Starting phenix.real_space_refine on Fri Jun 28 22:10:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6w_18967/06_2024/8r6w_18967_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6w_18967/06_2024/8r6w_18967.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6w_18967/06_2024/8r6w_18967_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6w_18967/06_2024/8r6w_18967_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6w_18967/06_2024/8r6w_18967_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6w_18967/06_2024/8r6w_18967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6w_18967/06_2024/8r6w_18967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6w_18967/06_2024/8r6w_18967_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6w_18967/06_2024/8r6w_18967_updated.pdb" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 40 5.49 5 S 95 5.16 5 C 10315 2.51 5 N 2886 2.21 5 O 3203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 283": "OD1" <-> "OD2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 937": "OE1" <-> "OE2" Residue "A TYR 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1983": "OD1" <-> "OD2" Residue "A PHE 1996": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 16539 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1974, 15661 Classifications: {'peptide': 1974} Link IDs: {'PCIS': 2, 'PTRANS': 70, 'TRANS': 1901} Chain breaks: 7 Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Classifications: {'RNA': 4} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 3} Chain: "P" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 341 Classifications: {'RNA': 16} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 12} Chain: "T" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 361 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 13} Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 95 Unusual residues: {'M7G': 1} Classifications: {'RNA': 3, 'undetermined': 1} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1, None: 1} Not linked: pdbres="M7G C 1 " pdbres=" A C 2 " Time building chain proxies: 9.64, per 1000 atoms: 0.58 Number of scatterers: 16539 At special positions: 0 Unit cell: (123.25, 116.45, 126.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 95 16.00 P 40 15.00 O 3203 8.00 N 2886 7.00 C 10315 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.75 Conformation dependent library (CDL) restraints added in 2.9 seconds 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 79 helices and 10 sheets defined 43.5% alpha, 5.5% beta 9 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 9.99 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 95 through 98 No H-bonds generated for 'chain 'A' and resid 95 through 98' Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 150 through 159 removed outlier: 3.876A pdb=" N ILE A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 206 Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.721A pdb=" N ILE A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 244 removed outlier: 3.758A pdb=" N GLY A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 263 through 284 Processing helix chain 'A' and resid 293 through 316 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 360 through 373 removed outlier: 3.635A pdb=" N LEU A 369 " --> pdb=" O TRP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.525A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 removed outlier: 3.964A pdb=" N HIS A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'A' and resid 478 through 493 removed outlier: 4.877A pdb=" N MET A 493 " --> pdb=" O LYS A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.509A pdb=" N TRP A 517 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TRP A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 610 removed outlier: 3.999A pdb=" N THR A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 639 through 654 Processing helix chain 'A' and resid 659 through 670 removed outlier: 4.264A pdb=" N ILE A 663 " --> pdb=" O THR A 659 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 690 removed outlier: 3.507A pdb=" N LEU A 690 " --> pdb=" O LEU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 715 Processing helix chain 'A' and resid 743 through 755 removed outlier: 4.095A pdb=" N TYR A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLY A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TYR A 754 " --> pdb=" O TRP A 750 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR A 755 " --> pdb=" O TYR A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 779 removed outlier: 4.747A pdb=" N MET A 777 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 779 " --> pdb=" O VAL A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'A' and resid 803 through 820 Processing helix chain 'A' and resid 825 through 838 Processing helix chain 'A' and resid 857 through 859 No H-bonds generated for 'chain 'A' and resid 857 through 859' Processing helix chain 'A' and resid 874 through 883 Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 927 through 946 removed outlier: 4.230A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 943 " --> pdb=" O MET A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 961 removed outlier: 4.408A pdb=" N ILE A 961 " --> pdb=" O LYS A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 972 Processing helix chain 'A' and resid 995 through 1005 Processing helix chain 'A' and resid 1008 through 1022 removed outlier: 4.511A pdb=" N ARG A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE A1013 " --> pdb=" O LYS A1009 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG A1022 " --> pdb=" O ILE A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1037 removed outlier: 3.603A pdb=" N HIS A1035 " --> pdb=" O ARG A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1057 Processing helix chain 'A' and resid 1086 through 1107 Processing helix chain 'A' and resid 1139 through 1162 removed outlier: 4.047A pdb=" N VAL A1156 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LYS A1157 " --> pdb=" O LEU A1153 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE A1158 " --> pdb=" O HIS A1154 " (cutoff:3.500A) Proline residue: A1161 - end of helix Processing helix chain 'A' and resid 1196 through 1200 Processing helix chain 'A' and resid 1212 through 1227 Processing helix chain 'A' and resid 1232 through 1250 Processing helix chain 'A' and resid 1256 through 1267 removed outlier: 4.092A pdb=" N GLY A1259 " --> pdb=" O PRO A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1299 Processing helix chain 'A' and resid 1302 through 1314 Processing helix chain 'A' and resid 1346 through 1354 Processing helix chain 'A' and resid 1361 through 1367 Processing helix chain 'A' and resid 1379 through 1391 Processing helix chain 'A' and resid 1404 through 1413 removed outlier: 3.732A pdb=" N ALA A1411 " --> pdb=" O ARG A1407 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY A1412 " --> pdb=" O VAL A1408 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL A1413 " --> pdb=" O VAL A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1447 removed outlier: 3.922A pdb=" N ILE A1447 " --> pdb=" O MET A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1452 No H-bonds generated for 'chain 'A' and resid 1449 through 1452' Processing helix chain 'A' and resid 1458 through 1464 Processing helix chain 'A' and resid 1468 through 1480 Processing helix chain 'A' and resid 1513 through 1522 Processing helix chain 'A' and resid 1531 through 1544 Processing helix chain 'A' and resid 1552 through 1558 removed outlier: 3.747A pdb=" N LEU A1556 " --> pdb=" O PRO A1552 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG A1557 " --> pdb=" O SER A1553 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A1558 " --> pdb=" O GLU A1554 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1552 through 1558' Processing helix chain 'A' and resid 1564 through 1573 Processing helix chain 'A' and resid 1596 through 1602 removed outlier: 3.634A pdb=" N VAL A1600 " --> pdb=" O THR A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1637 removed outlier: 3.920A pdb=" N MET A1635 " --> pdb=" O HIS A1631 " (cutoff:3.500A) Processing helix chain 'A' and resid 1643 through 1656 Processing helix chain 'A' and resid 1671 through 1682 removed outlier: 3.611A pdb=" N LEU A1681 " --> pdb=" O LEU A1677 " (cutoff:3.500A) Processing helix chain 'A' and resid 1688 through 1695 Processing helix chain 'A' and resid 1758 through 1772 Processing helix chain 'A' and resid 1859 through 1867 Processing helix chain 'A' and resid 1869 through 1871 No H-bonds generated for 'chain 'A' and resid 1869 through 1871' Processing helix chain 'A' and resid 1891 through 1901 Processing helix chain 'A' and resid 1914 through 1930 removed outlier: 4.208A pdb=" N GLN A1930 " --> pdb=" O SER A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1980 through 1982 No H-bonds generated for 'chain 'A' and resid 1980 through 1982' Processing helix chain 'A' and resid 1998 through 2003 Processing helix chain 'A' and resid 2017 through 2026 Processing helix chain 'A' and resid 2030 through 2036 removed outlier: 3.997A pdb=" N GLY A2033 " --> pdb=" O GLY A2030 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A2035 " --> pdb=" O ARG A2032 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2047 No H-bonds generated for 'chain 'A' and resid 2045 through 2047' Processing helix chain 'A' and resid 2049 through 2053 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 41 removed outlier: 4.198A pdb=" N THR A 46 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 113 through 117 removed outlier: 3.690A pdb=" N THR A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 127 through 129 removed outlier: 6.096A pdb=" N ILE A 170 " --> pdb=" O SER A 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 410 through 412 Processing sheet with id= E, first strand: chain 'A' and resid 719 through 722 Processing sheet with id= F, first strand: chain 'A' and resid 906 through 908 Processing sheet with id= G, first strand: chain 'A' and resid 978 through 984 Processing sheet with id= H, first strand: chain 'A' and resid 1178 through 1180 Processing sheet with id= I, first strand: chain 'A' and resid 1699 through 1702 removed outlier: 3.520A pdb=" N LEU A1700 " --> pdb=" O VAL A1728 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A1740 " --> pdb=" O GLY A1721 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1708 through 1712 removed outlier: 3.909A pdb=" N ARG A1712 " --> pdb=" O GLY A1716 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLY A1716 " --> pdb=" O ARG A1712 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 6.81 Time building geometry restraints manager: 7.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4702 1.34 - 1.45: 3030 1.45 - 1.57: 8994 1.57 - 1.69: 78 1.69 - 1.81: 154 Bond restraints: 16958 Sorted by residual: bond pdb=" C3' M7G C 1 " pdb=" C4' M7G C 1 " ideal model delta sigma weight residual 1.305 1.525 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C5 M7G C 1 " pdb=" C6 M7G C 1 " ideal model delta sigma weight residual 1.534 1.339 0.195 2.00e-02 2.50e+03 9.48e+01 bond pdb=" C4' M7G C 1 " pdb=" O4' M7G C 1 " ideal model delta sigma weight residual 1.615 1.446 0.169 2.00e-02 2.50e+03 7.13e+01 bond pdb=" C4 M7G C 1 " pdb=" N3 M7G C 1 " ideal model delta sigma weight residual 1.492 1.341 0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" C1' M7G C 1 " pdb=" O4' M7G C 1 " ideal model delta sigma weight residual 1.305 1.456 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 16953 not shown) Histogram of bond angle deviations from ideal: 83.45 - 93.61: 3 93.61 - 103.78: 322 103.78 - 113.94: 10018 113.94 - 124.10: 12117 124.10 - 134.26: 619 Bond angle restraints: 23079 Sorted by residual: angle pdb=" O3A M7G C 1 " pdb=" PB M7G C 1 " pdb=" O3B M7G C 1 " ideal model delta sigma weight residual 109.47 83.45 26.02 3.00e+00 1.11e-01 7.52e+01 angle pdb=" C1' M7G C 1 " pdb=" N9 M7G C 1 " pdb=" C4 M7G C 1 " ideal model delta sigma weight residual 103.02 128.68 -25.66 3.00e+00 1.11e-01 7.32e+01 angle pdb=" O1B M7G C 1 " pdb=" PB M7G C 1 " pdb=" O3B M7G C 1 " ideal model delta sigma weight residual 109.47 86.75 22.72 3.00e+00 1.11e-01 5.73e+01 angle pdb=" O2B M7G C 1 " pdb=" PB M7G C 1 " pdb=" O3B M7G C 1 " ideal model delta sigma weight residual 109.47 87.72 21.75 3.00e+00 1.11e-01 5.26e+01 angle pdb=" C1' M7G C 1 " pdb=" N9 M7G C 1 " pdb=" C8 M7G C 1 " ideal model delta sigma weight residual 139.43 123.21 16.22 3.00e+00 1.11e-01 2.92e+01 ... (remaining 23074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 9786 35.34 - 70.69: 449 70.69 - 106.03: 42 106.03 - 141.37: 0 141.37 - 176.72: 5 Dihedral angle restraints: 10282 sinusoidal: 4573 harmonic: 5709 Sorted by residual: dihedral pdb=" O4' C T 19 " pdb=" C1' C T 19 " pdb=" N1 C T 19 " pdb=" C2 C T 19 " ideal model delta sinusoidal sigma weight residual 200.00 41.31 158.69 1 1.50e+01 4.44e-03 8.24e+01 dihedral pdb=" O4' U T 21 " pdb=" C1' U T 21 " pdb=" N1 U T 21 " pdb=" C2 U T 21 " ideal model delta sinusoidal sigma weight residual -128.00 48.72 -176.72 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U T 18 " pdb=" C1' U T 18 " pdb=" N1 U T 18 " pdb=" C2 U T 18 " ideal model delta sinusoidal sigma weight residual -160.00 -70.14 -89.86 1 1.50e+01 4.44e-03 4.26e+01 ... (remaining 10279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2421 0.084 - 0.167: 162 0.167 - 0.251: 4 0.251 - 0.335: 0 0.335 - 0.418: 1 Chirality restraints: 2588 Sorted by residual: chirality pdb=" C3' M7G C 1 " pdb=" C2' M7G C 1 " pdb=" C4' M7G C 1 " pdb=" O3' M7G C 1 " both_signs ideal model delta sigma weight residual False -2.39 -2.81 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C3' U T 20 " pdb=" C4' U T 20 " pdb=" O3' U T 20 " pdb=" C2' U T 20 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C4' M7G C 1 " pdb=" C3' M7G C 1 " pdb=" C5' M7G C 1 " pdb=" O4' M7G C 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.73 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2585 not shown) Planarity restraints: 2795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A1712 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO A1713 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A1713 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1713 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1878 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A1879 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A1879 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1879 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A1006 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO A1007 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A1007 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1007 " 0.026 5.00e-02 4.00e+02 ... (remaining 2792 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1922 2.75 - 3.29: 16524 3.29 - 3.83: 28812 3.83 - 4.36: 33176 4.36 - 4.90: 55674 Nonbonded interactions: 136108 Sorted by model distance: nonbonded pdb=" OP1 C P 10 " pdb=" O2' G P 11 " model vdw 2.217 2.440 nonbonded pdb=" OG SER A 132 " pdb=" OD1 ASN A 134 " model vdw 2.237 2.440 nonbonded pdb=" OG SER A1780 " pdb=" O GLY A1803 " model vdw 2.256 2.440 nonbonded pdb=" O MET A1729 " pdb=" OG1 THR A1732 " model vdw 2.266 2.440 nonbonded pdb=" OG1 THR A 558 " pdb=" O HIS A 563 " model vdw 2.268 2.440 ... (remaining 136103 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 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: 7.110 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 52.180 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.220 16958 Z= 0.321 Angle : 0.793 26.020 23079 Z= 0.408 Chirality : 0.043 0.418 2588 Planarity : 0.005 0.054 2795 Dihedral : 18.605 176.716 6594 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.87 % Favored : 91.98 % Rotamer: Outliers : 9.45 % Allowed : 11.54 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.57 (0.18), residues: 1958 helix: 0.30 (0.17), residues: 917 sheet: -0.32 (0.48), residues: 136 loop : -2.68 (0.18), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 520 HIS 0.006 0.001 HIS A 285 PHE 0.018 0.001 PHE A 649 TYR 0.015 0.002 TYR A 861 ARG 0.004 0.000 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 259 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 VAL cc_start: 0.8195 (t) cc_final: 0.7927 (m) REVERT: A 54 ASP cc_start: 0.7740 (m-30) cc_final: 0.7472 (m-30) REVERT: A 92 ASP cc_start: 0.8003 (t0) cc_final: 0.7303 (p0) REVERT: A 280 ASP cc_start: 0.8341 (t70) cc_final: 0.8033 (t0) REVERT: A 412 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.7462 (mtpp) REVERT: A 582 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7834 (mpp80) REVERT: A 651 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8387 (mt) REVERT: A 653 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8278 (mm) REVERT: A 743 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8734 (tp) REVERT: A 800 GLU cc_start: 0.7647 (mt-10) cc_final: 0.6751 (mt-10) REVERT: A 937 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7675 (mm-30) REVERT: A 1018 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7839 (mt) REVERT: A 1020 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8496 (ptm) REVERT: A 1065 MET cc_start: 0.8332 (mmm) cc_final: 0.8048 (mmt) REVERT: A 1110 TYR cc_start: 0.7209 (OUTLIER) cc_final: 0.6061 (t80) REVERT: A 1418 ARG cc_start: 0.8004 (tpp80) cc_final: 0.7179 (mmt180) REVERT: A 1478 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8034 (mm) REVERT: A 1489 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8553 (m) REVERT: A 1540 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8734 (ptpp) REVERT: A 1612 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: A 1690 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8299 (t0) REVERT: A 1745 ASN cc_start: 0.6742 (m-40) cc_final: 0.6375 (m-40) REVERT: A 1757 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7314 (mtp180) REVERT: A 1787 MET cc_start: 0.6021 (pmm) cc_final: 0.5623 (ptp) REVERT: A 1995 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7149 (mm-30) outliers start: 163 outliers final: 39 residues processed: 387 average time/residue: 0.3598 time to fit residues: 196.3216 Evaluate side-chains 204 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 149 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 ARG Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1024 LYS Chi-restraints excluded: chain A residue 1078 MET Chi-restraints excluded: chain A residue 1110 TYR Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1174 ASN Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1233 SER Chi-restraints excluded: chain A residue 1341 TYR Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1401 LYS Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1489 VAL Chi-restraints excluded: chain A residue 1540 LYS Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1635 MET Chi-restraints excluded: chain A residue 1690 ASP Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1796 LYS Chi-restraints excluded: chain A residue 1833 LEU Chi-restraints excluded: chain A residue 1995 GLU Chi-restraints excluded: chain A residue 2000 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 9.9990 chunk 150 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 285 HIS A 300 ASN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 HIS A 824 GLN A 914 ASN A 916 HIS A 979 ASN A1174 ASN A1188 HIS A1239 GLN ** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1467 GLN A1569 ASN ** A1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1776 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 16958 Z= 0.350 Angle : 0.683 9.590 23079 Z= 0.355 Chirality : 0.043 0.210 2588 Planarity : 0.005 0.063 2795 Dihedral : 16.169 175.591 2888 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.71 % Favored : 92.13 % Rotamer: Outliers : 5.39 % Allowed : 16.23 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.25 (0.19), residues: 1958 helix: 0.57 (0.17), residues: 905 sheet: -0.79 (0.40), residues: 177 loop : -2.43 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 335 HIS 0.010 0.002 HIS A1452 PHE 0.026 0.002 PHE A 649 TYR 0.021 0.002 TYR A 668 ARG 0.012 0.001 ARG A1422 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 142 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7813 (m-30) cc_final: 0.7590 (m-30) REVERT: A 92 ASP cc_start: 0.7955 (t0) cc_final: 0.7387 (p0) REVERT: A 192 MET cc_start: 0.7556 (mtm) cc_final: 0.7079 (mtm) REVERT: A 280 ASP cc_start: 0.8439 (t70) cc_final: 0.8212 (t0) REVERT: A 392 ILE cc_start: 0.9128 (mm) cc_final: 0.8848 (mm) REVERT: A 445 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: A 507 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8900 (mptt) REVERT: A 710 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8139 (ttp) REVERT: A 712 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8099 (ttt-90) REVERT: A 800 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7504 (mt-10) REVERT: A 860 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8259 (mm) REVERT: A 883 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: A 1065 MET cc_start: 0.8676 (mmm) cc_final: 0.8475 (mmt) REVERT: A 1612 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: A 1915 MET cc_start: 0.7154 (mpp) cc_final: 0.6915 (mpp) REVERT: A 1919 PHE cc_start: 0.8844 (m-10) cc_final: 0.8590 (m-80) outliers start: 93 outliers final: 51 residues processed: 222 average time/residue: 0.3231 time to fit residues: 104.8381 Evaluate side-chains 175 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 117 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 ARG Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1341 TYR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1401 LYS Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1528 LYS Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1626 ILE Chi-restraints excluded: chain A residue 1635 MET Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1754 SER Chi-restraints excluded: chain A residue 1755 ASP Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1828 VAL Chi-restraints excluded: chain A residue 1856 ASP Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2001 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 123 optimal weight: 0.0040 chunk 49 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 195 optimal weight: 7.9990 chunk 161 optimal weight: 0.0370 chunk 179 optimal weight: 7.9990 chunk 61 optimal weight: 0.0870 chunk 145 optimal weight: 0.7980 overall best weight: 0.3850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN A 526 GLN ** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1896 HIS ** A1908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16958 Z= 0.145 Angle : 0.538 9.969 23079 Z= 0.279 Chirality : 0.037 0.203 2588 Planarity : 0.004 0.050 2795 Dihedral : 15.630 175.936 2820 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.74 % Favored : 93.11 % Rotamer: Outliers : 3.77 % Allowed : 18.43 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.78 (0.19), residues: 1958 helix: 1.07 (0.18), residues: 902 sheet: -0.45 (0.42), residues: 171 loop : -2.33 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 520 HIS 0.008 0.001 HIS A1452 PHE 0.011 0.001 PHE A1874 TYR 0.012 0.001 TYR A1341 ARG 0.005 0.000 ARG A 907 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 133 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7710 (m-30) cc_final: 0.7485 (m-30) REVERT: A 92 ASP cc_start: 0.7936 (t0) cc_final: 0.7326 (p0) REVERT: A 280 ASP cc_start: 0.8275 (t70) cc_final: 0.8070 (t0) REVERT: A 392 ILE cc_start: 0.9056 (mm) cc_final: 0.8798 (mm) REVERT: A 635 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7887 (mtm180) REVERT: A 712 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8150 (ttt-90) REVERT: A 713 ILE cc_start: 0.8882 (tt) cc_final: 0.8361 (mt) REVERT: A 767 LEU cc_start: 0.8657 (mp) cc_final: 0.8444 (mt) REVERT: A 797 LYS cc_start: 0.7813 (mptt) cc_final: 0.7608 (mptt) REVERT: A 800 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7622 (mt-10) REVERT: A 860 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8428 (mm) REVERT: A 883 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: A 1061 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7612 (m-30) REVERT: A 1065 MET cc_start: 0.8649 (mmm) cc_final: 0.8387 (tpp) REVERT: A 1157 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8076 (ptpp) REVERT: A 1418 ARG cc_start: 0.7834 (tpp80) cc_final: 0.6953 (mmt180) REVERT: A 1757 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7391 (mtm180) REVERT: A 1913 ARG cc_start: 0.7006 (tpm170) cc_final: 0.6588 (tpm170) REVERT: A 2040 CYS cc_start: 0.7606 (OUTLIER) cc_final: 0.6776 (m) outliers start: 65 outliers final: 36 residues processed: 189 average time/residue: 0.2957 time to fit residues: 83.4385 Evaluate side-chains 162 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 118 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 635 ARG Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 ARG Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1401 LYS Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1450 MET Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1528 LYS Chi-restraints excluded: chain A residue 1538 TRP Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1856 ASP Chi-restraints excluded: chain A residue 1907 THR Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2040 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 8.9990 chunk 136 optimal weight: 0.9980 chunk 93 optimal weight: 0.0000 chunk 20 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 121 optimal weight: 0.0570 chunk 181 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 0.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 979 ASN ** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16958 Z= 0.139 Angle : 0.511 9.422 23079 Z= 0.264 Chirality : 0.037 0.226 2588 Planarity : 0.003 0.049 2795 Dihedral : 15.235 175.718 2802 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.74 % Favored : 93.11 % Rotamer: Outliers : 3.88 % Allowed : 18.96 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.60 (0.19), residues: 1958 helix: 1.29 (0.18), residues: 898 sheet: -0.43 (0.42), residues: 166 loop : -2.28 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 520 HIS 0.008 0.001 HIS A1452 PHE 0.010 0.001 PHE A 649 TYR 0.030 0.001 TYR A1323 ARG 0.006 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 128 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7623 (m-30) cc_final: 0.7419 (m-30) REVERT: A 92 ASP cc_start: 0.7924 (t0) cc_final: 0.7292 (p0) REVERT: A 156 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6790 (mmt-90) REVERT: A 392 ILE cc_start: 0.9040 (mm) cc_final: 0.8777 (mm) REVERT: A 507 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8907 (mptt) REVERT: A 635 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7939 (mtm180) REVERT: A 710 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8257 (ttp) REVERT: A 712 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8098 (ttt-90) REVERT: A 797 LYS cc_start: 0.7800 (mptt) cc_final: 0.7500 (mptt) REVERT: A 800 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7406 (mt-10) REVERT: A 883 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: A 1061 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7636 (m-30) REVERT: A 1157 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8010 (ptpp) REVERT: A 1418 ARG cc_start: 0.7835 (tpp80) cc_final: 0.7019 (mmt180) REVERT: A 1467 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7750 (mm110) REVERT: A 1757 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7255 (mtm180) REVERT: A 1913 ARG cc_start: 0.7113 (tpm170) cc_final: 0.6879 (tpm170) REVERT: A 2026 MET cc_start: 0.7268 (mmm) cc_final: 0.6736 (mtm) outliers start: 67 outliers final: 41 residues processed: 186 average time/residue: 0.3177 time to fit residues: 86.8361 Evaluate side-chains 169 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 118 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 635 ARG Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1233 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1401 LYS Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1450 MET Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1578 SER Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1856 ASP Chi-restraints excluded: chain A residue 1903 ASN Chi-restraints excluded: chain A residue 2001 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 164 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1846 ASN A1896 HIS ** A1908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16958 Z= 0.152 Angle : 0.506 9.251 23079 Z= 0.262 Chirality : 0.037 0.200 2588 Planarity : 0.004 0.053 2795 Dihedral : 15.136 175.451 2797 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.35 % Favored : 92.54 % Rotamer: Outliers : 4.17 % Allowed : 19.19 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.48 (0.19), residues: 1958 helix: 1.40 (0.18), residues: 896 sheet: -0.45 (0.41), residues: 171 loop : -2.22 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 520 HIS 0.007 0.001 HIS A1452 PHE 0.013 0.001 PHE A 649 TYR 0.015 0.001 TYR A1323 ARG 0.005 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 125 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7920 (t0) cc_final: 0.7298 (p0) REVERT: A 192 MET cc_start: 0.7638 (mtm) cc_final: 0.7434 (mtp) REVERT: A 221 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8345 (mp) REVERT: A 392 ILE cc_start: 0.9068 (mm) cc_final: 0.8825 (mm) REVERT: A 507 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8912 (mptt) REVERT: A 635 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7940 (mtm180) REVERT: A 710 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8235 (ttp) REVERT: A 712 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8173 (ttt-90) REVERT: A 883 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: A 1157 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7962 (ptpp) REVERT: A 1334 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8284 (pp) REVERT: A 1418 ARG cc_start: 0.7731 (tpp80) cc_final: 0.6859 (mmt180) REVERT: A 1467 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7777 (mm110) REVERT: A 1485 THR cc_start: 0.7746 (p) cc_final: 0.7544 (p) REVERT: A 1757 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7169 (mtp180) REVERT: A 1758 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.6061 (tm) REVERT: A 1913 ARG cc_start: 0.7101 (tpm170) cc_final: 0.6629 (tpm170) REVERT: A 2026 MET cc_start: 0.7139 (mmm) cc_final: 0.6743 (mtm) outliers start: 72 outliers final: 47 residues processed: 186 average time/residue: 0.2951 time to fit residues: 83.4914 Evaluate side-chains 171 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 113 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 635 ARG Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1233 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1401 LYS Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1450 MET Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1578 SER Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1793 PHE Chi-restraints excluded: chain A residue 1856 ASP Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1903 ASN Chi-restraints excluded: chain A residue 1907 THR Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2001 VAL Chi-restraints excluded: chain A residue 2044 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 101 optimal weight: 0.0030 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 979 ASN ** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1846 ASN ** A1908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 16958 Z= 0.257 Angle : 0.560 10.984 23079 Z= 0.288 Chirality : 0.039 0.203 2588 Planarity : 0.004 0.054 2795 Dihedral : 15.171 174.698 2795 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.92 % Favored : 91.98 % Rotamer: Outliers : 4.35 % Allowed : 19.01 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.60 (0.19), residues: 1958 helix: 1.26 (0.18), residues: 897 sheet: -0.75 (0.40), residues: 183 loop : -2.19 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 520 HIS 0.029 0.001 HIS A1896 PHE 0.019 0.001 PHE A 649 TYR 0.011 0.001 TYR A1323 ARG 0.006 0.000 ARG A 739 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 116 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7927 (t0) cc_final: 0.7383 (p0) REVERT: A 221 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8295 (mp) REVERT: A 240 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8351 (ttt-90) REVERT: A 392 ILE cc_start: 0.9162 (mm) cc_final: 0.8923 (mm) REVERT: A 507 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8912 (mptt) REVERT: A 710 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8121 (ttp) REVERT: A 712 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8305 (ttt-90) REVERT: A 860 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8509 (mm) REVERT: A 887 MET cc_start: 0.7548 (tmm) cc_final: 0.7221 (tmm) REVERT: A 1061 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7650 (m-30) REVERT: A 1157 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8017 (ptpp) REVERT: A 1334 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8340 (pp) REVERT: A 1418 ARG cc_start: 0.7669 (tpp80) cc_final: 0.6795 (mmt180) REVERT: A 1467 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7905 (mm110) REVERT: A 1757 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7291 (mtp180) REVERT: A 1758 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.5982 (tm) REVERT: A 1782 TYR cc_start: 0.6683 (t80) cc_final: 0.6211 (t80) REVERT: A 1787 MET cc_start: 0.7690 (ptm) cc_final: 0.7404 (ptm) REVERT: A 1913 ARG cc_start: 0.7199 (tpm170) cc_final: 0.6807 (tpm170) REVERT: A 2026 MET cc_start: 0.7428 (mmm) cc_final: 0.6888 (mtm) outliers start: 75 outliers final: 48 residues processed: 180 average time/residue: 0.3233 time to fit residues: 86.7680 Evaluate side-chains 168 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 108 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1233 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1401 LYS Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1450 MET Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1626 ILE Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1894 TRP Chi-restraints excluded: chain A residue 1903 ASN Chi-restraints excluded: chain A residue 1907 THR Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2001 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 109 optimal weight: 0.0020 chunk 140 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1846 ASN ** A1908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16958 Z= 0.174 Angle : 0.525 8.677 23079 Z= 0.270 Chirality : 0.038 0.201 2588 Planarity : 0.004 0.048 2795 Dihedral : 15.130 175.180 2795 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.51 % Favored : 92.39 % Rotamer: Outliers : 4.12 % Allowed : 20.23 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.48 (0.19), residues: 1958 helix: 1.39 (0.18), residues: 890 sheet: -0.70 (0.40), residues: 183 loop : -2.13 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1547 HIS 0.008 0.001 HIS A1452 PHE 0.013 0.001 PHE A 649 TYR 0.018 0.001 TYR A1323 ARG 0.006 0.000 ARG A1694 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 115 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7876 (t0) cc_final: 0.7379 (p0) REVERT: A 221 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8285 (mp) REVERT: A 240 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8420 (ttt-90) REVERT: A 507 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8932 (mptt) REVERT: A 635 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7898 (mtm180) REVERT: A 710 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8156 (ttp) REVERT: A 712 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8229 (ttt-90) REVERT: A 860 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8517 (mm) REVERT: A 1006 MET cc_start: 0.8103 (tpp) cc_final: 0.7741 (tpt) REVERT: A 1061 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7621 (m-30) REVERT: A 1157 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8000 (ptpp) REVERT: A 1235 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8571 (p) REVERT: A 1418 ARG cc_start: 0.7664 (tpp80) cc_final: 0.6786 (mmt180) REVERT: A 1467 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7813 (mm110) REVERT: A 1757 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7382 (mtm180) REVERT: A 1758 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.6083 (tm) REVERT: A 1782 TYR cc_start: 0.6830 (t80) cc_final: 0.6364 (t80) REVERT: A 1787 MET cc_start: 0.7591 (ptm) cc_final: 0.7345 (ptm) REVERT: A 1913 ARG cc_start: 0.7132 (tpm170) cc_final: 0.6690 (tpm170) REVERT: A 1995 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7165 (mm-30) REVERT: A 2026 MET cc_start: 0.7362 (mmm) cc_final: 0.6849 (mtm) outliers start: 71 outliers final: 49 residues processed: 175 average time/residue: 0.2950 time to fit residues: 77.4088 Evaluate side-chains 170 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 107 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 635 ARG Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1174 ASN Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1233 SER Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1401 LYS Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1450 MET Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1793 PHE Chi-restraints excluded: chain A residue 1856 ASP Chi-restraints excluded: chain A residue 1894 TRP Chi-restraints excluded: chain A residue 1903 ASN Chi-restraints excluded: chain A residue 1907 THR Chi-restraints excluded: chain A residue 1995 GLU Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2001 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 0.7980 chunk 76 optimal weight: 0.0570 chunk 114 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 174 optimal weight: 0.0030 overall best weight: 1.5712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1057 HIS A1091 HIS A1292 ASN A1691 GLN ** A1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16958 Z= 0.205 Angle : 0.537 9.393 23079 Z= 0.276 Chirality : 0.038 0.202 2588 Planarity : 0.004 0.055 2795 Dihedral : 15.105 174.931 2795 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.87 % Favored : 92.03 % Rotamer: Outliers : 3.94 % Allowed : 20.52 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.50 (0.19), residues: 1958 helix: 1.36 (0.18), residues: 891 sheet: -0.71 (0.39), residues: 183 loop : -2.12 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1547 HIS 0.008 0.001 HIS A1452 PHE 0.015 0.001 PHE A 649 TYR 0.017 0.001 TYR A1323 ARG 0.004 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 107 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7903 (t0) cc_final: 0.7399 (p0) REVERT: A 221 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8292 (mp) REVERT: A 240 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8395 (ttt-90) REVERT: A 507 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8937 (mptt) REVERT: A 635 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7894 (mtm180) REVERT: A 710 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8150 (ttp) REVERT: A 712 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8272 (ttt-90) REVERT: A 860 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8536 (mm) REVERT: A 1061 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7657 (m-30) REVERT: A 1123 GLU cc_start: 0.8186 (pm20) cc_final: 0.7516 (pm20) REVERT: A 1157 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7997 (ptpp) REVERT: A 1235 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8573 (p) REVERT: A 1418 ARG cc_start: 0.7626 (tpp80) cc_final: 0.6820 (mmt180) REVERT: A 1467 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7879 (mm110) REVERT: A 1493 ARG cc_start: 0.6776 (ttm170) cc_final: 0.6547 (ttm170) REVERT: A 1757 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7344 (mtp180) REVERT: A 1758 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5842 (tm) REVERT: A 1782 TYR cc_start: 0.6914 (t80) cc_final: 0.6408 (t80) REVERT: A 1913 ARG cc_start: 0.7177 (tpm170) cc_final: 0.6787 (tpm170) REVERT: A 1995 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7198 (mm-30) outliers start: 68 outliers final: 49 residues processed: 167 average time/residue: 0.3168 time to fit residues: 79.0410 Evaluate side-chains 166 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 103 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 635 ARG Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1174 ASN Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1233 SER Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1401 LYS Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1793 PHE Chi-restraints excluded: chain A residue 1894 TRP Chi-restraints excluded: chain A residue 1903 ASN Chi-restraints excluded: chain A residue 1907 THR Chi-restraints excluded: chain A residue 1995 GLU Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2001 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 161 optimal weight: 0.0570 chunk 169 optimal weight: 9.9990 chunk 117 optimal weight: 0.6980 chunk 189 optimal weight: 0.9980 overall best weight: 2.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1459 ASN ** A1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 16958 Z= 0.304 Angle : 0.602 10.024 23079 Z= 0.310 Chirality : 0.040 0.204 2588 Planarity : 0.004 0.055 2795 Dihedral : 15.184 174.945 2794 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.17 % Favored : 91.73 % Rotamer: Outliers : 4.17 % Allowed : 20.52 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.69 (0.19), residues: 1958 helix: 1.19 (0.18), residues: 890 sheet: -0.85 (0.39), residues: 184 loop : -2.19 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1547 HIS 0.007 0.001 HIS A1452 PHE 0.021 0.002 PHE A 649 TYR 0.016 0.002 TYR A1323 ARG 0.004 0.000 ARG A2032 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 105 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8359 (ttt-90) REVERT: A 448 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7894 (mp0) REVERT: A 507 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8939 (mptt) REVERT: A 710 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8153 (ttp) REVERT: A 712 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8407 (ttt-90) REVERT: A 860 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8466 (mm) REVERT: A 920 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7547 (tpp-160) REVERT: A 1006 MET cc_start: 0.8304 (tpp) cc_final: 0.7893 (tpt) REVERT: A 1061 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7597 (m-30) REVERT: A 1123 GLU cc_start: 0.8268 (pm20) cc_final: 0.7567 (pm20) REVERT: A 1157 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8064 (ptpp) REVERT: A 1235 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8625 (p) REVERT: A 1418 ARG cc_start: 0.7605 (tpp80) cc_final: 0.6796 (mmt180) REVERT: A 1467 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8035 (mm110) REVERT: A 1757 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7472 (mtm180) REVERT: A 1758 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.5911 (tm) REVERT: A 1782 TYR cc_start: 0.7046 (t80) cc_final: 0.6468 (t80) REVERT: A 1913 ARG cc_start: 0.7203 (tpm170) cc_final: 0.6585 (tpm170) REVERT: A 1995 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7224 (mm-30) outliers start: 72 outliers final: 47 residues processed: 168 average time/residue: 0.3103 time to fit residues: 78.6621 Evaluate side-chains 162 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 102 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1174 ASN Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1401 LYS Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1894 TRP Chi-restraints excluded: chain A residue 1903 ASN Chi-restraints excluded: chain A residue 1907 THR Chi-restraints excluded: chain A residue 1995 GLU Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2001 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 198 optimal weight: 20.0000 chunk 182 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 121 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16958 Z= 0.181 Angle : 0.546 10.696 23079 Z= 0.279 Chirality : 0.038 0.200 2588 Planarity : 0.004 0.055 2795 Dihedral : 15.115 175.474 2793 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.71 % Favored : 92.19 % Rotamer: Outliers : 3.59 % Allowed : 21.10 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.64 (0.19), residues: 1958 helix: 1.27 (0.18), residues: 897 sheet: -0.82 (0.38), residues: 183 loop : -2.25 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1547 HIS 0.007 0.001 HIS A1452 PHE 0.013 0.001 PHE A 649 TYR 0.015 0.001 TYR A1323 ARG 0.004 0.000 ARG A 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 109 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7890 (t0) cc_final: 0.7430 (p0) REVERT: A 240 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8349 (ttt-90) REVERT: A 507 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8931 (mptt) REVERT: A 635 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7775 (mtm180) REVERT: A 710 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8122 (ttp) REVERT: A 712 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8229 (ttt-90) REVERT: A 860 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8454 (mm) REVERT: A 920 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7610 (tpp-160) REVERT: A 1006 MET cc_start: 0.8200 (tpp) cc_final: 0.7799 (tpt) REVERT: A 1061 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: A 1123 GLU cc_start: 0.8204 (pm20) cc_final: 0.7634 (pm20) REVERT: A 1157 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8002 (ptpp) REVERT: A 1235 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8597 (p) REVERT: A 1418 ARG cc_start: 0.7572 (tpp80) cc_final: 0.6775 (mmt180) REVERT: A 1467 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7850 (mm110) REVERT: A 1757 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7249 (mtm180) REVERT: A 1758 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.5955 (tm) REVERT: A 1782 TYR cc_start: 0.7098 (t80) cc_final: 0.6583 (t80) REVERT: A 1787 MET cc_start: 0.7770 (ttp) cc_final: 0.7496 (ttm) REVERT: A 1809 MET cc_start: 0.6428 (tmm) cc_final: 0.6227 (tmm) REVERT: A 1913 ARG cc_start: 0.7176 (tpm170) cc_final: 0.6719 (tpm170) REVERT: A 1919 PHE cc_start: 0.9040 (m-80) cc_final: 0.8774 (m-80) REVERT: A 1995 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7241 (mm-30) outliers start: 62 outliers final: 43 residues processed: 165 average time/residue: 0.3120 time to fit residues: 76.8258 Evaluate side-chains 162 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 105 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 635 ARG Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1174 ASN Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1401 LYS Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1757 ARG Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1793 PHE Chi-restraints excluded: chain A residue 1894 TRP Chi-restraints excluded: chain A residue 1903 ASN Chi-restraints excluded: chain A residue 1907 THR Chi-restraints excluded: chain A residue 1995 GLU Chi-restraints excluded: chain A residue 2000 VAL Chi-restraints excluded: chain A residue 2001 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 158 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 162 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN A1204 GLN A1280 ASN ** A1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.082820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.066759 restraints weight = 53381.270| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.51 r_work: 0.3335 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16958 Z= 0.165 Angle : 0.542 11.061 23079 Z= 0.276 Chirality : 0.038 0.199 2588 Planarity : 0.004 0.055 2795 Dihedral : 15.038 175.308 2793 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.61 % Favored : 92.29 % Rotamer: Outliers : 3.25 % Allowed : 21.57 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.53 (0.19), residues: 1958 helix: 1.37 (0.18), residues: 896 sheet: -0.73 (0.38), residues: 183 loop : -2.21 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1547 HIS 0.007 0.001 HIS A1452 PHE 0.012 0.001 PHE A 649 TYR 0.016 0.001 TYR A1323 ARG 0.004 0.000 ARG A 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3475.35 seconds wall clock time: 63 minutes 7.81 seconds (3787.81 seconds total)