-01 5.29e+00 angle pdb=" C20 CLR A2603 " pdb=" C22 CLR A2603 " pdb=" C23 CLR A2603 " ideal model delta sigma weight residual 115.57 109.24 6.33 3.00e+00 1.11e-01 4.45e+00 ... (remaining 18513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 7720 23.43 - 46.87: 325 46.87 - 70.30: 33 70.30 - 93.74: 28 93.74 - 117.17: 18 Dihedral angle restraints: 8124 sinusoidal: 2951 harmonic: 5173 Sorted by residual: dihedral pdb=" CB CYS A 626 " pdb=" SG CYS A 626 " pdb=" SG CYS A1465 " pdb=" CB CYS A1465 " ideal model delta sinusoidal sigma weight residual 93.00 175.96 -82.96 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 81 " pdb=" CB CYS A 81 " ideal model delta sinusoidal sigma weight residual 93.00 22.31 70.69 1 1.00e+01 1.00e-02 6.43e+01 dihedral pdb=" CA PRO A 625 " pdb=" C PRO A 625 " pdb=" N CYS A 626 " pdb=" CA CYS A 626 " ideal model delta harmonic sigma weight residual 180.00 155.95 24.05 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 8121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1966 0.068 - 0.135: 192 0.135 - 0.203: 4 0.203 - 0.271: 2 0.271 - 0.338: 4 Chirality restraints: 2168 Sorted by residual: chirality pdb=" C14 CLR A2603 " pdb=" C13 CLR A2603 " pdb=" C15 CLR A2603 " pdb=" C8 CLR A2603 " both_signs ideal model delta sigma weight residual False -2.32 -2.66 0.34 2.00e-01 2.50e+01 2.86e+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 -2.55 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C5 BMA C 5 " pdb=" C4 BMA C 5 " pdb=" C6 BMA C 5 " pdb=" O5 BMA C 5 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2165 not shown) Planarity restraints: 2347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 759 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.42e+00 pdb=" N PRO A 760 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A2076 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.64e+00 pdb=" N PRO A2077 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A2077 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A2077 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1721 " -0.008 2.00e-02 2.50e+03 8.90e-03 1.39e+00 pdb=" CG PHE A1721 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A1721 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A1721 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A1721 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A1721 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A1721 " -0.000 2.00e-02 2.50e+03 ... (remaining 2344 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1395 2.75 - 3.28: 13558 3.28 - 3.82: 21814 3.82 - 4.36: 23202 4.36 - 4.90: 40150 Nonbonded interactions: 100119 Sorted by model distance: nonbonded pdb=" OD2 ASP A1706 " pdb=" OH TYR A1754 " model vdw 2.207 2.440 nonbonded pdb=" OG1 THR A1493 " pdb=" OD1 ASP A1495 " model vdw 2.255 2.440 nonbonded pdb=" OE1 GLU A 925 " pdb=" OG1 THR A1083 " model vdw 2.256 2.440 nonbonded pdb=" NE2 GLN A1464 " pdb=" O VAL A1476 " model vdw 2.267 2.520 nonbonded pdb=" OD2 ASP A1507 " pdb=" O6 NAG C 1 " model vdw 2.287 2.440 ... (remaining 100114 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 7.210 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 38.560 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.002 0.081 13578 Z= 0.170 Angle : 0.564 7.477 18518 Z= 0.281 Chirality : 0.042 0.338 2168 Planarity : 0.003 0.053 2343 Dihedral : 14.926 117.173 4760 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.76 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.18), residues: 1756 helix: -0.64 (0.15), residues: 978 sheet: -1.91 (0.36), residues: 166 loop : -3.44 (0.20), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.000 TRP A1705 HIS 0.001 0.000 HIS A1626 PHE 0.021 0.001 PHE A1721 TYR 0.008 0.001 TYR A 793 ARG 0.003 0.000 ARG A1336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.9676 (tt) cc_final: 0.9475 (pp) REVERT: A 18 ARG cc_start: 0.9263 (mmt90) cc_final: 0.8823 (mmm160) REVERT: A 112 LEU cc_start: 0.9422 (tt) cc_final: 0.8996 (mp) REVERT: A 286 MET cc_start: 0.9409 (ptp) cc_final: 0.9029 (ptt) REVERT: A 396 MET cc_start: 0.9570 (mmm) cc_final: 0.9341 (mmm) REVERT: A 605 ILE cc_start: 0.9628 (mm) cc_final: 0.9319 (tp) REVERT: A 622 MET cc_start: 0.8335 (mtt) cc_final: 0.7739 (mtt) REVERT: A 640 MET cc_start: 0.9173 (tpp) cc_final: 0.8835 (tpp) REVERT: A 683 PHE cc_start: 0.8936 (t80) cc_final: 0.8596 (m-10) REVERT: A 724 VAL cc_start: 0.8793 (m) cc_final: 0.8559 (p) REVERT: A 735 LEU cc_start: 0.8767 (tp) cc_final: 0.8495 (tp) REVERT: A 827 MET cc_start: 0.8625 (tpt) cc_final: 0.8355 (tpp) REVERT: A 839 THR cc_start: 0.7987 (m) cc_final: 0.7733 (m) REVERT: A 921 LEU cc_start: 0.9354 (tt) cc_final: 0.8924 (mm) REVERT: A 927 GLN cc_start: 0.9132 (mt0) cc_final: 0.8902 (mp10) REVERT: A 1037 MET cc_start: 0.9419 (mmm) cc_final: 0.9190 (mpp) REVERT: A 1086 LEU cc_start: 0.9257 (mt) cc_final: 0.8958 (tt) REVERT: A 1333 LEU cc_start: 0.9326 (mp) cc_final: 0.9125 (mp) REVERT: A 1610 ASN cc_start: 0.9327 (m-40) cc_final: 0.8977 (m-40) REVERT: A 1662 ILE cc_start: 0.9148 (mt) cc_final: 0.8883 (mt) REVERT: A 1665 MET cc_start: 0.9570 (tpp) cc_final: 0.9299 (tpp) REVERT: A 1707 MET cc_start: 0.9428 (mmm) cc_final: 0.9142 (mmp) REVERT: A 1710 TYR cc_start: 0.9025 (t80) cc_final: 0.8589 (t80) REVERT: A 1776 PHE cc_start: 0.9164 (t80) cc_final: 0.8823 (m-10) REVERT: A 1822 MET cc_start: 0.9319 (ttt) cc_final: 0.8876 (tmm) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2606 time to fit residues: 101.2904 Evaluate side-chains 155 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 9.9990 chunk 134 optimal weight: 0.6980 chunk 74 optimal weight: 30.0000 chunk 46 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 0.0980 chunk 139 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 161 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 52 HIS A 79 ASN A 551 HIS A 621 GLN A 820 ASN A1327 GLN A1385 ASN A1422 ASN A1443 GLN A1515 GLN A1617 ASN ** A1688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1812 HIS ** A1825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2049 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13578 Z= 0.168 Angle : 0.568 9.819 18518 Z= 0.269 Chirality : 0.041 0.191 2168 Planarity : 0.003 0.058 2343 Dihedral : 9.968 91.502 2137 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.08 % Allowed : 5.70 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.20), residues: 1756 helix: 0.67 (0.17), residues: 978 sheet: -1.48 (0.39), residues: 164 loop : -2.96 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1705 HIS 0.002 0.001 HIS A 551 PHE 0.027 0.001 PHE A 403 TYR 0.012 0.001 TYR A1754 ARG 0.006 0.000 ARG A 530 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.9302 (mmt90) cc_final: 0.8812 (mmm160) REVERT: A 112 LEU cc_start: 0.9464 (tt) cc_final: 0.9064 (mp) REVERT: A 275 MET cc_start: 0.7263 (ppp) cc_final: 0.5613 (ppp) REVERT: A 286 MET cc_start: 0.9457 (ptp) cc_final: 0.8892 (ptt) REVERT: A 396 MET cc_start: 0.9565 (mmm) cc_final: 0.9353 (mmm) REVERT: A 622 MET cc_start: 0.8562 (mtt) cc_final: 0.7986 (mtt) REVERT: A 644 MET cc_start: 0.9031 (tpt) cc_final: 0.8748 (tmm) REVERT: A 683 PHE cc_start: 0.9020 (t80) cc_final: 0.8653 (m-10) REVERT: A 694 LEU cc_start: 0.9063 (mm) cc_final: 0.8848 (mm) REVERT: A 724 VAL cc_start: 0.8794 (m) cc_final: 0.8436 (p) REVERT: A 735 LEU cc_start: 0.8930 (tp) cc_final: 0.8669 (tp) REVERT: A 828 MET cc_start: 0.8754 (ttm) cc_final: 0.8388 (ttm) REVERT: A 839 THR cc_start: 0.8051 (m) cc_final: 0.7848 (m) REVERT: A 927 GLN cc_start: 0.9201 (mt0) cc_final: 0.8920 (mp10) REVERT: A 987 MET cc_start: 0.8713 (mpp) cc_final: 0.8351 (mpp) REVERT: A 1074 LEU cc_start: 0.9714 (tp) cc_final: 0.9513 (mm) REVERT: A 1086 LEU cc_start: 0.9298 (mt) cc_final: 0.9043 (tt) REVERT: A 1473 MET cc_start: 0.9036 (tmm) cc_final: 0.8823 (tmm) REVERT: A 1662 ILE cc_start: 0.9151 (mt) cc_final: 0.8674 (mt) REVERT: A 1665 MET cc_start: 0.9594 (tpp) cc_final: 0.9322 (tpp) REVERT: A 1707 MET cc_start: 0.9489 (mmm) cc_final: 0.9126 (mmp) REVERT: A 1708 CYS cc_start: 0.9427 (m) cc_final: 0.9076 (p) REVERT: A 1710 TYR cc_start: 0.9070 (t80) cc_final: 0.8807 (t80) REVERT: A 1822 MET cc_start: 0.9328 (ttt) cc_final: 0.8878 (tmm) REVERT: A 2057 MET cc_start: 0.9237 (mmt) cc_final: 0.8783 (mmt) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.1914 time to fit residues: 56.9481 Evaluate side-chains 141 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 161 optimal weight: 0.4980 chunk 174 optimal weight: 20.0000 chunk 144 optimal weight: 4.9990 chunk 160 optimal weight: 30.0000 chunk 55 optimal weight: 0.9990 chunk 129 optimal weight: 0.3980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1498 GLN ** A1515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1600 HIS A1610 ASN ** A1642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1688 GLN ** A1825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13578 Z= 0.154 Angle : 0.569 11.081 18518 Z= 0.267 Chirality : 0.041 0.183 2168 Planarity : 0.003 0.059 2343 Dihedral : 7.975 76.451 2137 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1756 helix: 1.15 (0.17), residues: 976 sheet: -1.40 (0.40), residues: 166 loop : -2.66 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 533 HIS 0.001 0.000 HIS A1600 PHE 0.024 0.001 PHE A 683 TYR 0.008 0.001 TYR A 997 ARG 0.007 0.000 ARG A 530 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.9331 (mmt90) cc_final: 0.9072 (tpm170) REVERT: A 112 LEU cc_start: 0.9491 (tt) cc_final: 0.9057 (mp) REVERT: A 275 MET cc_start: 0.7347 (ppp) cc_final: 0.6968 (ppp) REVERT: A 286 MET cc_start: 0.9452 (ptp) cc_final: 0.9104 (ptt) REVERT: A 396 MET cc_start: 0.9492 (mmm) cc_final: 0.9157 (mmm) REVERT: A 524 MET cc_start: 0.9413 (mmt) cc_final: 0.9006 (mmm) REVERT: A 622 MET cc_start: 0.8645 (mtt) cc_final: 0.7975 (mtt) REVERT: A 735 LEU cc_start: 0.8962 (tp) cc_final: 0.8694 (tp) REVERT: A 827 MET cc_start: 0.8690 (tpp) cc_final: 0.8384 (tpp) REVERT: A 927 GLN cc_start: 0.9215 (mt0) cc_final: 0.8945 (mp10) REVERT: A 987 MET cc_start: 0.8770 (mpp) cc_final: 0.8401 (mpp) REVERT: A 1074 LEU cc_start: 0.9743 (tp) cc_final: 0.9501 (mm) REVERT: A 1086 LEU cc_start: 0.9284 (mt) cc_final: 0.9021 (tt) REVERT: A 1468 ASP cc_start: 0.8289 (t0) cc_final: 0.7862 (p0) REVERT: A 1473 MET cc_start: 0.9066 (tmm) cc_final: 0.8848 (tmm) REVERT: A 1610 ASN cc_start: 0.9244 (m110) cc_final: 0.8848 (m-40) REVERT: A 1656 LEU cc_start: 0.9174 (tt) cc_final: 0.8926 (pp) REVERT: A 1665 MET cc_start: 0.9608 (tpp) cc_final: 0.9374 (tpp) REVERT: A 1707 MET cc_start: 0.9487 (mmm) cc_final: 0.9142 (mmp) REVERT: A 1710 TYR cc_start: 0.9128 (t80) cc_final: 0.8892 (t80) REVERT: A 1776 PHE cc_start: 0.9142 (t80) cc_final: 0.8828 (m-10) REVERT: A 1822 MET cc_start: 0.9287 (ttt) cc_final: 0.9041 (tmm) REVERT: A 2057 MET cc_start: 0.9277 (mmt) cc_final: 0.8772 (mmt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1909 time to fit residues: 54.6895 Evaluate side-chains 128 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 143 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 744 ASN A1498 GLN ** A1515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1688 GLN ** A1825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13578 Z= 0.207 Angle : 0.579 7.521 18518 Z= 0.286 Chirality : 0.041 0.201 2168 Planarity : 0.003 0.055 2343 Dihedral : 6.127 56.555 2137 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1756 helix: 1.51 (0.17), residues: 992 sheet: -1.35 (0.39), residues: 179 loop : -2.52 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 533 HIS 0.003 0.001 HIS A1812 PHE 0.026 0.002 PHE A 725 TYR 0.012 0.001 TYR A 754 ARG 0.003 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.9373 (mmt90) cc_final: 0.9038 (tpm170) REVERT: A 286 MET cc_start: 0.9465 (ptp) cc_final: 0.8901 (ptt) REVERT: A 396 MET cc_start: 0.9451 (mmm) cc_final: 0.9153 (mmm) REVERT: A 524 MET cc_start: 0.9435 (mmt) cc_final: 0.9032 (mmm) REVERT: A 622 MET cc_start: 0.8958 (mtt) cc_final: 0.8277 (mtt) REVERT: A 644 MET cc_start: 0.8794 (tmm) cc_final: 0.8541 (tmm) REVERT: A 794 PHE cc_start: 0.9211 (t80) cc_final: 0.8908 (t80) REVERT: A 830 PHE cc_start: 0.9141 (t80) cc_final: 0.8773 (m-10) REVERT: A 927 GLN cc_start: 0.9289 (mt0) cc_final: 0.8962 (mp10) REVERT: A 987 MET cc_start: 0.8946 (mpp) cc_final: 0.8586 (mpp) REVERT: A 1329 PHE cc_start: 0.9189 (t80) cc_final: 0.8922 (t80) REVERT: A 1456 MET cc_start: 0.8836 (tpt) cc_final: 0.8477 (tpt) REVERT: A 1473 MET cc_start: 0.9149 (tmm) cc_final: 0.8909 (tmm) REVERT: A 1610 ASN cc_start: 0.9278 (m110) cc_final: 0.8778 (m110) REVERT: A 1656 LEU cc_start: 0.9208 (tt) cc_final: 0.8975 (pp) REVERT: A 1710 TYR cc_start: 0.9245 (t80) cc_final: 0.8819 (t80) REVERT: A 1776 PHE cc_start: 0.9184 (t80) cc_final: 0.8867 (m-10) REVERT: A 1822 MET cc_start: 0.9264 (ttt) cc_final: 0.9015 (tmm) REVERT: A 1856 MET cc_start: 0.8846 (mtp) cc_final: 0.8158 (ttm) REVERT: A 2057 MET cc_start: 0.9352 (mmt) cc_final: 0.8826 (mmt) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1933 time to fit residues: 50.4975 Evaluate side-chains 127 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 6.9990 chunk 2 optimal weight: 0.0060 chunk 128 optimal weight: 0.3980 chunk 70 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 154 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1498 GLN ** A1515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 13578 Z= 0.149 Angle : 0.564 11.764 18518 Z= 0.269 Chirality : 0.040 0.190 2168 Planarity : 0.003 0.055 2343 Dihedral : 5.899 59.216 2137 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.08 % Allowed : 2.85 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.04 (0.21), residues: 1756 helix: 1.61 (0.17), residues: 989 sheet: -1.23 (0.39), residues: 179 loop : -2.40 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 533 HIS 0.003 0.000 HIS A1812 PHE 0.029 0.001 PHE A 755 TYR 0.009 0.001 TYR A1710 ARG 0.006 0.000 ARG A 530 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.9370 (mmt90) cc_final: 0.9013 (tpm170) REVERT: A 112 LEU cc_start: 0.9133 (pp) cc_final: 0.8816 (mt) REVERT: A 286 MET cc_start: 0.9469 (ptp) cc_final: 0.9107 (ptt) REVERT: A 396 MET cc_start: 0.9487 (mmm) cc_final: 0.9049 (mmm) REVERT: A 524 MET cc_start: 0.9414 (mmt) cc_final: 0.8992 (mmm) REVERT: A 622 MET cc_start: 0.8925 (mtt) cc_final: 0.8346 (mtt) REVERT: A 644 MET cc_start: 0.8959 (tmm) cc_final: 0.8575 (tmm) REVERT: A 830 PHE cc_start: 0.9145 (t80) cc_final: 0.8769 (m-10) REVERT: A 927 GLN cc_start: 0.9272 (mt0) cc_final: 0.8977 (mp10) REVERT: A 987 MET cc_start: 0.8935 (mpp) cc_final: 0.8551 (mpp) REVERT: A 1329 PHE cc_start: 0.9185 (t80) cc_final: 0.8908 (t80) REVERT: A 1456 MET cc_start: 0.8854 (tpt) cc_final: 0.8524 (tpt) REVERT: A 1473 MET cc_start: 0.9188 (tmm) cc_final: 0.8872 (ppp) REVERT: A 1610 ASN cc_start: 0.9074 (m110) cc_final: 0.8783 (m-40) REVERT: A 1665 MET cc_start: 0.9387 (tpp) cc_final: 0.8952 (tpp) REVERT: A 1776 PHE cc_start: 0.9179 (t80) cc_final: 0.8875 (m-10) REVERT: A 1822 MET cc_start: 0.9252 (ttt) cc_final: 0.9024 (tmm) REVERT: A 1856 MET cc_start: 0.8828 (mtp) cc_final: 0.8242 (ttm) REVERT: A 2057 MET cc_start: 0.9333 (mmt) cc_final: 0.8804 (mmt) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.1904 time to fit residues: 49.2048 Evaluate side-chains 129 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 42 optimal weight: 8.9990 chunk 172 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 732 GLN A1498 GLN ** A1619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13578 Z= 0.296 Angle : 0.659 7.878 18518 Z= 0.336 Chirality : 0.043 0.274 2168 Planarity : 0.004 0.046 2343 Dihedral : 5.915 58.058 2137 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1756 helix: 1.41 (0.17), residues: 997 sheet: -1.25 (0.43), residues: 156 loop : -2.35 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 533 HIS 0.005 0.001 HIS A1626 PHE 0.019 0.002 PHE A 794 TYR 0.024 0.002 TYR A 754 ARG 0.006 0.001 ARG A1489 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.559 Fit side-chains REVERT: A 61 MET cc_start: 0.9301 (mmm) cc_final: 0.9071 (mmm) REVERT: A 286 MET cc_start: 0.9480 (ptp) cc_final: 0.8942 (ptt) REVERT: A 359 MET cc_start: 0.9609 (ppp) cc_final: 0.9385 (ppp) REVERT: A 396 MET cc_start: 0.9574 (mmm) cc_final: 0.9169 (mmm) REVERT: A 524 MET cc_start: 0.9418 (mmt) cc_final: 0.9196 (mmm) REVERT: A 622 MET cc_start: 0.9169 (mtt) cc_final: 0.8513 (mtt) REVERT: A 644 MET cc_start: 0.9121 (tmm) cc_final: 0.8566 (tmm) REVERT: A 749 CYS cc_start: 0.8508 (m) cc_final: 0.8196 (t) REVERT: A 827 MET cc_start: 0.8701 (tpp) cc_final: 0.8006 (tpp) REVERT: A 830 PHE cc_start: 0.9208 (t80) cc_final: 0.8568 (t80) REVERT: A 987 MET cc_start: 0.9134 (mpp) cc_final: 0.8743 (mpp) REVERT: A 1456 MET cc_start: 0.8941 (tpt) cc_final: 0.8726 (tpp) REVERT: A 1473 MET cc_start: 0.9209 (tmm) cc_final: 0.9006 (tmm) REVERT: A 1610 ASN cc_start: 0.9366 (m110) cc_final: 0.9016 (m110) REVERT: A 1665 MET cc_start: 0.9457 (tpp) cc_final: 0.9238 (tpp) REVERT: A 1716 LEU cc_start: 0.9078 (tt) cc_final: 0.8834 (mm) REVERT: A 1776 PHE cc_start: 0.9174 (t80) cc_final: 0.8876 (m-10) REVERT: A 1822 MET cc_start: 0.9287 (ttt) cc_final: 0.9048 (tmm) REVERT: A 2057 MET cc_start: 0.9366 (mmt) cc_final: 0.8819 (mmt) REVERT: A 2067 PHE cc_start: 0.8770 (t80) cc_final: 0.8561 (t80) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1849 time to fit residues: 43.2249 Evaluate side-chains 105 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 144 optimal weight: 20.0000 chunk 96 optimal weight: 0.7980 chunk 171 optimal weight: 7.9990 chunk 107 optimal weight: 0.1980 chunk 104 optimal weight: 0.1980 chunk 79 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1498 GLN ** A1688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 13578 Z= 0.152 Angle : 0.590 7.395 18518 Z= 0.284 Chirality : 0.041 0.234 2168 Planarity : 0.003 0.049 2343 Dihedral : 5.669 53.541 2137 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1756 helix: 1.65 (0.17), residues: 991 sheet: -1.16 (0.42), residues: 166 loop : -2.22 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.001 TRP A 533 HIS 0.002 0.001 HIS A1626 PHE 0.029 0.001 PHE A 755 TYR 0.011 0.001 TYR A 997 ARG 0.003 0.000 ARG A 530 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.563 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.9160 (mmm) cc_final: 0.8799 (mmm) REVERT: A 286 MET cc_start: 0.9477 (ptp) cc_final: 0.9122 (ptt) REVERT: A 359 MET cc_start: 0.9609 (ppp) cc_final: 0.9366 (ppp) REVERT: A 396 MET cc_start: 0.9546 (mmm) cc_final: 0.9058 (mmm) REVERT: A 524 MET cc_start: 0.9418 (mmt) cc_final: 0.9162 (mmm) REVERT: A 622 MET cc_start: 0.9179 (mtt) cc_final: 0.8681 (mtt) REVERT: A 644 MET cc_start: 0.9117 (tmm) cc_final: 0.8523 (tmm) REVERT: A 674 MET cc_start: 0.9104 (ttt) cc_final: 0.8606 (tmm) REVERT: A 749 CYS cc_start: 0.8514 (m) cc_final: 0.8185 (t) REVERT: A 827 MET cc_start: 0.8670 (tpp) cc_final: 0.8064 (tpp) REVERT: A 830 PHE cc_start: 0.9206 (t80) cc_final: 0.8592 (t80) REVERT: A 927 GLN cc_start: 0.9299 (mt0) cc_final: 0.8958 (mp10) REVERT: A 987 MET cc_start: 0.9107 (mpp) cc_final: 0.8762 (mpp) REVERT: A 1091 MET cc_start: 0.9195 (mmp) cc_final: 0.8985 (mmp) REVERT: A 1329 PHE cc_start: 0.9204 (t80) cc_final: 0.8954 (t80) REVERT: A 1473 MET cc_start: 0.9277 (tmm) cc_final: 0.8974 (ppp) REVERT: A 1610 ASN cc_start: 0.9327 (m110) cc_final: 0.8948 (m-40) REVERT: A 1665 MET cc_start: 0.9454 (tpp) cc_final: 0.9110 (tpp) REVERT: A 1707 MET cc_start: 0.9250 (mmm) cc_final: 0.8918 (mmp) REVERT: A 1708 CYS cc_start: 0.9444 (m) cc_final: 0.9220 (m) REVERT: A 1716 LEU cc_start: 0.9054 (tt) cc_final: 0.8810 (mm) REVERT: A 1744 LEU cc_start: 0.9452 (mm) cc_final: 0.9246 (mm) REVERT: A 1776 PHE cc_start: 0.9171 (t80) cc_final: 0.8876 (m-10) REVERT: A 1856 MET cc_start: 0.8662 (mtp) cc_final: 0.7833 (ttm) REVERT: A 2057 MET cc_start: 0.9317 (mmt) cc_final: 0.8779 (mmt) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1904 time to fit residues: 46.4874 Evaluate side-chains 111 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 30.0000 chunk 102 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 109 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 156 optimal weight: 20.0000 chunk 164 optimal weight: 0.0020 overall best weight: 1.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1498 GLN ** A1688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13578 Z= 0.178 Angle : 0.576 8.584 18518 Z= 0.282 Chirality : 0.041 0.207 2168 Planarity : 0.003 0.054 2343 Dihedral : 5.548 53.324 2137 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.21), residues: 1756 helix: 1.69 (0.17), residues: 989 sheet: -1.01 (0.43), residues: 165 loop : -2.16 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP A 533 HIS 0.003 0.001 HIS A1626 PHE 0.023 0.001 PHE A 403 TYR 0.010 0.001 TYR A 754 ARG 0.006 0.000 ARG A 530 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.479 Fit side-chains revert: symmetry clash REVERT: A 286 MET cc_start: 0.9475 (ptp) cc_final: 0.9122 (ptt) REVERT: A 359 MET cc_start: 0.9594 (ppp) cc_final: 0.9357 (ppp) REVERT: A 396 MET cc_start: 0.9596 (mmm) cc_final: 0.9123 (mmm) REVERT: A 622 MET cc_start: 0.9180 (mtt) cc_final: 0.8635 (mtt) REVERT: A 644 MET cc_start: 0.9154 (tmm) cc_final: 0.8517 (tmm) REVERT: A 674 MET cc_start: 0.9106 (ttt) cc_final: 0.8626 (tmm) REVERT: A 749 CYS cc_start: 0.8463 (m) cc_final: 0.8166 (t) REVERT: A 827 MET cc_start: 0.8679 (tpp) cc_final: 0.8021 (tpp) REVERT: A 828 MET cc_start: 0.9109 (mtp) cc_final: 0.8903 (ttm) REVERT: A 830 PHE cc_start: 0.9185 (t80) cc_final: 0.8572 (t80) REVERT: A 987 MET cc_start: 0.9122 (mpp) cc_final: 0.8796 (mpp) REVERT: A 1473 MET cc_start: 0.9270 (tmm) cc_final: 0.8969 (ppp) REVERT: A 1610 ASN cc_start: 0.9340 (m110) cc_final: 0.8964 (m110) REVERT: A 1665 MET cc_start: 0.9476 (tpp) cc_final: 0.9127 (tpp) REVERT: A 1707 MET cc_start: 0.9227 (mmm) cc_final: 0.8876 (mmp) REVERT: A 1716 LEU cc_start: 0.9086 (tt) cc_final: 0.8853 (mm) REVERT: A 1753 MET cc_start: 0.9449 (mtm) cc_final: 0.9056 (mpp) REVERT: A 1776 PHE cc_start: 0.9180 (t80) cc_final: 0.8888 (m-10) REVERT: A 1856 MET cc_start: 0.8682 (mtp) cc_final: 0.7899 (ttm) REVERT: A 2057 MET cc_start: 0.9231 (mmt) cc_final: 0.8972 (mmt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1794 time to fit residues: 41.2156 Evaluate side-chains 107 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 69 optimal weight: 50.0000 chunk 125 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 144 optimal weight: 20.0000 chunk 151 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 169 optimal weight: 40.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1498 GLN ** A1619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 13578 Z= 0.311 Angle : 0.674 8.268 18518 Z= 0.343 Chirality : 0.043 0.283 2168 Planarity : 0.004 0.054 2343 Dihedral : 5.923 58.339 2137 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1756 helix: 1.40 (0.17), residues: 999 sheet: -1.15 (0.42), residues: 168 loop : -2.26 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.002 TRP A 533 HIS 0.005 0.001 HIS A1626 PHE 0.015 0.002 PHE A1760 TYR 0.015 0.002 TYR A1206 ARG 0.004 0.000 ARG A1489 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.306 Fit side-chains revert: symmetry clash REVERT: A 275 MET cc_start: 0.9166 (ppp) cc_final: 0.8959 (ppp) REVERT: A 359 MET cc_start: 0.9613 (ppp) cc_final: 0.9309 (ppp) REVERT: A 396 MET cc_start: 0.9558 (mmm) cc_final: 0.9044 (mmm) REVERT: A 622 MET cc_start: 0.9218 (mtt) cc_final: 0.8565 (mtt) REVERT: A 640 MET cc_start: 0.9080 (tpp) cc_final: 0.8835 (tpp) REVERT: A 644 MET cc_start: 0.9181 (tmm) cc_final: 0.8535 (tmm) REVERT: A 674 MET cc_start: 0.9106 (ttt) cc_final: 0.8703 (tmm) REVERT: A 749 CYS cc_start: 0.8446 (m) cc_final: 0.8193 (t) REVERT: A 794 PHE cc_start: 0.9182 (t80) cc_final: 0.8982 (t80) REVERT: A 827 MET cc_start: 0.8652 (tpp) cc_final: 0.8025 (tpp) REVERT: A 830 PHE cc_start: 0.9210 (t80) cc_final: 0.8583 (t80) REVERT: A 987 MET cc_start: 0.9157 (mpp) cc_final: 0.8809 (mpp) REVERT: A 1473 MET cc_start: 0.9288 (tmm) cc_final: 0.9035 (tmm) REVERT: A 1610 ASN cc_start: 0.9335 (m110) cc_final: 0.8976 (m110) REVERT: A 1665 MET cc_start: 0.9433 (tpp) cc_final: 0.9110 (tpp) REVERT: A 1707 MET cc_start: 0.9237 (mmm) cc_final: 0.8913 (mmp) REVERT: A 1856 MET cc_start: 0.8731 (mtp) cc_final: 0.7938 (ttm) REVERT: A 2057 MET cc_start: 0.9191 (mmt) cc_final: 0.8857 (mmt) REVERT: A 2067 PHE cc_start: 0.8791 (t80) cc_final: 0.8558 (t80) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1831 time to fit residues: 40.0025 Evaluate side-chains 106 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 2.9990 chunk 80 optimal weight: 30.0000 chunk 117 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 chunk 163 optimal weight: 0.0040 chunk 141 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1812 HIS ** A1825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13578 Z= 0.185 Angle : 0.624 7.950 18518 Z= 0.307 Chirality : 0.042 0.247 2168 Planarity : 0.003 0.055 2343 Dihedral : 5.762 55.888 2137 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1756 helix: 1.54 (0.17), residues: 995 sheet: -1.09 (0.44), residues: 156 loop : -2.11 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.001 TRP A 533 HIS 0.007 0.001 HIS A1686 PHE 0.017 0.001 PHE A1329 TYR 0.012 0.001 TYR A1698 ARG 0.003 0.000 ARG A 530 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.512 Fit side-chains revert: symmetry clash REVERT: A 359 MET cc_start: 0.9619 (ppp) cc_final: 0.9368 (ppp) REVERT: A 396 MET cc_start: 0.9599 (mmm) cc_final: 0.9049 (mmm) REVERT: A 622 MET cc_start: 0.9224 (mtt) cc_final: 0.8642 (mtt) REVERT: A 640 MET cc_start: 0.9070 (tpp) cc_final: 0.8862 (tpp) REVERT: A 644 MET cc_start: 0.9199 (tmm) cc_final: 0.8528 (tmm) REVERT: A 674 MET cc_start: 0.9065 (ttt) cc_final: 0.8653 (tmm) REVERT: A 749 CYS cc_start: 0.8406 (m) cc_final: 0.8197 (t) REVERT: A 827 MET cc_start: 0.8593 (tpp) cc_final: 0.8057 (tpp) REVERT: A 830 PHE cc_start: 0.9205 (t80) cc_final: 0.8638 (t80) REVERT: A 987 MET cc_start: 0.9124 (mpp) cc_final: 0.8851 (mpp) REVERT: A 1057 ASP cc_start: 0.8643 (t0) cc_final: 0.7771 (p0) REVERT: A 1073 GLU cc_start: 0.9520 (mt-10) cc_final: 0.9216 (mt-10) REVERT: A 1473 MET cc_start: 0.9289 (tmm) cc_final: 0.9002 (ppp) REVERT: A 1610 ASN cc_start: 0.9342 (m110) cc_final: 0.8987 (m110) REVERT: A 1665 MET cc_start: 0.9414 (tpp) cc_final: 0.9152 (tpp) REVERT: A 1716 LEU cc_start: 0.9184 (tt) cc_final: 0.8951 (mm) REVERT: A 1776 PHE cc_start: 0.9199 (t80) cc_final: 0.8898 (m-10) REVERT: A 1856 MET cc_start: 0.8652 (mtp) cc_final: 0.7906 (ttm) REVERT: A 2057 MET cc_start: 0.9134 (mmt) cc_final: 0.8838 (mmt) REVERT: A 2067 PHE cc_start: 0.8736 (t80) cc_final: 0.8518 (t80) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1830 time to fit residues: 40.8837 Evaluate side-chains 113 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 8 optimal weight: 0.2980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1812 HIS ** A1825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.052752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.041805 restraints weight = 88100.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.043092 restraints weight = 53456.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.043810 restraints weight = 38163.672| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13578 Z= 0.169 Angle : 0.607 7.649 18518 Z= 0.297 Chirality : 0.042 0.233 2168 Planarity : 0.003 0.056 2343 Dihedral : 5.665 54.291 2137 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1756 helix: 1.58 (0.17), residues: 994 sheet: -1.03 (0.44), residues: 156 loop : -2.08 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.001 TRP A 533 HIS 0.003 0.001 HIS A1626 PHE 0.013 0.001 PHE A 532 TYR 0.009 0.001 TYR A 997 ARG 0.005 0.000 ARG A1680 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2336.87 seconds wall clock time: 43 minutes 15.70 seconds (2595.70 seconds total)