Starting phenix.real_space_refine on Sun May 3 09:23:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9enr_19842/05_2026/9enr_19842.cif Found real_map, /net/cci-nas-00/data/ceres_data/9enr_19842/05_2026/9enr_19842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9enr_19842/05_2026/9enr_19842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9enr_19842/05_2026/9enr_19842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9enr_19842/05_2026/9enr_19842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9enr_19842/05_2026/9enr_19842.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.025 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 1 5.49 5 S 72 5.16 5 C 7659 2.51 5 N 2081 2.21 5 O 2314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12127 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1551, 12044 Classifications: {'peptide': 1551} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 76, 'TRANS': 1474} Chain breaks: 5 Unresolved non-hydrogen bonds: 363 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 290 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 11, 'ARG:plan': 4, 'ASN:plan1': 12, 'GLN:plan1': 6, 'PHE:plan': 2, 'TYR:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 216 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'43Y': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 3.01, per 1000 atoms: 0.25 Number of scatterers: 12127 At special positions: 0 Unit cell: (93.9504, 99.8752, 154.891, 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 72 16.00 P 1 15.00 O 2314 8.00 N 2081 7.00 C 7659 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 178 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A1242 " - pdb=" SG CYS A1279 " distance=2.03 Simple disulfide: pdb=" SG CYS A1310 " - pdb=" SG CYS A1324 " distance=2.03 Simple disulfide: pdb=" SG CYS A1444 " - pdb=" SG CYS A1598 " distance=2.03 Simple disulfide: pdb=" SG CYS A1466 " - pdb=" SG CYS A1634 " distance=2.03 Simple disulfide: pdb=" SG CYS A1615 " - pdb=" SG CYS A1650 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 296 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 653.7 milliseconds 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2958 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 8 sheets defined 31.8% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 41 through 44 removed outlier: 3.680A pdb=" N SER A 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 41 through 44' Processing helix chain 'A' and resid 126 through 139 Processing helix chain 'A' and resid 188 through 195 removed outlier: 3.626A pdb=" N ILE A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 420 through 436 Processing helix chain 'A' and resid 437 through 440 removed outlier: 5.679A pdb=" N SER A 440 " --> pdb=" O GLU A 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 437 through 440' Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 446 through 459 Processing helix chain 'A' and resid 462 through 474 removed outlier: 3.862A pdb=" N GLN A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 505 removed outlier: 4.240A pdb=" N GLY A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 520 Processing helix chain 'A' and resid 524 through 534 removed outlier: 3.749A pdb=" N LYS A 533 " --> pdb=" O ASN A 529 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 537 No H-bonds generated for 'chain 'A' and resid 535 through 537' Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 555 through 560 removed outlier: 3.569A pdb=" N ASN A 560 " --> pdb=" O PRO A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 580 Processing helix chain 'A' and resid 582 through 590 removed outlier: 3.602A pdb=" N TYR A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 596 removed outlier: 3.579A pdb=" N PHE A 595 " --> pdb=" O PRO A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 625 removed outlier: 4.021A pdb=" N ASP A 608 " --> pdb=" O ASN A 604 " (cutoff:3.500A) Proline residue: A 612 - end of helix Processing helix chain 'A' and resid 626 through 641 removed outlier: 4.203A pdb=" N GLY A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 654 removed outlier: 3.981A pdb=" N SER A 647 " --> pdb=" O PRO A 643 " (cutoff:3.500A) Proline residue: A 651 - end of helix removed outlier: 3.751A pdb=" N GLU A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 670 Processing helix chain 'A' and resid 671 through 676 removed outlier: 3.659A pdb=" N THR A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU A 676 " --> pdb=" O GLY A 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 671 through 676' Processing helix chain 'A' and resid 678 through 692 removed outlier: 3.939A pdb=" N ASN A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 708 Processing helix chain 'A' and resid 713 through 727 removed outlier: 3.658A pdb=" N LEU A 717 " --> pdb=" O PRO A 713 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS A 725 " --> pdb=" O ALA A 721 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 751 through 760 removed outlier: 4.036A pdb=" N LYS A 756 " --> pdb=" O LYS A 752 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS A 757 " --> pdb=" O ASP A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 853 through 863 removed outlier: 3.884A pdb=" N LYS A 857 " --> pdb=" O SER A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 908 removed outlier: 3.523A pdb=" N LEU A 894 " --> pdb=" O ASP A 890 " (cutoff:3.500A) Proline residue: A 898 - end of helix Processing helix chain 'A' and resid 985 through 987 No H-bonds generated for 'chain 'A' and resid 985 through 987' Processing helix chain 'A' and resid 1014 through 1016 No H-bonds generated for 'chain 'A' and resid 1014 through 1016' Processing helix chain 'A' and resid 1052 through 1056 Processing helix chain 'A' and resid 1089 through 1096 Processing helix chain 'A' and resid 1146 through 1150 removed outlier: 3.722A pdb=" N ASP A1150 " --> pdb=" O PRO A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1183 removed outlier: 3.678A pdb=" N GLY A1182 " --> pdb=" O MET A1178 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG A1183 " --> pdb=" O ARG A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1303 Processing helix chain 'A' and resid 1304 through 1317 removed outlier: 3.630A pdb=" N LYS A1308 " --> pdb=" O THR A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1332 Processing helix chain 'A' and resid 1345 through 1361 Processing helix chain 'A' and resid 1587 through 1591 Processing helix chain 'A' and resid 1619 through 1627 Processing helix chain 'A' and resid 1637 through 1648 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 39 removed outlier: 4.995A pdb=" N ASN A 26 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 58 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N HIS A 47 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN A 79 " --> pdb=" O HIS A 47 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY A 49 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG A 77 " --> pdb=" O GLY A 49 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU A 51 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR A 75 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS A 53 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY A 73 " --> pdb=" O LYS A 53 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 98 through 99 current: chain 'A' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 116 through 121 current: chain 'A' and resid 211 through 213 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 211 through 213 current: chain 'A' and resid 270 through 279 Processing sheet with id=AA2, first strand: chain 'A' and resid 168 through 169 Processing sheet with id=AA3, first strand: chain 'A' and resid 776 through 784 removed outlier: 3.546A pdb=" N ARG A 776 " --> pdb=" O TYR A 797 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 797 " --> pdb=" O ARG A 776 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR A 778 " --> pdb=" O LEU A 795 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A 793 " --> pdb=" O ASP A 780 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN A 796 " --> pdb=" O TYR A 810 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 798 " --> pdb=" O ILE A 808 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE A 808 " --> pdb=" O VAL A 798 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 808 through 812 current: chain 'A' and resid 874 through 879 Processing sheet with id=AA4, first strand: chain 'A' and resid 913 through 922 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 913 through 922 current: chain 'A' and resid 935 through 955 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 961 through 966 current: chain 'A' and resid 989 through 1012 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1017 through 1024 current: chain 'A' and resid 1060 through 1061 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1060 through 1061 current: chain 'A' and resid 1117 through 1123 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1117 through 1123 current: chain 'A' and resid 1188 through 1199 removed outlier: 4.038A pdb=" N ARG A1223 " --> pdb=" O SER A1214 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N SER A1216 " --> pdb=" O LYS A1221 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LYS A1221 " --> pdb=" O SER A1216 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A1237 " --> pdb=" O MET A1232 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N MET A1267 " --> pdb=" O LEU A1291 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A1269 " --> pdb=" O GLY A1289 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1067 through 1068 removed outlier: 3.591A pdb=" N THR A1085 " --> pdb=" O THR A1068 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1398 through 1400 Processing sheet with id=AA7, first strand: chain 'A' and resid 1451 through 1452 removed outlier: 3.538A pdb=" N TYR A1557 " --> pdb=" O GLY A1565 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE A1554 " --> pdb=" O LYS A1546 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A1546 " --> pdb=" O PHE A1554 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1468 through 1472 removed outlier: 6.529A pdb=" N VAL A1496 " --> pdb=" O VAL A1470 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR A1472 " --> pdb=" O VAL A1494 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A1494 " --> pdb=" O THR A1472 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A1508 " --> pdb=" O PHE A1519 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2042 1.31 - 1.44: 3088 1.44 - 1.56: 7101 1.56 - 1.69: 2 1.69 - 1.81: 129 Bond restraints: 12362 Sorted by residual: bond pdb=" C2 43Y A1801 " pdb=" O2 43Y A1801 " ideal model delta sigma weight residual 1.468 1.398 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C3 43Y A1801 " pdb=" O3 43Y A1801 " ideal model delta sigma weight residual 1.457 1.411 0.046 2.00e-02 2.50e+03 5.38e+00 bond pdb=" C31 43Y A1801 " pdb=" C32 43Y A1801 " ideal model delta sigma weight residual 1.500 1.541 -0.041 2.00e-02 2.50e+03 4.27e+00 bond pdb=" C11 43Y A1801 " pdb=" C9 43Y A1801 " ideal model delta sigma weight residual 1.499 1.539 -0.040 2.00e-02 2.50e+03 3.99e+00 bond pdb=" C31 43Y A1801 " pdb=" O2 43Y A1801 " ideal model delta sigma weight residual 1.372 1.411 -0.039 2.00e-02 2.50e+03 3.84e+00 ... (remaining 12357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 16586 2.75 - 5.50: 137 5.50 - 8.26: 9 8.26 - 11.01: 3 11.01 - 13.76: 4 Bond angle restraints: 16739 Sorted by residual: angle pdb=" O1P 43Y A1801 " pdb=" P 43Y A1801 " pdb=" O2P 43Y A1801 " ideal model delta sigma weight residual 123.24 109.48 13.76 3.00e+00 1.11e-01 2.10e+01 angle pdb=" O3P 43Y A1801 " pdb=" P 43Y A1801 " pdb=" O4P 43Y A1801 " ideal model delta sigma weight residual 97.79 109.83 -12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" C32 43Y A1801 " pdb=" C31 43Y A1801 " pdb=" O2 43Y A1801 " ideal model delta sigma weight residual 108.45 119.86 -11.41 3.00e+00 1.11e-01 1.45e+01 angle pdb=" C9 43Y A1801 " pdb=" C11 43Y A1801 " pdb=" O3 43Y A1801 " ideal model delta sigma weight residual 108.61 119.92 -11.31 3.00e+00 1.11e-01 1.42e+01 angle pdb=" C32 43Y A1801 " pdb=" C31 43Y A1801 " pdb=" O31 43Y A1801 " ideal model delta sigma weight residual 130.12 119.84 10.28 3.00e+00 1.11e-01 1.17e+01 ... (remaining 16734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.92: 7443 31.92 - 63.84: 205 63.84 - 95.75: 23 95.75 - 127.67: 5 127.67 - 159.59: 4 Dihedral angle restraints: 7680 sinusoidal: 3133 harmonic: 4547 Sorted by residual: dihedral pdb=" CB CYS A1242 " pdb=" SG CYS A1242 " pdb=" SG CYS A1279 " pdb=" CB CYS A1279 " ideal model delta sinusoidal sigma weight residual -86.00 -172.42 86.42 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYS A1466 " pdb=" SG CYS A1466 " pdb=" SG CYS A1634 " pdb=" CB CYS A1634 " ideal model delta sinusoidal sigma weight residual -86.00 -17.49 -68.51 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" CA CYS A1324 " pdb=" C CYS A1324 " pdb=" N GLN A1325 " pdb=" CA GLN A1325 " ideal model delta harmonic sigma weight residual 180.00 156.76 23.24 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 7677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1502 0.051 - 0.102: 312 0.102 - 0.153: 93 0.153 - 0.204: 3 0.204 - 0.256: 3 Chirality restraints: 1913 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA CYS A1310 " pdb=" N CYS A1310 " pdb=" C CYS A1310 " pdb=" CB CYS A1310 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C2 43Y A1801 " pdb=" C1 43Y A1801 " pdb=" C3 43Y A1801 " pdb=" O2 43Y A1801 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1910 not shown) Planarity restraints: 2153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 314 " 0.052 5.00e-02 4.00e+02 7.89e-02 9.95e+00 pdb=" N PRO A 315 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 315 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 315 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 507 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO A 508 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 508 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 508 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 296 " -0.019 2.00e-02 2.50e+03 1.81e-02 4.09e+00 pdb=" CG ASN A 296 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 296 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 296 " 0.022 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " -0.020 2.00e-02 2.50e+03 ... (remaining 2150 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1964 2.77 - 3.30: 11613 3.30 - 3.83: 19144 3.83 - 4.37: 21339 4.37 - 4.90: 37767 Nonbonded interactions: 91827 Sorted by model distance: nonbonded pdb=" NH1 ARG A 77 " pdb=" OE2 GLU A 987 " model vdw 2.234 3.120 nonbonded pdb=" O ALA A 721 " pdb=" OG1 THR A 724 " model vdw 2.250 3.040 nonbonded pdb=" OE1 GLN A 139 " pdb=" OG SER A 271 " model vdw 2.251 3.040 nonbonded pdb=" OD1 ASN A 462 " pdb=" NE2 GLN A 465 " model vdw 2.279 3.120 nonbonded pdb=" OG1 THR A1401 " pdb=" O MET A1404 " model vdw 2.290 3.040 ... (remaining 91822 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.210 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.780 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 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 : 0.004 0.070 12373 Z= 0.164 Angle : 0.664 13.760 16766 Z= 0.324 Chirality : 0.046 0.256 1913 Planarity : 0.005 0.079 2152 Dihedral : 15.563 159.591 4704 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.22), residues: 1539 helix: 1.56 (0.26), residues: 399 sheet: -0.19 (0.26), residues: 436 loop : -1.28 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1595 TYR 0.020 0.001 TYR A1438 PHE 0.029 0.002 PHE A 705 TRP 0.027 0.002 TRP A1023 HIS 0.005 0.001 HIS A1603 Details of bonding type rmsd covalent geometry : bond 0.00366 (12362) covalent geometry : angle 0.65594 (16739) SS BOND : bond 0.00247 ( 6) SS BOND : angle 2.94977 ( 12) hydrogen bonds : bond 0.20175 ( 436) hydrogen bonds : angle 7.27656 ( 1224) link_ALPHA1-3 : bond 0.00494 ( 1) link_ALPHA1-3 : angle 1.46312 ( 3) link_ALPHA1-6 : bond 0.00365 ( 1) link_ALPHA1-6 : angle 1.56847 ( 3) link_BETA1-4 : bond 0.00348 ( 2) link_BETA1-4 : angle 1.64205 ( 6) link_NAG-ASN : bond 0.00300 ( 1) link_NAG-ASN : angle 4.46840 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 90 ILE cc_start: 0.7913 (mm) cc_final: 0.7709 (mt) REVERT: A 197 GLU cc_start: 0.7253 (pm20) cc_final: 0.7026 (pm20) REVERT: A 211 MET cc_start: 0.7698 (mpp) cc_final: 0.7362 (mpp) REVERT: A 259 ILE cc_start: 0.7568 (mt) cc_final: 0.7027 (mt) REVERT: A 314 ASN cc_start: 0.6884 (m110) cc_final: 0.6469 (m110) REVERT: A 752 LYS cc_start: 0.8382 (ttpt) cc_final: 0.8017 (ttpp) REVERT: A 963 ILE cc_start: 0.7794 (mm) cc_final: 0.7552 (mm) REVERT: A 1087 LYS cc_start: 0.7934 (tptp) cc_final: 0.7673 (tptp) REVERT: A 1094 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6750 (mm-30) REVERT: A 1178 MET cc_start: 0.7504 (mmm) cc_final: 0.7117 (mmm) REVERT: A 1204 GLU cc_start: 0.7240 (mp0) cc_final: 0.6966 (mp0) REVERT: A 1232 MET cc_start: 0.6792 (mmt) cc_final: 0.6492 (mmt) REVERT: A 1322 ARG cc_start: 0.7085 (ttt90) cc_final: 0.6861 (ttm-80) REVERT: A 1588 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7228 (mm-30) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.1204 time to fit residues: 52.5100 Evaluate side-chains 292 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 ASN A 269 GLN A 483 ASN A 588 ASN A1089 ASN ** A1550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1614 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.157326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129305 restraints weight = 17661.036| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.76 r_work: 0.3510 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 12373 Z= 0.288 Angle : 0.710 8.804 16766 Z= 0.372 Chirality : 0.050 0.184 1913 Planarity : 0.005 0.056 2152 Dihedral : 11.017 153.744 1779 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.99 % Allowed : 9.35 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.22), residues: 1539 helix: 1.39 (0.26), residues: 403 sheet: -0.35 (0.25), residues: 444 loop : -1.51 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1595 TYR 0.027 0.002 TYR A1116 PHE 0.027 0.003 PHE A 572 TRP 0.031 0.003 TRP A1023 HIS 0.009 0.001 HIS A 697 Details of bonding type rmsd covalent geometry : bond 0.00671 (12362) covalent geometry : angle 0.70519 (16739) SS BOND : bond 0.00230 ( 6) SS BOND : angle 1.57546 ( 12) hydrogen bonds : bond 0.06488 ( 436) hydrogen bonds : angle 5.71138 ( 1224) link_ALPHA1-3 : bond 0.01551 ( 1) link_ALPHA1-3 : angle 1.46036 ( 3) link_ALPHA1-6 : bond 0.00729 ( 1) link_ALPHA1-6 : angle 2.36786 ( 3) link_BETA1-4 : bond 0.00395 ( 2) link_BETA1-4 : angle 2.43522 ( 6) link_NAG-ASN : bond 0.00552 ( 1) link_NAG-ASN : angle 4.07239 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 311 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 30 TYR cc_start: 0.7842 (m-80) cc_final: 0.7418 (m-80) REVERT: A 90 ILE cc_start: 0.7983 (mm) cc_final: 0.7709 (mt) REVERT: A 164 TYR cc_start: 0.7432 (m-10) cc_final: 0.6911 (m-10) REVERT: A 197 GLU cc_start: 0.7853 (pm20) cc_final: 0.7616 (pm20) REVERT: A 201 MET cc_start: 0.7637 (ppp) cc_final: 0.7421 (ppp) REVERT: A 211 MET cc_start: 0.8090 (mpp) cc_final: 0.7634 (mpp) REVERT: A 314 ASN cc_start: 0.6814 (m110) cc_final: 0.6538 (m110) REVERT: A 695 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7255 (mm-30) REVERT: A 793 MET cc_start: 0.8172 (ttt) cc_final: 0.7904 (ttm) REVERT: A 918 MET cc_start: 0.7304 (mpp) cc_final: 0.6939 (mpp) REVERT: A 922 TYR cc_start: 0.8377 (t80) cc_final: 0.7895 (t80) REVERT: A 963 ILE cc_start: 0.8027 (mm) cc_final: 0.7737 (mm) REVERT: A 1083 VAL cc_start: 0.8069 (t) cc_final: 0.7813 (p) REVERT: A 1087 LYS cc_start: 0.8123 (tptp) cc_final: 0.7816 (tptp) REVERT: A 1094 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6923 (mm-30) REVERT: A 1167 GLN cc_start: 0.7465 (mp10) cc_final: 0.7216 (mp10) REVERT: A 1204 GLU cc_start: 0.7595 (mp0) cc_final: 0.7357 (mp0) REVERT: A 1230 VAL cc_start: 0.8567 (m) cc_final: 0.8203 (t) REVERT: A 1322 ARG cc_start: 0.7465 (ttt90) cc_final: 0.7229 (ttm-80) REVERT: A 1339 ILE cc_start: 0.7996 (mt) cc_final: 0.7734 (mp) REVERT: A 1535 LYS cc_start: 0.8470 (tmtt) cc_final: 0.8197 (tptp) REVERT: A 1550 ASN cc_start: 0.7742 (t0) cc_final: 0.7455 (t0) REVERT: A 1588 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7816 (mm-30) REVERT: A 1603 HIS cc_start: 0.6305 (m170) cc_final: 0.6070 (m170) outliers start: 26 outliers final: 20 residues processed: 318 average time/residue: 0.1251 time to fit residues: 54.9565 Evaluate side-chains 321 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 301 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1238 ASP Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1564 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 0.0570 chunk 60 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 0.0970 chunk 137 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 GLN A1089 ASN A1550 ASN A1614 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.159104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.130918 restraints weight = 17833.582| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.90 r_work: 0.3541 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12373 Z= 0.127 Angle : 0.604 10.576 16766 Z= 0.310 Chirality : 0.046 0.174 1913 Planarity : 0.004 0.052 2152 Dihedral : 9.979 140.174 1779 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.22 % Allowed : 12.64 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.22), residues: 1539 helix: 1.68 (0.26), residues: 406 sheet: -0.17 (0.25), residues: 447 loop : -1.33 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1115 TYR 0.022 0.001 TYR A 904 PHE 0.016 0.001 PHE A 563 TRP 0.016 0.002 TRP A1023 HIS 0.006 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00284 (12362) covalent geometry : angle 0.60059 (16739) SS BOND : bond 0.00563 ( 6) SS BOND : angle 1.49070 ( 12) hydrogen bonds : bond 0.04360 ( 436) hydrogen bonds : angle 5.22709 ( 1224) link_ALPHA1-3 : bond 0.01462 ( 1) link_ALPHA1-3 : angle 1.62529 ( 3) link_ALPHA1-6 : bond 0.00598 ( 1) link_ALPHA1-6 : angle 2.07231 ( 3) link_BETA1-4 : bond 0.00345 ( 2) link_BETA1-4 : angle 1.62247 ( 6) link_NAG-ASN : bond 0.00133 ( 1) link_NAG-ASN : angle 2.51168 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 307 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 30 TYR cc_start: 0.7866 (m-80) cc_final: 0.7381 (m-80) REVERT: A 164 TYR cc_start: 0.7444 (m-10) cc_final: 0.6898 (m-10) REVERT: A 197 GLU cc_start: 0.7791 (pm20) cc_final: 0.7520 (pm20) REVERT: A 211 MET cc_start: 0.7975 (mpp) cc_final: 0.7572 (mpp) REVERT: A 273 THR cc_start: 0.8352 (m) cc_final: 0.8129 (m) REVERT: A 304 LYS cc_start: 0.7747 (tppt) cc_final: 0.7507 (tppt) REVERT: A 314 ASN cc_start: 0.6748 (m110) cc_final: 0.6297 (m110) REVERT: A 415 LYS cc_start: 0.7925 (ttpp) cc_final: 0.7492 (ttpp) REVERT: A 610 TYR cc_start: 0.7957 (m-10) cc_final: 0.7306 (m-10) REVERT: A 695 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7249 (mm-30) REVERT: A 906 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6542 (pm20) REVERT: A 918 MET cc_start: 0.7379 (mpp) cc_final: 0.7001 (mpp) REVERT: A 963 ILE cc_start: 0.7949 (mm) cc_final: 0.7642 (mm) REVERT: A 1087 LYS cc_start: 0.8025 (tptp) cc_final: 0.7723 (tptp) REVERT: A 1094 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6872 (mm-30) REVERT: A 1144 MET cc_start: 0.7847 (mmm) cc_final: 0.7556 (mmm) REVERT: A 1167 GLN cc_start: 0.7418 (mp10) cc_final: 0.7140 (mp10) REVERT: A 1204 GLU cc_start: 0.7589 (mp0) cc_final: 0.7147 (mp0) REVERT: A 1230 VAL cc_start: 0.8517 (m) cc_final: 0.8154 (t) REVERT: A 1322 ARG cc_start: 0.7314 (ttt90) cc_final: 0.7045 (ttm-80) REVERT: A 1457 LYS cc_start: 0.7963 (tppt) cc_final: 0.7674 (ttmt) REVERT: A 1535 LYS cc_start: 0.8481 (tmtt) cc_final: 0.8201 (tptp) REVERT: A 1550 ASN cc_start: 0.7717 (t0) cc_final: 0.7429 (t0) REVERT: A 1588 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7685 (mm-30) REVERT: A 1603 HIS cc_start: 0.6321 (m170) cc_final: 0.6034 (m170) outliers start: 29 outliers final: 19 residues processed: 317 average time/residue: 0.1146 time to fit residues: 51.0712 Evaluate side-chains 323 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 303 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1238 ASP Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1337 VAL Chi-restraints excluded: chain A residue 1445 MET Chi-restraints excluded: chain A residue 1531 VAL Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1564 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 33 optimal weight: 0.3980 chunk 138 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 GLN A 398 GLN A1089 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.159133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.130852 restraints weight = 17652.615| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.91 r_work: 0.3533 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12373 Z= 0.144 Angle : 0.605 10.572 16766 Z= 0.308 Chirality : 0.046 0.189 1913 Planarity : 0.004 0.052 2152 Dihedral : 9.330 141.024 1779 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.76 % Allowed : 14.18 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.22), residues: 1539 helix: 1.71 (0.26), residues: 404 sheet: -0.06 (0.26), residues: 439 loop : -1.29 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1595 TYR 0.024 0.001 TYR A 904 PHE 0.036 0.002 PHE A 705 TRP 0.016 0.002 TRP A1023 HIS 0.004 0.001 HIS A 697 Details of bonding type rmsd covalent geometry : bond 0.00334 (12362) covalent geometry : angle 0.60206 (16739) SS BOND : bond 0.00202 ( 6) SS BOND : angle 1.25041 ( 12) hydrogen bonds : bond 0.04328 ( 436) hydrogen bonds : angle 5.10228 ( 1224) link_ALPHA1-3 : bond 0.01366 ( 1) link_ALPHA1-3 : angle 1.77087 ( 3) link_ALPHA1-6 : bond 0.00536 ( 1) link_ALPHA1-6 : angle 2.04929 ( 3) link_BETA1-4 : bond 0.00357 ( 2) link_BETA1-4 : angle 1.60450 ( 6) link_NAG-ASN : bond 0.00213 ( 1) link_NAG-ASN : angle 2.64525 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 306 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 30 TYR cc_start: 0.7856 (m-80) cc_final: 0.7383 (m-80) REVERT: A 164 TYR cc_start: 0.7448 (m-10) cc_final: 0.6865 (m-10) REVERT: A 197 GLU cc_start: 0.7817 (pm20) cc_final: 0.7540 (pm20) REVERT: A 211 MET cc_start: 0.7996 (mpp) cc_final: 0.7603 (mpp) REVERT: A 273 THR cc_start: 0.8340 (m) cc_final: 0.8111 (m) REVERT: A 314 ASN cc_start: 0.6722 (m110) cc_final: 0.6276 (m110) REVERT: A 415 LYS cc_start: 0.7913 (ttpp) cc_final: 0.7479 (ttpp) REVERT: A 610 TYR cc_start: 0.7960 (m-10) cc_final: 0.7606 (m-10) REVERT: A 662 PHE cc_start: 0.7448 (t80) cc_final: 0.7192 (t80) REVERT: A 695 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7320 (mm-30) REVERT: A 918 MET cc_start: 0.7345 (mpp) cc_final: 0.6990 (mpp) REVERT: A 1087 LYS cc_start: 0.8052 (tptp) cc_final: 0.7768 (tptp) REVERT: A 1094 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6962 (mm-30) REVERT: A 1167 GLN cc_start: 0.7468 (mp10) cc_final: 0.7144 (mp10) REVERT: A 1204 GLU cc_start: 0.7599 (mp0) cc_final: 0.7209 (mp0) REVERT: A 1230 VAL cc_start: 0.8503 (m) cc_final: 0.8269 (t) REVERT: A 1322 ARG cc_start: 0.7345 (ttt90) cc_final: 0.7124 (ttm-80) REVERT: A 1457 LYS cc_start: 0.7971 (tppt) cc_final: 0.7612 (ttmt) REVERT: A 1535 LYS cc_start: 0.8479 (tmtt) cc_final: 0.8188 (tptp) REVERT: A 1550 ASN cc_start: 0.7734 (t0) cc_final: 0.7336 (t0) REVERT: A 1588 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7812 (mm-30) REVERT: A 1603 HIS cc_start: 0.6284 (m170) cc_final: 0.5887 (m170) outliers start: 36 outliers final: 29 residues processed: 323 average time/residue: 0.1196 time to fit residues: 53.7936 Evaluate side-chains 334 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 305 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1238 ASP Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1310 CYS Chi-restraints excluded: chain A residue 1337 VAL Chi-restraints excluded: chain A residue 1445 MET Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1531 VAL Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1564 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 80 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 70 optimal weight: 0.0050 chunk 30 optimal weight: 50.0000 chunk 104 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 GLN A 398 GLN A 412 HIS A1089 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.158672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130301 restraints weight = 17641.340| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.91 r_work: 0.3523 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12373 Z= 0.168 Angle : 0.620 11.249 16766 Z= 0.316 Chirality : 0.047 0.201 1913 Planarity : 0.004 0.051 2152 Dihedral : 8.831 143.600 1779 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.22 % Allowed : 14.33 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.22), residues: 1539 helix: 1.69 (0.26), residues: 405 sheet: -0.02 (0.26), residues: 434 loop : -1.34 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 519 TYR 0.024 0.002 TYR A 904 PHE 0.032 0.002 PHE A 705 TRP 0.017 0.002 TRP A1023 HIS 0.005 0.001 HIS A 697 Details of bonding type rmsd covalent geometry : bond 0.00392 (12362) covalent geometry : angle 0.61643 (16739) SS BOND : bond 0.00086 ( 6) SS BOND : angle 1.34135 ( 12) hydrogen bonds : bond 0.04569 ( 436) hydrogen bonds : angle 5.08551 ( 1224) link_ALPHA1-3 : bond 0.01233 ( 1) link_ALPHA1-3 : angle 1.80273 ( 3) link_ALPHA1-6 : bond 0.00618 ( 1) link_ALPHA1-6 : angle 2.09745 ( 3) link_BETA1-4 : bond 0.00342 ( 2) link_BETA1-4 : angle 1.66517 ( 6) link_NAG-ASN : bond 0.00323 ( 1) link_NAG-ASN : angle 2.86047 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 308 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 30 TYR cc_start: 0.7874 (m-80) cc_final: 0.7397 (m-80) REVERT: A 164 TYR cc_start: 0.7461 (m-10) cc_final: 0.6882 (m-10) REVERT: A 197 GLU cc_start: 0.7796 (pm20) cc_final: 0.7515 (pm20) REVERT: A 211 MET cc_start: 0.8001 (mpp) cc_final: 0.7601 (mpp) REVERT: A 273 THR cc_start: 0.8333 (m) cc_final: 0.8100 (m) REVERT: A 314 ASN cc_start: 0.6701 (m110) cc_final: 0.6264 (m110) REVERT: A 415 LYS cc_start: 0.7931 (ttpp) cc_final: 0.7485 (ttpp) REVERT: A 610 TYR cc_start: 0.7981 (m-10) cc_final: 0.7690 (m-10) REVERT: A 662 PHE cc_start: 0.7420 (t80) cc_final: 0.7131 (t80) REVERT: A 695 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7265 (mm-30) REVERT: A 918 MET cc_start: 0.7341 (mpp) cc_final: 0.6999 (mpp) REVERT: A 963 ILE cc_start: 0.7968 (mm) cc_final: 0.7687 (mm) REVERT: A 1087 LYS cc_start: 0.8027 (tptp) cc_final: 0.7757 (tptp) REVERT: A 1092 MET cc_start: 0.7900 (tpp) cc_final: 0.7508 (tpp) REVERT: A 1094 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7000 (mm-30) REVERT: A 1167 GLN cc_start: 0.7509 (mp10) cc_final: 0.7161 (mp10) REVERT: A 1204 GLU cc_start: 0.7617 (mp0) cc_final: 0.7283 (mp0) REVERT: A 1322 ARG cc_start: 0.7375 (ttt90) cc_final: 0.7121 (ttm-80) REVERT: A 1457 LYS cc_start: 0.7952 (tppt) cc_final: 0.7713 (ttmt) REVERT: A 1516 LYS cc_start: 0.7701 (pptt) cc_final: 0.7420 (pptt) REVERT: A 1535 LYS cc_start: 0.8493 (tmtt) cc_final: 0.8153 (tptp) REVERT: A 1550 ASN cc_start: 0.7772 (t0) cc_final: 0.7351 (t0) REVERT: A 1588 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7833 (mm-30) outliers start: 42 outliers final: 35 residues processed: 325 average time/residue: 0.1217 time to fit residues: 55.3446 Evaluate side-chains 342 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 307 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1310 CYS Chi-restraints excluded: chain A residue 1337 VAL Chi-restraints excluded: chain A residue 1445 MET Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1470 VAL Chi-restraints excluded: chain A residue 1531 VAL Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1564 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 20 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 GLN A1089 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.157236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129451 restraints weight = 17496.578| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.78 r_work: 0.3516 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12373 Z= 0.227 Angle : 0.668 12.635 16766 Z= 0.340 Chirality : 0.048 0.210 1913 Planarity : 0.005 0.051 2152 Dihedral : 8.647 149.380 1779 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.22 % Allowed : 15.94 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.22), residues: 1539 helix: 1.52 (0.26), residues: 404 sheet: -0.08 (0.26), residues: 433 loop : -1.44 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 519 TYR 0.026 0.002 TYR A 904 PHE 0.028 0.002 PHE A 705 TRP 0.021 0.002 TRP A1023 HIS 0.009 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00530 (12362) covalent geometry : angle 0.66356 (16739) SS BOND : bond 0.00140 ( 6) SS BOND : angle 1.55859 ( 12) hydrogen bonds : bond 0.05213 ( 436) hydrogen bonds : angle 5.18080 ( 1224) link_ALPHA1-3 : bond 0.01391 ( 1) link_ALPHA1-3 : angle 1.92584 ( 3) link_ALPHA1-6 : bond 0.00687 ( 1) link_ALPHA1-6 : angle 2.13678 ( 3) link_BETA1-4 : bond 0.00402 ( 2) link_BETA1-4 : angle 1.92850 ( 6) link_NAG-ASN : bond 0.00469 ( 1) link_NAG-ASN : angle 3.28995 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 308 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 30 TYR cc_start: 0.7859 (m-80) cc_final: 0.7311 (m-80) REVERT: A 164 TYR cc_start: 0.7425 (m-10) cc_final: 0.6851 (m-10) REVERT: A 197 GLU cc_start: 0.7800 (pm20) cc_final: 0.7546 (pm20) REVERT: A 211 MET cc_start: 0.8065 (mpp) cc_final: 0.7698 (mpp) REVERT: A 273 THR cc_start: 0.8381 (m) cc_final: 0.8157 (m) REVERT: A 303 GLU cc_start: 0.6931 (pp20) cc_final: 0.6718 (pp20) REVERT: A 314 ASN cc_start: 0.6775 (m110) cc_final: 0.6369 (m110) REVERT: A 415 LYS cc_start: 0.7960 (ttpp) cc_final: 0.7506 (ttpp) REVERT: A 610 TYR cc_start: 0.8057 (m-10) cc_final: 0.7702 (m-10) REVERT: A 662 PHE cc_start: 0.7455 (t80) cc_final: 0.7200 (t80) REVERT: A 695 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7286 (mm-30) REVERT: A 918 MET cc_start: 0.7299 (mpp) cc_final: 0.6960 (mpp) REVERT: A 963 ILE cc_start: 0.7988 (mm) cc_final: 0.7701 (mm) REVERT: A 992 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8430 (mp) REVERT: A 1083 VAL cc_start: 0.8098 (t) cc_final: 0.7841 (p) REVERT: A 1087 LYS cc_start: 0.8057 (tptp) cc_final: 0.7847 (tptp) REVERT: A 1092 MET cc_start: 0.7913 (tpp) cc_final: 0.7487 (tpp) REVERT: A 1094 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7084 (mm-30) REVERT: A 1167 GLN cc_start: 0.7577 (mp10) cc_final: 0.7216 (mp10) REVERT: A 1204 GLU cc_start: 0.7630 (mp0) cc_final: 0.7288 (mp0) REVERT: A 1230 VAL cc_start: 0.8535 (t) cc_final: 0.8329 (t) REVERT: A 1247 ILE cc_start: 0.6768 (mp) cc_final: 0.6182 (tt) REVERT: A 1322 ARG cc_start: 0.7433 (ttt90) cc_final: 0.7180 (ttm-80) REVERT: A 1457 LYS cc_start: 0.7970 (tppt) cc_final: 0.7743 (ttmt) REVERT: A 1535 LYS cc_start: 0.8449 (tmtt) cc_final: 0.8203 (tptp) REVERT: A 1550 ASN cc_start: 0.7831 (t0) cc_final: 0.7400 (t0) REVERT: A 1588 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7806 (mm-30) outliers start: 42 outliers final: 35 residues processed: 325 average time/residue: 0.1161 time to fit residues: 52.9227 Evaluate side-chains 342 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 306 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1310 CYS Chi-restraints excluded: chain A residue 1337 VAL Chi-restraints excluded: chain A residue 1445 MET Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1470 VAL Chi-restraints excluded: chain A residue 1531 VAL Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1564 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 38 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN A1089 ASN A1129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.154773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.127011 restraints weight = 17488.647| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.81 r_work: 0.3474 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 12373 Z= 0.372 Angle : 0.782 14.526 16766 Z= 0.403 Chirality : 0.053 0.222 1913 Planarity : 0.006 0.053 2152 Dihedral : 8.908 158.768 1779 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.75 % Allowed : 16.55 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.22), residues: 1539 helix: 1.01 (0.25), residues: 403 sheet: -0.39 (0.25), residues: 441 loop : -1.65 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 989 TYR 0.032 0.003 TYR A1116 PHE 0.037 0.003 PHE A 572 TRP 0.025 0.003 TRP A 22 HIS 0.010 0.002 HIS A 990 Details of bonding type rmsd covalent geometry : bond 0.00866 (12362) covalent geometry : angle 0.77640 (16739) SS BOND : bond 0.00329 ( 6) SS BOND : angle 1.97166 ( 12) hydrogen bonds : bond 0.06646 ( 436) hydrogen bonds : angle 5.54632 ( 1224) link_ALPHA1-3 : bond 0.01193 ( 1) link_ALPHA1-3 : angle 1.72080 ( 3) link_ALPHA1-6 : bond 0.00506 ( 1) link_ALPHA1-6 : angle 2.08927 ( 3) link_BETA1-4 : bond 0.00498 ( 2) link_BETA1-4 : angle 2.66124 ( 6) link_NAG-ASN : bond 0.00696 ( 1) link_NAG-ASN : angle 3.69239 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 313 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 30 TYR cc_start: 0.7863 (m-80) cc_final: 0.7286 (m-80) REVERT: A 164 TYR cc_start: 0.7489 (m-10) cc_final: 0.6996 (m-10) REVERT: A 197 GLU cc_start: 0.7918 (pm20) cc_final: 0.7629 (pm20) REVERT: A 211 MET cc_start: 0.8164 (mpp) cc_final: 0.7837 (mpp) REVERT: A 273 THR cc_start: 0.8411 (m) cc_final: 0.8192 (m) REVERT: A 303 GLU cc_start: 0.7027 (pp20) cc_final: 0.6710 (pp20) REVERT: A 314 ASN cc_start: 0.6748 (m110) cc_final: 0.6327 (m110) REVERT: A 394 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7226 (tm-30) REVERT: A 395 ASP cc_start: 0.7485 (t0) cc_final: 0.7124 (t0) REVERT: A 415 LYS cc_start: 0.7968 (ttpp) cc_final: 0.7525 (ttpp) REVERT: A 485 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8111 (tmmt) REVERT: A 610 TYR cc_start: 0.8040 (m-10) cc_final: 0.7709 (m-10) REVERT: A 662 PHE cc_start: 0.7521 (t80) cc_final: 0.7302 (t80) REVERT: A 695 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7243 (mm-30) REVERT: A 891 LYS cc_start: 0.8054 (ttpt) cc_final: 0.7740 (ttpp) REVERT: A 918 MET cc_start: 0.7344 (mpp) cc_final: 0.7027 (mpp) REVERT: A 1087 LYS cc_start: 0.8098 (tptp) cc_final: 0.7865 (tptp) REVERT: A 1092 MET cc_start: 0.7955 (tpp) cc_final: 0.7470 (tpp) REVERT: A 1094 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7107 (mm-30) REVERT: A 1167 GLN cc_start: 0.7631 (mp10) cc_final: 0.7200 (mp10) REVERT: A 1178 MET cc_start: 0.7838 (mtm) cc_final: 0.7591 (mtt) REVERT: A 1204 GLU cc_start: 0.7600 (mp0) cc_final: 0.7301 (mp0) REVERT: A 1322 ARG cc_start: 0.7556 (ttt90) cc_final: 0.7316 (ttm-80) REVERT: A 1457 LYS cc_start: 0.7980 (tppt) cc_final: 0.7720 (ttmt) REVERT: A 1516 LYS cc_start: 0.7775 (pptt) cc_final: 0.7503 (pptt) REVERT: A 1548 GLU cc_start: 0.7523 (pt0) cc_final: 0.7322 (pt0) REVERT: A 1550 ASN cc_start: 0.7906 (t0) cc_final: 0.7477 (t0) REVERT: A 1588 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7785 (mm-30) REVERT: A 1591 ARG cc_start: 0.7592 (mmm-85) cc_final: 0.6968 (mmm-85) outliers start: 49 outliers final: 38 residues processed: 335 average time/residue: 0.1233 time to fit residues: 56.9824 Evaluate side-chains 346 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 307 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1310 CYS Chi-restraints excluded: chain A residue 1337 VAL Chi-restraints excluded: chain A residue 1445 MET Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1470 VAL Chi-restraints excluded: chain A residue 1531 VAL Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1564 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 HIS A1089 ASN A1129 GLN A1622 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.157989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130048 restraints weight = 17473.025| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.83 r_work: 0.3529 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12373 Z= 0.144 Angle : 0.662 14.486 16766 Z= 0.334 Chirality : 0.047 0.217 1913 Planarity : 0.005 0.055 2152 Dihedral : 8.405 160.177 1779 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.61 % Allowed : 19.39 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.22), residues: 1539 helix: 1.46 (0.26), residues: 403 sheet: -0.17 (0.25), residues: 448 loop : -1.45 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1051 TYR 0.024 0.001 TYR A 904 PHE 0.043 0.002 PHE A 705 TRP 0.021 0.002 TRP A1228 HIS 0.009 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00331 (12362) covalent geometry : angle 0.65861 (16739) SS BOND : bond 0.00067 ( 6) SS BOND : angle 1.65235 ( 12) hydrogen bonds : bond 0.04414 ( 436) hydrogen bonds : angle 5.15453 ( 1224) link_ALPHA1-3 : bond 0.01327 ( 1) link_ALPHA1-3 : angle 1.95854 ( 3) link_ALPHA1-6 : bond 0.00764 ( 1) link_ALPHA1-6 : angle 1.97986 ( 3) link_BETA1-4 : bond 0.00342 ( 2) link_BETA1-4 : angle 1.57542 ( 6) link_NAG-ASN : bond 0.00098 ( 1) link_NAG-ASN : angle 2.30636 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 313 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 TYR cc_start: 0.7819 (m-80) cc_final: 0.7260 (m-80) REVERT: A 164 TYR cc_start: 0.7441 (m-10) cc_final: 0.6948 (m-10) REVERT: A 197 GLU cc_start: 0.7857 (pm20) cc_final: 0.7578 (pm20) REVERT: A 211 MET cc_start: 0.8085 (mpp) cc_final: 0.7687 (mpp) REVERT: A 266 PHE cc_start: 0.7817 (t80) cc_final: 0.7546 (t80) REVERT: A 303 GLU cc_start: 0.6900 (pp20) cc_final: 0.6651 (pp20) REVERT: A 314 ASN cc_start: 0.6613 (m110) cc_final: 0.6234 (m110) REVERT: A 415 LYS cc_start: 0.7937 (ttpp) cc_final: 0.7510 (ttpp) REVERT: A 610 TYR cc_start: 0.7986 (m-10) cc_final: 0.7625 (m-10) REVERT: A 662 PHE cc_start: 0.7346 (t80) cc_final: 0.7066 (t80) REVERT: A 695 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7272 (mm-30) REVERT: A 910 GLU cc_start: 0.7611 (tp30) cc_final: 0.7212 (tp30) REVERT: A 918 MET cc_start: 0.7326 (mpp) cc_final: 0.7006 (mpp) REVERT: A 1087 LYS cc_start: 0.8042 (tptp) cc_final: 0.7818 (tptp) REVERT: A 1092 MET cc_start: 0.7862 (tpp) cc_final: 0.7382 (tpp) REVERT: A 1094 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7098 (mm-30) REVERT: A 1167 GLN cc_start: 0.7553 (mp10) cc_final: 0.7186 (mp10) REVERT: A 1178 MET cc_start: 0.7765 (mtm) cc_final: 0.7516 (mtm) REVERT: A 1204 GLU cc_start: 0.7570 (mp0) cc_final: 0.7255 (mp0) REVERT: A 1322 ARG cc_start: 0.7452 (ttt90) cc_final: 0.7193 (ttm-80) REVERT: A 1457 LYS cc_start: 0.7934 (tppt) cc_final: 0.7661 (ttmt) REVERT: A 1516 LYS cc_start: 0.7696 (pptt) cc_final: 0.7423 (pptt) REVERT: A 1535 LYS cc_start: 0.8435 (tmtt) cc_final: 0.8019 (tptp) REVERT: A 1550 ASN cc_start: 0.7877 (t0) cc_final: 0.7448 (t0) REVERT: A 1588 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7717 (mm-30) REVERT: A 1591 ARG cc_start: 0.7554 (mmm-85) cc_final: 0.6944 (mmm-85) REVERT: A 1604 ASP cc_start: 0.6695 (t0) cc_final: 0.6435 (t0) outliers start: 34 outliers final: 30 residues processed: 328 average time/residue: 0.1302 time to fit residues: 59.2688 Evaluate side-chains 338 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 308 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1310 CYS Chi-restraints excluded: chain A residue 1337 VAL Chi-restraints excluded: chain A residue 1445 MET Chi-restraints excluded: chain A residue 1531 VAL Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1564 ILE Chi-restraints excluded: chain A residue 1622 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 148 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 153 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN A1129 GLN A1622 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.155610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.127766 restraints weight = 17371.403| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.80 r_work: 0.3494 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 12373 Z= 0.279 Angle : 0.745 14.476 16766 Z= 0.378 Chirality : 0.051 0.220 1913 Planarity : 0.005 0.060 2152 Dihedral : 8.551 158.584 1779 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.99 % Allowed : 19.39 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.22), residues: 1539 helix: 1.16 (0.26), residues: 404 sheet: -0.31 (0.25), residues: 446 loop : -1.55 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1051 TYR 0.028 0.002 TYR A 814 PHE 0.049 0.003 PHE A 705 TRP 0.030 0.003 TRP A1228 HIS 0.009 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00650 (12362) covalent geometry : angle 0.73969 (16739) SS BOND : bond 0.00201 ( 6) SS BOND : angle 2.19721 ( 12) hydrogen bonds : bond 0.05741 ( 436) hydrogen bonds : angle 5.35642 ( 1224) link_ALPHA1-3 : bond 0.01262 ( 1) link_ALPHA1-3 : angle 1.80163 ( 3) link_ALPHA1-6 : bond 0.00675 ( 1) link_ALPHA1-6 : angle 2.04577 ( 3) link_BETA1-4 : bond 0.00386 ( 2) link_BETA1-4 : angle 2.18692 ( 6) link_NAG-ASN : bond 0.00624 ( 1) link_NAG-ASN : angle 3.41328 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 313 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 30 TYR cc_start: 0.7845 (m-80) cc_final: 0.7275 (m-80) REVERT: A 164 TYR cc_start: 0.7459 (m-10) cc_final: 0.6967 (m-10) REVERT: A 197 GLU cc_start: 0.7908 (pm20) cc_final: 0.7614 (pm20) REVERT: A 211 MET cc_start: 0.8118 (mpp) cc_final: 0.7661 (mpp) REVERT: A 266 PHE cc_start: 0.7839 (t80) cc_final: 0.7589 (t80) REVERT: A 303 GLU cc_start: 0.6989 (pp20) cc_final: 0.6736 (pp20) REVERT: A 314 ASN cc_start: 0.6650 (m110) cc_final: 0.6287 (m110) REVERT: A 415 LYS cc_start: 0.7972 (ttpp) cc_final: 0.7522 (ttpp) REVERT: A 610 TYR cc_start: 0.8024 (m-10) cc_final: 0.7655 (m-10) REVERT: A 662 PHE cc_start: 0.7441 (t80) cc_final: 0.7197 (t80) REVERT: A 695 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7262 (mm-30) REVERT: A 910 GLU cc_start: 0.7651 (tp30) cc_final: 0.7206 (tp30) REVERT: A 918 MET cc_start: 0.7320 (mpp) cc_final: 0.7008 (mpp) REVERT: A 963 ILE cc_start: 0.7989 (mm) cc_final: 0.7723 (mm) REVERT: A 1087 LYS cc_start: 0.8104 (tptp) cc_final: 0.7873 (tptp) REVERT: A 1092 MET cc_start: 0.7861 (tpp) cc_final: 0.7358 (tpp) REVERT: A 1094 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7076 (mm-30) REVERT: A 1167 GLN cc_start: 0.7638 (mp10) cc_final: 0.7236 (mp10) REVERT: A 1178 MET cc_start: 0.7792 (mtm) cc_final: 0.7520 (mtm) REVERT: A 1204 GLU cc_start: 0.7580 (mp0) cc_final: 0.7279 (mp0) REVERT: A 1322 ARG cc_start: 0.7498 (ttt90) cc_final: 0.7259 (ttm-80) REVERT: A 1457 LYS cc_start: 0.7952 (tppt) cc_final: 0.7689 (ttmt) REVERT: A 1535 LYS cc_start: 0.8444 (tmtt) cc_final: 0.8122 (tptp) REVERT: A 1550 ASN cc_start: 0.7912 (t0) cc_final: 0.7493 (t0) REVERT: A 1588 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7797 (mm-30) REVERT: A 1604 ASP cc_start: 0.6777 (t0) cc_final: 0.6517 (t0) outliers start: 39 outliers final: 35 residues processed: 329 average time/residue: 0.1213 time to fit residues: 55.3997 Evaluate side-chains 345 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 310 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1337 VAL Chi-restraints excluded: chain A residue 1445 MET Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1470 VAL Chi-restraints excluded: chain A residue 1531 VAL Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1564 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 154 optimal weight: 30.0000 chunk 11 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 78 optimal weight: 0.0970 chunk 64 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 ASN A 269 GLN A1089 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.158295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.130665 restraints weight = 17505.143| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.78 r_work: 0.3534 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12373 Z= 0.144 Angle : 0.689 14.889 16766 Z= 0.343 Chirality : 0.047 0.223 1913 Planarity : 0.005 0.057 2152 Dihedral : 8.225 158.757 1779 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.53 % Allowed : 19.92 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.22), residues: 1539 helix: 1.45 (0.26), residues: 403 sheet: -0.18 (0.25), residues: 447 loop : -1.43 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 519 TYR 0.028 0.002 TYR A 814 PHE 0.036 0.002 PHE A 705 TRP 0.033 0.002 TRP A1228 HIS 0.009 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00336 (12362) covalent geometry : angle 0.68407 (16739) SS BOND : bond 0.00066 ( 6) SS BOND : angle 2.31752 ( 12) hydrogen bonds : bond 0.04292 ( 436) hydrogen bonds : angle 5.10703 ( 1224) link_ALPHA1-3 : bond 0.01409 ( 1) link_ALPHA1-3 : angle 2.00982 ( 3) link_ALPHA1-6 : bond 0.00831 ( 1) link_ALPHA1-6 : angle 1.95303 ( 3) link_BETA1-4 : bond 0.00287 ( 2) link_BETA1-4 : angle 1.41184 ( 6) link_NAG-ASN : bond 0.00095 ( 1) link_NAG-ASN : angle 2.31030 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 307 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 30 TYR cc_start: 0.7830 (m-80) cc_final: 0.7301 (m-80) REVERT: A 164 TYR cc_start: 0.7423 (m-10) cc_final: 0.6971 (m-10) REVERT: A 197 GLU cc_start: 0.7798 (pm20) cc_final: 0.7542 (pm20) REVERT: A 211 MET cc_start: 0.8057 (mpp) cc_final: 0.7719 (mpp) REVERT: A 221 ASN cc_start: 0.6913 (t0) cc_final: 0.6710 (t0) REVERT: A 266 PHE cc_start: 0.7820 (t80) cc_final: 0.7489 (t80) REVERT: A 303 GLU cc_start: 0.6901 (pp20) cc_final: 0.6694 (pp20) REVERT: A 314 ASN cc_start: 0.6617 (m110) cc_final: 0.6235 (m110) REVERT: A 415 LYS cc_start: 0.7927 (ttpp) cc_final: 0.7518 (ttpp) REVERT: A 610 TYR cc_start: 0.8038 (m-10) cc_final: 0.7530 (m-10) REVERT: A 662 PHE cc_start: 0.7288 (t80) cc_final: 0.7028 (t80) REVERT: A 695 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7273 (mm-30) REVERT: A 887 PHE cc_start: 0.7943 (m-10) cc_final: 0.7579 (m-80) REVERT: A 910 GLU cc_start: 0.7583 (tp30) cc_final: 0.7218 (tp30) REVERT: A 918 MET cc_start: 0.7277 (mpp) cc_final: 0.6955 (mpp) REVERT: A 1087 LYS cc_start: 0.8057 (tptp) cc_final: 0.7838 (tptp) REVERT: A 1092 MET cc_start: 0.7824 (tpp) cc_final: 0.7352 (tpp) REVERT: A 1094 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7037 (mm-30) REVERT: A 1167 GLN cc_start: 0.7590 (mp10) cc_final: 0.7218 (mp10) REVERT: A 1178 MET cc_start: 0.7738 (mtm) cc_final: 0.7512 (mtm) REVERT: A 1204 GLU cc_start: 0.7542 (mp0) cc_final: 0.7256 (mp0) REVERT: A 1322 ARG cc_start: 0.7401 (ttt90) cc_final: 0.7150 (ttm-80) REVERT: A 1457 LYS cc_start: 0.7937 (tppt) cc_final: 0.7673 (ttmt) REVERT: A 1516 LYS cc_start: 0.7730 (pptt) cc_final: 0.7473 (pptt) REVERT: A 1550 ASN cc_start: 0.7833 (t0) cc_final: 0.7417 (t0) REVERT: A 1588 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7761 (mm-30) REVERT: A 1603 HIS cc_start: 0.6389 (m170) cc_final: 0.6048 (m170) REVERT: A 1604 ASP cc_start: 0.6711 (t0) cc_final: 0.6446 (t0) outliers start: 33 outliers final: 30 residues processed: 322 average time/residue: 0.1241 time to fit residues: 55.3724 Evaluate side-chains 338 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 308 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1238 ASP Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1310 CYS Chi-restraints excluded: chain A residue 1337 VAL Chi-restraints excluded: chain A residue 1445 MET Chi-restraints excluded: chain A residue 1531 VAL Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1564 ILE Chi-restraints excluded: chain A residue 1622 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 142 optimal weight: 0.0470 chunk 58 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 6 optimal weight: 0.0980 chunk 101 optimal weight: 3.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.158667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.130614 restraints weight = 17466.962| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.85 r_work: 0.3532 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12373 Z= 0.151 Angle : 0.690 14.579 16766 Z= 0.342 Chirality : 0.047 0.223 1913 Planarity : 0.005 0.057 2152 Dihedral : 8.072 159.085 1779 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.45 % Allowed : 19.92 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.22), residues: 1539 helix: 1.48 (0.26), residues: 405 sheet: -0.08 (0.26), residues: 444 loop : -1.39 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 719 TYR 0.032 0.002 TYR A 690 PHE 0.036 0.002 PHE A 705 TRP 0.041 0.002 TRP A1228 HIS 0.009 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00353 (12362) covalent geometry : angle 0.68564 (16739) SS BOND : bond 0.00093 ( 6) SS BOND : angle 2.17697 ( 12) hydrogen bonds : bond 0.04271 ( 436) hydrogen bonds : angle 5.00613 ( 1224) link_ALPHA1-3 : bond 0.01197 ( 1) link_ALPHA1-3 : angle 1.85170 ( 3) link_ALPHA1-6 : bond 0.00828 ( 1) link_ALPHA1-6 : angle 1.92066 ( 3) link_BETA1-4 : bond 0.00353 ( 2) link_BETA1-4 : angle 1.51164 ( 6) link_NAG-ASN : bond 0.00225 ( 1) link_NAG-ASN : angle 2.46878 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2999.85 seconds wall clock time: 52 minutes 13.34 seconds (3133.34 seconds total)