Starting phenix.real_space_refine on Sat Jan 20 01:34:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tby_25801/01_2024/7tby_25801_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tby_25801/01_2024/7tby_25801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tby_25801/01_2024/7tby_25801.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tby_25801/01_2024/7tby_25801.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tby_25801/01_2024/7tby_25801_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tby_25801/01_2024/7tby_25801_updated.pdb" } resolution = 4.0 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 69 5.16 5 C 8591 2.51 5 N 2233 2.21 5 O 2388 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 ARG 43": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A ASP 528": "OD1" <-> "OD2" Residue "A PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 799": "OE1" <-> "OE2" Residue "A PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 843": "OE1" <-> "OE2" Residue "A GLU 925": "OE1" <-> "OE2" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1057": "OD1" <-> "OD2" Residue "A ARG 1069": "NH1" <-> "NH2" Residue "A ARG 1082": "NH1" <-> "NH2" Residue "A ARG 1100": "NH1" <-> "NH2" Residue "A GLU 1246": "OE1" <-> "OE2" Residue "A PHE 1248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1336": "NH1" <-> "NH2" Residue "A ASP 1398": "OD1" <-> "OD2" Residue "A ASP 1411": "OD1" <-> "OD2" Residue "A GLU 1420": "OE1" <-> "OE2" Residue "A ARG 1503": "NH1" <-> "NH2" Residue "A ASP 1571": "OD1" <-> "OD2" Residue "A ARG 1680": "NH1" <-> "NH2" Residue "A ASP 1706": "OD1" <-> "OD2" Residue "A TYR 1710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1833": "OE1" <-> "OE2" 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 2105": "OE1" <-> "OE2" Residue "A ARG 2113": "NH1" <-> "NH2" Residue "A PHE 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2178": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13281 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1788, 13136 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: 7.41, per 1000 atoms: 0.56 Number of scatterers: 13281 At special positions: 0 Unit cell: (81.674, 93.462, 216.394, 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 69 16.00 O 2388 8.00 N 2233 7.00 C 8591 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=2.03 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 A2502 " - " ASN A1637 " " NAG A2503 " - " ASN A 98 " " NAG B 1 " - " ASN A 400 " " NAG C 1 " - " ASN A1504 " Time building additional restraints: 5.51 Conformation dependent library (CDL) restraints added in 2.5 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: 75 helices and 9 sheets defined 53.4% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.37 Creating SS restraints... Processing helix chain 'A' and resid 4 through 21 removed outlier: 3.850A pdb=" N GLN A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 45 Proline residue: A 32 - end of helix removed outlier: 3.565A pdb=" N SER A 45 " --> pdb=" O SER A 41 " (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 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 117 Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 253 through 273 Processing helix chain 'A' and resid 277 through 288 Processing helix chain 'A' and resid 297 through 308 removed outlier: 3.721A pdb=" N TYR A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) 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: 4.767A pdb=" N LEU A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA A 407 " --> pdb=" O PHE A 403 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N PHE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 429 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 504 removed outlier: 4.642A pdb=" N CYS A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 528 Processing helix chain 'A' and resid 560 through 562 No H-bonds generated for 'chain 'A' and resid 560 through 562' 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 637 Processing helix chain 'A' and resid 640 through 664 removed outlier: 4.733A pdb=" N ALA A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 4.677A 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: 4.124A pdb=" N THR A 738 " --> pdb=" O PHE A 734 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 765 removed outlier: 4.602A pdb=" N GLY A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 4.292A 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 799 Processing helix chain 'A' and resid 821 through 845 removed outlier: 4.145A 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: 3.886A pdb=" N ALA A1046 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE A1047 " --> pdb=" O VAL A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1078 removed outlier: 3.620A 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 1366 Proline residue: A1354 - end of helix removed outlier: 3.684A pdb=" N LEU A1366 " --> pdb=" O LEU A1362 " (cutoff:3.500A) 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: 4.050A 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 1582 Processing helix chain 'A' and resid 1602 through 1617 Processing helix chain 'A' and resid 1640 through 1680 removed outlier: 4.239A pdb=" N THR A1651 " --> pdb=" O ALA A1647 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N SER A1652 " --> pdb=" O LEU A1648 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL A1653 " --> pdb=" O MET A1649 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS A1660 " --> pdb=" O LEU A1656 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A1661 " --> pdb=" O VAL A1657 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE A1667 " --> pdb=" O PHE A1663 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VAL A1668 " --> pdb=" O ALA A1664 " (cutoff:3.500A) Proline residue: A1669 - end of helix removed outlier: 3.769A 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: 4.056A 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 1752 Proline residue: A1751 - end of helix 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 1786 Processing helix chain 'A' and resid 1800 through 1809 removed outlier: 4.226A pdb=" N LEU A1808 " --> pdb=" O LYS A1804 " (cutoff:3.500A) removed outlier: 5.814A 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: 3.671A pdb=" N GLN A1871 " --> pdb=" O THR A1867 " (cutoff:3.500A) removed outlier: 3.665A 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 removed outlier: 3.820A pdb=" N VAL A2007 " --> pdb=" O GLY A2003 " (cutoff:3.500A) 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: 3.857A 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: 4.603A pdb=" N LYS A2199 " --> pdb=" O SER A2195 " (cutoff:3.500A) removed outlier: 4.025A 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: 3.747A 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: 6.958A pdb=" N GLY A1628 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N TYR A 554 " --> pdb=" O GLY A1628 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR A1630 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE A 556 " --> pdb=" O THR A1630 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N PHE A1632 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 616 through 621 removed outlier: 4.772A pdb=" N GLY A1533 " --> pdb=" O TYR A1388 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE A1390 " --> pdb=" O GLY A1533 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE A1496 " --> pdb=" O THR A1389 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL A1391 " --> pdb=" O ILE A1496 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN A1498 " --> pdb=" O VAL A1391 " (cutoff:3.500A) removed outlier: 8.163A 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: 3.668A pdb=" N TYR A 958 " --> pdb=" O SER A 900 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A 900 " --> pdb=" O TYR A 958 " (cutoff:3.500A) removed outlier: 6.798A 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: 3.809A pdb=" N SER A1236 " --> pdb=" O VAL A1131 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A1198 " --> pdb=" O THR A1205 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A1207 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU A1196 " --> pdb=" O VAL A1207 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1988 through 1990 removed outlier: 7.275A pdb=" N VAL A2065 " --> pdb=" O GLY A1989 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 2205 through 2209 removed outlier: 3.574A pdb=" N GLN A2177 " --> pdb=" O GLU A2170 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU A2170 " --> pdb=" O GLN A2177 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLN A2179 " --> pdb=" O LEU A2168 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU A2168 " --> pdb=" O GLN A2179 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1101 through 1105 removed outlier: 6.120A pdb=" N SER A1105 " --> pdb=" O LEU A1109 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU A1109 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 2114 through 2117 removed outlier: 3.612A pdb=" N GLY A2126 " --> pdb=" O MET A2114 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS A2124 " --> pdb=" O ILE A2116 " (cutoff:3.500A) 657 hydrogen bonds defined for protein. 1941 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: 4.73 Time building geometry restraints manager: 5.98 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: 2922 1.46 - 1.58: 6312 1.58 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 13585 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 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 C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C1 NAG A2503 " pdb=" O5 NAG A2503 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.11e+00 bond pdb=" C13 CLR A2501 " pdb=" C17 CLR A2501 " ideal model delta sigma weight residual 1.550 1.518 0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" C LEU A 759 " pdb=" N PRO A 760 " ideal model delta sigma weight residual 1.333 1.355 -0.022 1.44e-02 4.82e+03 2.36e+00 ... (remaining 13580 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.05: 425 107.05 - 113.79: 7540 113.79 - 120.53: 5270 120.53 - 127.27: 5134 127.27 - 134.02: 159 Bond angle restraints: 18528 Sorted by residual: angle pdb=" N VAL A1681 " pdb=" CA VAL A1681 " pdb=" C VAL A1681 " ideal model delta sigma weight residual 106.21 110.43 -4.22 1.07e+00 8.73e-01 1.56e+01 angle pdb=" N VAL A1693 " pdb=" CA VAL A1693 " pdb=" C VAL A1693 " ideal model delta sigma weight residual 113.71 109.98 3.73 9.50e-01 1.11e+00 1.55e+01 angle pdb=" C TYR A 385 " pdb=" N THR A 386 " pdb=" CA THR A 386 " ideal model delta sigma weight residual 122.29 127.84 -5.55 1.48e+00 4.57e-01 1.41e+01 angle pdb=" C SER A 639 " pdb=" N MET A 640 " pdb=" CA MET A 640 " ideal model delta sigma weight residual 120.09 124.46 -4.37 1.25e+00 6.40e-01 1.22e+01 angle pdb=" CA THR A 386 " pdb=" C THR A 386 " pdb=" N PRO A 387 " ideal model delta sigma weight residual 117.69 120.45 -2.76 9.30e-01 1.16e+00 8.79e+00 ... (remaining 18523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.47: 7686 23.47 - 46.95: 357 46.95 - 70.42: 40 70.42 - 93.90: 25 93.90 - 117.37: 18 Dihedral angle restraints: 8126 sinusoidal: 2952 harmonic: 5174 Sorted by residual: dihedral pdb=" CB CYS A 355 " pdb=" SG CYS A 355 " pdb=" SG CYS A 504 " pdb=" CB CYS A 504 " ideal model delta sinusoidal sigma weight residual 93.00 143.54 -50.54 1 1.00e+01 1.00e-02 3.50e+01 dihedral pdb=" CB CYS A 75 " pdb=" SG CYS A 75 " pdb=" SG CYS A 309 " pdb=" CB CYS A 309 " ideal model delta sinusoidal sigma weight residual 93.00 141.10 -48.10 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" C1 NAG C 2 " pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " pdb=" C4 NAG C 2 " ideal model delta sinusoidal sigma weight residual -64.11 53.26 -117.37 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 8123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1848 0.056 - 0.113: 289 0.113 - 0.169: 24 0.169 - 0.225: 2 0.225 - 0.281: 5 Chirality restraints: 2168 Sorted by residual: chirality pdb=" C13 CLR A2501 " pdb=" C12 CLR A2501 " pdb=" C14 CLR A2501 " pdb=" C17 CLR A2501 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 1.98e+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 1.98e+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 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 2165 not shown) Planarity restraints: 2348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 759 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO A 760 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A2076 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO A2077 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A2077 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A2077 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1064 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO A1065 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A1065 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A1065 " 0.018 5.00e-02 4.00e+02 ... (remaining 2345 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 309 2.70 - 3.25: 13713 3.25 - 3.80: 20727 3.80 - 4.35: 25050 4.35 - 4.90: 41256 Nonbonded interactions: 101055 Sorted by model distance: nonbonded pdb=" OD2 ASP A1706 " pdb=" OH TYR A1754 " model vdw 2.155 2.440 nonbonded pdb=" O PRO A 641 " pdb=" OG1 THR A 645 " model vdw 2.173 2.440 nonbonded pdb=" OD2 ASP A 108 " pdb=" OG SER A 277 " model vdw 2.234 2.440 nonbonded pdb=" O ASN A 361 " pdb=" OG SER A 365 " model vdw 2.259 2.440 nonbonded pdb=" OG1 THR A1493 " pdb=" OD1 ASP A1495 " model vdw 2.268 2.440 ... (remaining 101050 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: 1.360 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: 7.200 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 38.170 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 0.081 13585 Z= 0.180 Angle : 0.608 7.842 18528 Z= 0.333 Chirality : 0.042 0.281 2168 Planarity : 0.003 0.039 2344 Dihedral : 15.630 117.373 4762 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % 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: -2.45 (0.18), residues: 1756 helix: -0.44 (0.15), residues: 977 sheet: -2.22 (0.37), residues: 161 loop : -3.38 (0.21), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1705 HIS 0.002 0.000 HIS A 52 PHE 0.015 0.001 PHE A1721 TYR 0.007 0.001 TYR A1237 ARG 0.002 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 227 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.9410 (tp) cc_final: 0.9123 (tt) REVERT: A 373 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8603 (mtpt) REVERT: A 586 MET cc_start: 0.9262 (tpp) cc_final: 0.8939 (mmt) REVERT: A 640 MET cc_start: 0.9188 (tpp) cc_final: 0.8866 (tpp) REVERT: A 1649 MET cc_start: 0.5336 (ppp) cc_final: 0.4694 (ppp) REVERT: A 1716 LEU cc_start: 0.8993 (tp) cc_final: 0.8631 (tt) REVERT: A 1720 ILE cc_start: 0.8675 (mt) cc_final: 0.8412 (mt) REVERT: A 1821 ASP cc_start: 0.8805 (m-30) cc_final: 0.8598 (m-30) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2644 time to fit residues: 89.0429 Evaluate side-chains 132 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.617 ------------------------------------------------------------------------------- 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: 0.9990 chunk 134 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 161 optimal weight: 0.0670 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 78 ASN A 551 HIS A 800 GLN A 820 ASN A1106 HIS A1121 GLN A1422 ASN A1600 HIS A1626 HIS A1688 GLN A1725 GLN ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2049 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13585 Z= 0.182 Angle : 0.573 9.856 18528 Z= 0.272 Chirality : 0.042 0.224 2168 Planarity : 0.003 0.042 2344 Dihedral : 10.467 91.264 2138 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.87 % Allowed : 13.44 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.05 (0.20), residues: 1756 helix: 0.76 (0.17), residues: 983 sheet: -1.82 (0.38), residues: 168 loop : -2.85 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1705 HIS 0.002 0.001 HIS A2006 PHE 0.019 0.001 PHE A1530 TYR 0.012 0.001 TYR A 997 ARG 0.005 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 159 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.9443 (tp) cc_final: 0.9228 (tt) REVERT: A 373 LYS cc_start: 0.8939 (mmtt) cc_final: 0.8715 (mtpt) REVERT: A 640 MET cc_start: 0.9193 (tpp) cc_final: 0.8758 (tpp) REVERT: A 1419 MET cc_start: 0.7697 (pmm) cc_final: 0.7253 (pmm) REVERT: A 1649 MET cc_start: 0.5559 (ppp) cc_final: 0.5286 (ppp) REVERT: A 2069 ASP cc_start: 0.8766 (t0) cc_final: 0.7315 (p0) outliers start: 23 outliers final: 14 residues processed: 154 average time/residue: 0.1969 time to fit residues: 48.6760 Evaluate side-chains 133 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 1245 GLU Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 174 optimal weight: 0.0070 chunk 144 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 overall best weight: 2.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1825 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13585 Z= 0.205 Angle : 0.594 11.172 18528 Z= 0.284 Chirality : 0.042 0.204 2168 Planarity : 0.003 0.038 2344 Dihedral : 7.760 71.235 2138 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.04 % Allowed : 17.35 % Favored : 80.62 % 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: -0.41 (0.21), residues: 1756 helix: 1.29 (0.17), residues: 991 sheet: -1.61 (0.39), residues: 169 loop : -2.63 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1705 HIS 0.002 0.001 HIS A1812 PHE 0.019 0.001 PHE A1530 TYR 0.011 0.001 TYR A 754 ARG 0.003 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 148 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 PHE cc_start: 0.8534 (t80) cc_final: 0.8329 (t80) REVERT: A 275 MET cc_start: 0.7045 (ppp) cc_final: 0.6797 (ppp) REVERT: A 281 MET cc_start: 0.8097 (tmm) cc_final: 0.7841 (tmm) REVERT: A 373 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8793 (mtpt) REVERT: A 449 TRP cc_start: 0.7384 (m100) cc_final: 0.6976 (m100) REVERT: A 640 MET cc_start: 0.9232 (tpp) cc_final: 0.8784 (tpp) REVERT: A 1707 MET cc_start: 0.8941 (mmm) cc_final: 0.8637 (mmm) REVERT: A 2069 ASP cc_start: 0.8777 (t0) cc_final: 0.7379 (p0) outliers start: 25 outliers final: 18 residues processed: 141 average time/residue: 0.1999 time to fit residues: 45.5044 Evaluate side-chains 133 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1245 GLU Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 154 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1451 ASN ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13585 Z= 0.182 Angle : 0.568 9.952 18528 Z= 0.271 Chirality : 0.041 0.190 2168 Planarity : 0.003 0.038 2344 Dihedral : 6.476 58.071 2138 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.44 % Allowed : 19.14 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1756 helix: 1.56 (0.17), residues: 991 sheet: -1.51 (0.39), residues: 169 loop : -2.51 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 533 HIS 0.002 0.000 HIS A1812 PHE 0.023 0.001 PHE A1530 TYR 0.011 0.001 TYR A 754 ARG 0.003 0.000 ARG A 565 *********************** 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 155 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 PHE cc_start: 0.8530 (t80) cc_final: 0.8302 (t80) REVERT: A 281 MET cc_start: 0.8234 (tmm) cc_final: 0.7940 (tmm) REVERT: A 373 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8817 (mtpt) REVERT: A 449 TRP cc_start: 0.7412 (m100) cc_final: 0.6987 (m100) REVERT: A 502 MET cc_start: 0.8458 (tmm) cc_final: 0.8225 (tmm) REVERT: A 640 MET cc_start: 0.9239 (tpp) cc_final: 0.8782 (tpp) REVERT: A 644 MET cc_start: 0.8600 (tpp) cc_final: 0.8367 (tpp) REVERT: A 1456 MET cc_start: 0.8987 (tpp) cc_final: 0.8679 (tpt) REVERT: A 1524 LYS cc_start: 0.6802 (mttt) cc_final: 0.5913 (tppt) REVERT: A 2069 ASP cc_start: 0.8799 (t0) cc_final: 0.7378 (p0) outliers start: 30 outliers final: 21 residues processed: 145 average time/residue: 0.2031 time to fit residues: 47.4441 Evaluate side-chains 137 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1245 GLU Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 70 optimal weight: 0.3980 chunk 146 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 ASN ** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1641 GLN ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13585 Z= 0.302 Angle : 0.628 7.621 18528 Z= 0.315 Chirality : 0.043 0.194 2168 Planarity : 0.004 0.035 2344 Dihedral : 6.021 55.163 2138 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.99 % Allowed : 19.30 % Favored : 76.71 % 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: -0.05 (0.21), residues: 1756 helix: 1.59 (0.17), residues: 988 sheet: -1.45 (0.39), residues: 178 loop : -2.48 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1705 HIS 0.003 0.001 HIS A 311 PHE 0.023 0.002 PHE A1663 TYR 0.020 0.001 TYR A 754 ARG 0.004 0.000 ARG A1680 *********************** 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 161 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 112 time to evaluate : 1.380 Fit side-chains revert: symmetry clash REVERT: A 34 PHE cc_start: 0.8593 (t80) cc_final: 0.8283 (t80) REVERT: A 275 MET cc_start: 0.7312 (ppp) cc_final: 0.7053 (ppp) REVERT: A 373 LYS cc_start: 0.9105 (mmtt) cc_final: 0.8901 (mtpt) REVERT: A 449 TRP cc_start: 0.7536 (m100) cc_final: 0.7096 (m100) REVERT: A 502 MET cc_start: 0.8523 (tmm) cc_final: 0.8281 (tmm) REVERT: A 640 MET cc_start: 0.9314 (tpp) cc_final: 0.8821 (tpp) REVERT: A 644 MET cc_start: 0.8803 (tpp) cc_final: 0.8455 (tpp) REVERT: A 755 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7773 (t80) REVERT: A 1456 MET cc_start: 0.8985 (tpp) cc_final: 0.8691 (tpt) REVERT: A 1524 LYS cc_start: 0.7129 (mttt) cc_final: 0.6113 (tppt) REVERT: A 1707 MET cc_start: 0.8940 (mmm) cc_final: 0.8710 (mmm) outliers start: 49 outliers final: 31 residues processed: 150 average time/residue: 0.2245 time to fit residues: 52.9804 Evaluate side-chains 141 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 109 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1245 GLU Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1867 THR Chi-restraints excluded: chain A residue 2007 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13585 Z= 0.206 Angle : 0.593 8.912 18528 Z= 0.289 Chirality : 0.041 0.193 2168 Planarity : 0.003 0.037 2344 Dihedral : 5.668 53.192 2138 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.85 % Allowed : 21.25 % Favored : 75.90 % 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: 1.75 (0.17), residues: 985 sheet: -1.49 (0.39), residues: 180 loop : -2.44 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1705 HIS 0.002 0.001 HIS A1812 PHE 0.020 0.001 PHE A1663 TYR 0.016 0.001 TYR A 754 ARG 0.002 0.000 ARG A 565 *********************** 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 151 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 116 time to evaluate : 1.620 Fit side-chains revert: symmetry clash REVERT: A 34 PHE cc_start: 0.8593 (t80) cc_final: 0.8276 (t80) REVERT: A 373 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8839 (mtpt) REVERT: A 449 TRP cc_start: 0.7561 (m100) cc_final: 0.7104 (m100) REVERT: A 502 MET cc_start: 0.8492 (tmm) cc_final: 0.8235 (tmm) REVERT: A 640 MET cc_start: 0.9307 (tpp) cc_final: 0.8850 (tpp) REVERT: A 644 MET cc_start: 0.8801 (tpp) cc_final: 0.8443 (tpp) REVERT: A 755 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7781 (t80) REVERT: A 1456 MET cc_start: 0.8959 (tpp) cc_final: 0.8699 (tpt) REVERT: A 1524 LYS cc_start: 0.7024 (mttt) cc_final: 0.6099 (tppt) REVERT: A 1656 LEU cc_start: 0.8914 (tt) cc_final: 0.8425 (pp) REVERT: A 1707 MET cc_start: 0.8928 (mmm) cc_final: 0.8691 (mmm) outliers start: 35 outliers final: 26 residues processed: 142 average time/residue: 0.2026 time to fit residues: 46.8958 Evaluate side-chains 132 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1245 GLU Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1832 LEU Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 10.0000 chunk 98 optimal weight: 0.4980 chunk 125 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 96 optimal weight: 30.0000 chunk 171 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 106 optimal weight: 0.0040 overall best weight: 2.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1443 GLN ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13585 Z= 0.203 Angle : 0.587 9.457 18528 Z= 0.286 Chirality : 0.042 0.437 2168 Planarity : 0.003 0.036 2344 Dihedral : 5.605 53.356 2138 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.75 % Allowed : 21.01 % Favored : 75.24 % 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: 0.18 (0.21), residues: 1756 helix: 1.80 (0.17), residues: 985 sheet: -1.39 (0.39), residues: 180 loop : -2.38 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 533 HIS 0.002 0.001 HIS A1600 PHE 0.023 0.001 PHE A1663 TYR 0.016 0.001 TYR A 754 ARG 0.002 0.000 ARG A 565 *********************** 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 157 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 111 time to evaluate : 1.504 Fit side-chains revert: symmetry clash REVERT: A 373 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8833 (mtpt) REVERT: A 411 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8044 (p0) REVERT: A 449 TRP cc_start: 0.7565 (m100) cc_final: 0.7099 (m100) REVERT: A 502 MET cc_start: 0.8500 (tmm) cc_final: 0.8201 (tmm) REVERT: A 640 MET cc_start: 0.9300 (tpp) cc_final: 0.8833 (tpp) REVERT: A 644 MET cc_start: 0.8818 (tpp) cc_final: 0.8458 (tpp) REVERT: A 755 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7819 (t80) REVERT: A 1446 MET cc_start: 0.7127 (mpp) cc_final: 0.6615 (pmm) REVERT: A 1524 LYS cc_start: 0.7094 (mttt) cc_final: 0.6171 (tppt) REVERT: A 1656 LEU cc_start: 0.8939 (tt) cc_final: 0.8481 (pp) REVERT: A 1707 MET cc_start: 0.8919 (mmm) cc_final: 0.8648 (mmm) outliers start: 46 outliers final: 34 residues processed: 146 average time/residue: 0.2116 time to fit residues: 49.1360 Evaluate side-chains 142 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 106 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1245 GLU Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1832 LEU Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2007 VAL Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 0.0020 chunk 102 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 164 optimal weight: 6.9990 overall best weight: 3.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A1464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13585 Z= 0.274 Angle : 0.632 11.005 18528 Z= 0.311 Chirality : 0.044 0.508 2168 Planarity : 0.003 0.034 2344 Dihedral : 5.519 52.108 2138 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.91 % Allowed : 21.34 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1756 helix: 1.75 (0.17), residues: 987 sheet: -1.37 (0.40), residues: 180 loop : -2.43 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1705 HIS 0.002 0.001 HIS A1600 PHE 0.020 0.001 PHE A1663 TYR 0.019 0.001 TYR A 754 ARG 0.004 0.000 ARG A2113 *********************** 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 152 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 104 time to evaluate : 1.641 Fit side-chains revert: symmetry clash REVERT: A 373 LYS cc_start: 0.9109 (mmtt) cc_final: 0.8836 (mtpt) REVERT: A 449 TRP cc_start: 0.7605 (m100) cc_final: 0.7107 (m100) REVERT: A 502 MET cc_start: 0.8506 (tmm) cc_final: 0.8205 (tmm) REVERT: A 640 MET cc_start: 0.9364 (tpp) cc_final: 0.8870 (tpp) REVERT: A 644 MET cc_start: 0.8853 (tpp) cc_final: 0.8487 (tpp) REVERT: A 755 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7869 (t80) REVERT: A 1446 MET cc_start: 0.7163 (mpp) cc_final: 0.6400 (pmm) REVERT: A 1524 LYS cc_start: 0.7161 (mttt) cc_final: 0.6223 (tppt) REVERT: A 1656 LEU cc_start: 0.8967 (tt) cc_final: 0.8530 (pp) outliers start: 48 outliers final: 37 residues processed: 144 average time/residue: 0.2092 time to fit residues: 48.5927 Evaluate side-chains 139 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 101 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1245 GLU Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1760 PHE Chi-restraints excluded: chain A residue 1832 LEU Chi-restraints excluded: chain A residue 2007 VAL Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU 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: 6.9990 chunk 164 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 169 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A1121 GLN ** A1464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13585 Z= 0.366 Angle : 0.692 9.623 18528 Z= 0.348 Chirality : 0.046 0.467 2168 Planarity : 0.004 0.033 2344 Dihedral : 5.684 51.070 2138 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.83 % Allowed : 21.58 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1756 helix: 1.55 (0.17), residues: 988 sheet: -1.32 (0.41), residues: 173 loop : -2.54 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1705 HIS 0.003 0.001 HIS A1812 PHE 0.027 0.002 PHE A 34 TYR 0.021 0.002 TYR A 754 ARG 0.004 0.000 ARG A1680 *********************** 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 150 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 103 time to evaluate : 1.576 Fit side-chains revert: symmetry clash REVERT: A 373 LYS cc_start: 0.9141 (mmtt) cc_final: 0.8892 (mtpt) REVERT: A 449 TRP cc_start: 0.7697 (m100) cc_final: 0.7148 (m100) REVERT: A 502 MET cc_start: 0.8547 (tmm) cc_final: 0.8230 (tmm) REVERT: A 640 MET cc_start: 0.9390 (tpp) cc_final: 0.8876 (tpp) REVERT: A 644 MET cc_start: 0.8852 (tpp) cc_final: 0.8418 (tpp) REVERT: A 755 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7884 (t80) REVERT: A 1446 MET cc_start: 0.7313 (mpp) cc_final: 0.6921 (pmm) REVERT: A 1524 LYS cc_start: 0.7117 (mttt) cc_final: 0.6214 (tppt) outliers start: 47 outliers final: 39 residues processed: 140 average time/residue: 0.2016 time to fit residues: 45.5720 Evaluate side-chains 140 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 100 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1245 GLU Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1760 PHE Chi-restraints excluded: chain A residue 1832 LEU Chi-restraints excluded: chain A residue 1867 THR Chi-restraints excluded: chain A residue 2007 VAL Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 163 optimal weight: 0.0570 chunk 141 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 chunk 112 optimal weight: 0.2980 chunk 150 optimal weight: 4.9990 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13585 Z= 0.165 Angle : 0.611 11.575 18528 Z= 0.293 Chirality : 0.043 0.467 2168 Planarity : 0.003 0.037 2344 Dihedral : 5.391 53.101 2138 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.69 % Allowed : 22.88 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1756 helix: 1.78 (0.17), residues: 988 sheet: -1.29 (0.41), residues: 170 loop : -2.41 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1705 HIS 0.002 0.000 HIS A1626 PHE 0.025 0.001 PHE A 36 TYR 0.016 0.001 TYR A 754 ARG 0.003 0.000 ARG A 565 ********************** 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 150 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 117 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8805 (mtpt) REVERT: A 449 TRP cc_start: 0.7627 (m100) cc_final: 0.7064 (m100) REVERT: A 502 MET cc_start: 0.8414 (tmm) cc_final: 0.8149 (tmm) REVERT: A 640 MET cc_start: 0.9332 (tpp) cc_final: 0.8851 (tpp) REVERT: A 644 MET cc_start: 0.8808 (tpp) cc_final: 0.8404 (tpp) REVERT: A 755 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7830 (t80) REVERT: A 1357 PHE cc_start: 0.8454 (m-80) cc_final: 0.8117 (m-10) REVERT: A 1414 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.7528 (t80) REVERT: A 1446 MET cc_start: 0.7179 (mpp) cc_final: 0.6757 (pmm) REVERT: A 1524 LYS cc_start: 0.7060 (mttt) cc_final: 0.6395 (mmmt) REVERT: A 1656 LEU cc_start: 0.9006 (tt) cc_final: 0.8536 (pp) outliers start: 33 outliers final: 28 residues processed: 143 average time/residue: 0.2021 time to fit residues: 46.3109 Evaluate side-chains 141 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 111 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1245 GLU Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1760 PHE Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1832 LEU Chi-restraints excluded: chain A residue 2007 VAL Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.071391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.058001 restraints weight = 55333.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.059432 restraints weight = 30404.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.059842 restraints weight = 21661.105| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13585 Z= 0.176 Angle : 0.609 11.231 18528 Z= 0.293 Chirality : 0.043 0.465 2168 Planarity : 0.003 0.039 2344 Dihedral : 5.218 53.270 2138 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.61 % Allowed : 23.29 % Favored : 74.10 % 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: 0.24 (0.21), residues: 1756 helix: 1.79 (0.17), residues: 991 sheet: -1.21 (0.41), residues: 170 loop : -2.36 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1705 HIS 0.002 0.000 HIS A 55 PHE 0.042 0.001 PHE A 36 TYR 0.016 0.001 TYR A 754 ARG 0.002 0.000 ARG A 565 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2483.12 seconds wall clock time: 46 minutes 7.86 seconds (2767.86 seconds total)