Starting phenix.real_space_refine on Sun Oct 25 01:16:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6w5t_21547/10_2026/6w5t_21547.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w5t_21547/10_2026/6w5t_21547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w5t_21547/10_2026/6w5t_21547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w5t_21547/10_2026/6w5t_21547.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6w5t_21547/10_2026/6w5t_21547.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6w5t_21547/10_2026/6w5t_21547.cif" model { file = "/net/cci-nas-00/data/ceres_data/6w5t_21547/10_2026/6w5t_21547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w5t_21547/10_2026/6w5t_21547.cif" } resolution = 3.7 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6688 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 71 5.16 5 C 6156 2.51 5 N 1496 2.21 5 O 1782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9505 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9189 Classifications: {'peptide': 1175} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1111} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 182 Unusual residues: {'CLR': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 2.19, per 1000 atoms: 0.23 Number of scatterers: 9505 At special positions: 0 Unit cell: (103.602, 91.348, 152.618, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 71 16.00 O 1782 8.00 N 1496 7.00 C 6156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 42 " distance=1.51 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.04 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 238 " distance=2.05 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 160 " distance=2.04 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.06 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=2.04 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 914 " distance=2.97 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 979 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 976 " 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 " NAG C 2 " - " MAN C 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1401 " - " ASN A 452 " " NAG A1402 " - " ASN A 459 " " NAG A1405 " - " ASN A 524 " " NAG A1409 " - " ASN A 598 " " NAG A1410 " - " ASN A 916 " " NAG A1414 " - " ASN A 961 " " NAG A1415 " - " ASN A 968 " " NAG A1416 " - " ASN A1064 " " NAG A1419 " - " ASN A 158 " " NAG B 1 " - " ASN A 478 " " NAG C 1 " - " ASN A 557 " " NAG D 1 " - " ASN A 931 " " NAG E 1 " - " ASN A 222 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 343.1 milliseconds 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 59.1% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 removed outlier: 3.599A pdb=" N CYS A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 87 through 95 Processing helix chain 'A' and resid 97 through 114 removed outlier: 3.608A pdb=" N ASN A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 185 through 195 removed outlier: 4.043A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 268 through 291 removed outlier: 3.991A pdb=" N ALA A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 295 Processing helix chain 'A' and resid 330 through 349 removed outlier: 4.150A pdb=" N CYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 376 through 382 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 436 through 453 removed outlier: 3.520A pdb=" N ASN A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.534A pdb=" N TYR A 487 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 508 through 519 removed outlier: 3.510A pdb=" N ARG A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 574 through 594 removed outlier: 3.652A pdb=" N GLU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 617 Processing helix chain 'A' and resid 620 through 639 removed outlier: 4.106A pdb=" N ILE A 626 " --> pdb=" O PHE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 679 Processing helix chain 'A' and resid 685 through 711 Proline residue: A 691 - end of helix Processing helix chain 'A' and resid 720 through 750 Proline residue: A 733 - end of helix Processing helix chain 'A' and resid 754 through 789 Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.634A pdb=" N PHE A 820 " --> pdb=" O CYS A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 833 through 852 removed outlier: 3.747A pdb=" N ILE A 837 " --> pdb=" O TRP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 870 through 883 removed outlier: 4.029A pdb=" N ASP A 874 " --> pdb=" O SER A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 907 Processing helix chain 'A' and resid 918 through 930 Processing helix chain 'A' and resid 941 through 951 removed outlier: 3.983A pdb=" N ASP A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 988 removed outlier: 4.073A pdb=" N GLN A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1005 removed outlier: 4.400A pdb=" N MET A 996 " --> pdb=" O GLY A 992 " (cutoff:3.500A) Proline residue: A1000 - end of helix Processing helix chain 'A' and resid 1047 through 1070 removed outlier: 3.720A pdb=" N GLY A1070 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1090 through 1092 No H-bonds generated for 'chain 'A' and resid 1090 through 1092' Processing helix chain 'A' and resid 1093 through 1117 Processing helix chain 'A' and resid 1120 through 1146 removed outlier: 3.537A pdb=" N ALA A1124 " --> pdb=" O GLU A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1177 removed outlier: 4.007A pdb=" N GLY A1162 " --> pdb=" O VAL A1158 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL A1165 " --> pdb=" O CYS A1161 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU A1166 " --> pdb=" O GLY A1162 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A1167 " --> pdb=" O ILE A1163 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A1172 " --> pdb=" O CYS A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1202 removed outlier: 4.301A pdb=" N SER A1197 " --> pdb=" O HIS A1193 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER A1200 " --> pdb=" O SER A1196 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A1202 " --> pdb=" O VAL A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1214 Processing helix chain 'A' and resid 1219 through 1242 removed outlier: 4.526A pdb=" N PHE A1226 " --> pdb=" O GLN A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1252 Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 127 removed outlier: 3.915A pdb=" N ASN A 122 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN A 145 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLU A 143 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR A 126 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL A 141 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N THR A 206 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 144 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL A 208 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR A 146 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 547 through 548 Processing sheet with id=AA3, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AA4, first strand: chain 'A' and resid 1039 through 1043 Processing sheet with id=AA5, first strand: chain 'A' and resid 958 through 960 Processing sheet with id=AA6, first strand: chain 'A' and resid 1023 through 1025 removed outlier: 5.328A pdb=" N ASN A1024 " --> pdb=" O GLY A1034 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1392 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: 1.58 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2947 1.35 - 1.48: 2625 1.48 - 1.61: 4081 1.61 - 1.74: 1 1.74 - 1.87: 99 Bond restraints: 9753 Sorted by residual: bond pdb=" CA CYS A 909 " pdb=" C CYS A 909 " ideal model delta sigma weight residual 1.524 1.579 -0.055 1.27e-02 6.20e+03 1.90e+01 bond pdb=" N CYS A 909 " pdb=" CA CYS A 909 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.19e-02 7.06e+03 1.47e+01 bond pdb=" CA TYR A 269 " pdb=" C TYR A 269 " ideal model delta sigma weight residual 1.522 1.473 0.049 1.39e-02 5.18e+03 1.23e+01 bond pdb=" C1 NAG A1405 " pdb=" O5 NAG A1405 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.26e+00 bond pdb=" C1 NAG A1410 " pdb=" O5 NAG A1410 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.65e+00 ... (remaining 9748 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.48: 13253 5.48 - 10.95: 38 10.95 - 16.43: 4 16.43 - 21.90: 0 21.90 - 27.38: 1 Bond angle restraints: 13296 Sorted by residual: angle pdb=" N CYS A 909 " pdb=" CA CYS A 909 " pdb=" C CYS A 909 " ideal model delta sigma weight residual 111.07 138.45 -27.38 1.07e+00 8.73e-01 6.55e+02 angle pdb=" N ASN A 823 " pdb=" CA ASN A 823 " pdb=" C ASN A 823 " ideal model delta sigma weight residual 111.14 121.36 -10.22 1.08e+00 8.57e-01 8.95e+01 angle pdb=" N SER A 602 " pdb=" CA SER A 602 " pdb=" C SER A 602 " ideal model delta sigma weight residual 108.41 97.30 11.11 1.63e+00 3.76e-01 4.64e+01 angle pdb=" CA CYS A 909 " pdb=" C CYS A 909 " pdb=" N GLY A 910 " ideal model delta sigma weight residual 117.07 124.47 -7.40 1.14e+00 7.69e-01 4.21e+01 angle pdb=" C GLY A 910 " pdb=" N GLY A 911 " pdb=" CA GLY A 911 " ideal model delta sigma weight residual 122.42 129.43 -7.01 1.13e+00 7.83e-01 3.85e+01 ... (remaining 13291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4965 17.90 - 35.81: 459 35.81 - 53.71: 125 53.71 - 71.61: 34 71.61 - 89.52: 9 Dihedral angle restraints: 5592 sinusoidal: 2170 harmonic: 3422 Sorted by residual: dihedral pdb=" CB CYS A 240 " pdb=" SG CYS A 240 " pdb=" SG CYS A 247 " pdb=" CB CYS A 247 " ideal model delta sinusoidal sigma weight residual -86.00 0.20 -86.20 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CA ASN A 70 " pdb=" C ASN A 70 " pdb=" N VAL A 71 " pdb=" CA VAL A 71 " ideal model delta harmonic sigma weight residual 180.00 -137.91 -42.09 0 5.00e+00 4.00e-02 7.08e+01 dihedral pdb=" CA GLY A 69 " pdb=" C GLY A 69 " pdb=" N ASN A 70 " pdb=" CA ASN A 70 " ideal model delta harmonic sigma weight residual 180.00 141.81 38.19 0 5.00e+00 4.00e-02 5.83e+01 ... (remaining 5589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.948: 1555 0.948 - 1.896: 0 1.896 - 2.844: 0 2.844 - 3.792: 0 3.792 - 4.740: 2 Chirality restraints: 1557 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 2.34 -4.74 2.00e-02 2.50e+03 5.62e+04 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 2.33 -4.73 2.00e-02 2.50e+03 5.59e+04 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.38e+02 ... (remaining 1554 not shown) Planarity restraints: 1677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG E 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.071 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.190 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " 0.343 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" C7 NAG C 2 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " 0.048 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " -0.518 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.344 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG E 1 " -0.088 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " 0.179 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.512 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.077 2.00e-02 2.50e+03 ... (remaining 1674 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 175 2.62 - 3.19: 9588 3.19 - 3.76: 14483 3.76 - 4.33: 20142 4.33 - 4.90: 32725 Nonbonded interactions: 77113 Sorted by model distance: nonbonded pdb=" O3 NAG B 2 " pdb=" O7 NAG B 2 " model vdw 2.054 3.040 nonbonded pdb=" OH TYR A 487 " pdb=" O VAL A 541 " model vdw 2.077 3.040 nonbonded pdb=" N GLU A 30 " pdb=" OE1 GLU A 30 " model vdw 2.134 3.120 nonbonded pdb=" OD1 ASN A 459 " pdb=" N2 NAG A1402 " model vdw 2.200 3.120 nonbonded pdb=" N GLN A 716 " pdb=" OE1 GLN A 716 " model vdw 2.206 3.120 ... (remaining 77108 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and resid 1 through 2) selection = (chain 'D' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 10.480 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 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 : 0.013 0.943 9787 Z= 0.654 Angle : 1.449 62.516 13383 Z= 0.811 Chirality : 0.182 4.740 1557 Planarity : 0.015 0.298 1664 Dihedral : 15.485 89.516 3347 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 48.42 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.97 % Favored : 91.52 % Rotamer: Outliers : 5.60 % Allowed : 8.95 % Favored : 85.45 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -2.80 (0.22), residues: 1167 helix: -0.92 (0.20), residues: 591 sheet: -2.19 (0.58), residues: 87 loop : -2.97 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 518 TYR 0.018 0.002 TYR A1225 PHE 0.031 0.002 PHE A 747 TRP 0.035 0.003 TRP A 27 HIS 0.004 0.001 HIS A1239 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.36 ( 9753) covalent geometry : angle 1.14424 / 0.71 (13296) SS BOND : bond 0.27857 / 14.17 ( 15) SS BOND : angle 15.44478 / 8.73 ( 30) hydrogen bonds : bond 0.14475 / 9.12 ( 482) hydrogen bonds : angle 6.57977 / 4.49 ( 1392) link_ALPHA1-3 : bond 0.00318 / 0.17 ( 1) link_ALPHA1-3 : angle 1.51178 / 0.82 ( 3) link_BETA1-4 : bond 0.04112 / 2.06 ( 5) link_BETA1-4 : angle 13.35003 / 7.36 ( 15) link_NAG-ASN : bond 0.00493 / 0.32 ( 13) link_NAG-ASN : angle 4.70561 / 3.03 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 246 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 PRO cc_start: 0.7137 (Cg_exo) cc_final: 0.6527 (Cg_endo) REVERT: A 83 LEU cc_start: 0.8865 (tt) cc_final: 0.8662 (tt) REVERT: A 93 PHE cc_start: 0.7739 (m-80) cc_final: 0.7238 (m-80) REVERT: A 192 TYR cc_start: 0.8081 (t80) cc_final: 0.7659 (t80) REVERT: A 272 MET cc_start: 0.8537 (mmp) cc_final: 0.8332 (mmm) REVERT: A 376 ASN cc_start: 0.8793 (t0) cc_final: 0.8496 (p0) REVERT: A 406 GLU cc_start: 0.8602 (mp0) cc_final: 0.8357 (mp0) REVERT: A 498 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7105 (mttt) REVERT: A 550 TYR cc_start: 0.8108 (p90) cc_final: 0.7790 (p90) REVERT: A 612 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7890 (mm-30) REVERT: A 714 ARG cc_start: 0.6922 (pmt170) cc_final: 0.6604 (ptp90) REVERT: A 726 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8572 (ttp-110) REVERT: A 825 TYR cc_start: 0.8789 (t80) cc_final: 0.8034 (t80) REVERT: A 1053 ASP cc_start: 0.7015 (t0) cc_final: 0.6808 (t0) REVERT: A 1089 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7088 (tm-30) REVERT: A 1110 PHE cc_start: 0.8557 (t80) cc_final: 0.8330 (t80) REVERT: A 1137 ASN cc_start: 0.9151 (m110) cc_final: 0.8803 (m110) REVERT: A 1235 LEU cc_start: 0.8425 (tt) cc_final: 0.7987 (mt) outliers start: 57 outliers final: 23 residues processed: 286 average time/residue: 0.0960 time to fit residues: 38.3861 Evaluate side-chains 197 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1032 ARG Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 100] chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN A 119 GLN A 136 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 823 ASN A1024 ASN A1137 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.143170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.111843 restraints weight = 16211.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.112957 restraints weight = 8994.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.113933 restraints weight = 7407.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.114425 restraints weight = 5563.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.114529 restraints weight = 5436.715| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9787 Z= 0.186 Angle : 0.927 12.560 13383 Z= 0.437 Chirality : 0.053 0.313 1557 Planarity : 0.005 0.047 1664 Dihedral : 8.785 90.132 1337 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.91 % Favored : 93.92 % Rotamer: Outliers : 3.34 % Allowed : 16.42 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.39 (0.24), residues: 1167 helix: 0.16 (0.21), residues: 611 sheet: -2.42 (0.52), residues: 89 loop : -2.05 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 372 TYR 0.027 0.002 TYR A 293 PHE 0.018 0.002 PHE A 101 TRP 0.031 0.002 TRP A 27 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 ( 9753) covalent geometry : angle 0.88731 / 0.43 (13296) SS BOND : bond 0.00405 / 0.21 ( 15) SS BOND : angle 2.48718 / 1.50 ( 30) hydrogen bonds : bond 0.05484 / 3.57 ( 482) hydrogen bonds : angle 5.28391 / 3.63 ( 1392) link_ALPHA1-3 : bond 0.01380 / 0.73 ( 1) link_ALPHA1-3 : angle 1.57353 / 0.81 ( 3) link_BETA1-4 : bond 0.01389 / 0.84 ( 5) link_BETA1-4 : angle 5.03960 / 2.96 ( 15) link_NAG-ASN : bond 0.00801 / 0.44 ( 13) link_NAG-ASN : angle 3.46185 / 1.95 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.363 Fit side-chains REVERT: A 78 ARG cc_start: 0.8678 (tpt-90) cc_final: 0.8409 (mmm-85) REVERT: A 93 PHE cc_start: 0.7677 (m-80) cc_final: 0.7438 (m-80) REVERT: A 127 GLU cc_start: 0.4891 (OUTLIER) cc_final: 0.4536 (pm20) REVERT: A 192 TYR cc_start: 0.8083 (t80) cc_final: 0.7816 (t80) REVERT: A 220 MET cc_start: 0.6248 (ppp) cc_final: 0.6017 (ppp) REVERT: A 277 MET cc_start: 0.7735 (mmt) cc_final: 0.7260 (mmm) REVERT: A 288 PHE cc_start: 0.6334 (m-10) cc_final: 0.6090 (m-10) REVERT: A 376 ASN cc_start: 0.8462 (t0) cc_final: 0.8161 (p0) REVERT: A 550 TYR cc_start: 0.8040 (p90) cc_final: 0.7780 (p90) REVERT: A 740 PHE cc_start: 0.8197 (t80) cc_final: 0.7903 (t80) REVERT: A 751 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7223 (pt) REVERT: A 825 TYR cc_start: 0.8694 (t80) cc_final: 0.7959 (t80) REVERT: A 1005 ASP cc_start: 0.8934 (t0) cc_final: 0.8619 (t0) REVERT: A 1089 GLU cc_start: 0.7365 (tm-30) cc_final: 0.7153 (tm-30) REVERT: A 1110 PHE cc_start: 0.8546 (t80) cc_final: 0.8283 (t80) REVERT: A 1127 MET cc_start: 0.8411 (ttp) cc_final: 0.8074 (tpp) outliers start: 34 outliers final: 23 residues processed: 225 average time/residue: 0.0798 time to fit residues: 26.5532 Evaluate side-chains 185 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [34, 7, 84, 110, 4, 51, 44, 0, 60, 72, 116] chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.136533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.105745 restraints weight = 16862.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.104994 restraints weight = 10094.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.106218 restraints weight = 9112.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106785 restraints weight = 6673.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.106988 restraints weight = 6365.213| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9787 Z= 0.245 Angle : 0.874 12.299 13383 Z= 0.421 Chirality : 0.051 0.263 1557 Planarity : 0.005 0.039 1664 Dihedral : 7.494 59.761 1298 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.60 % Favored : 93.23 % Rotamer: Outliers : 4.62 % Allowed : 19.57 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.05 (0.24), residues: 1167 helix: 0.35 (0.20), residues: 609 sheet: -2.06 (0.55), residues: 84 loop : -1.78 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 336 TYR 0.015 0.002 TYR A 899 PHE 0.029 0.002 PHE A 503 TRP 0.022 0.002 TRP A 27 HIS 0.004 0.001 HIS A 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 ( 9753) covalent geometry : angle 0.84087 / 0.41 (13296) SS BOND : bond 0.00465 / 0.27 ( 15) SS BOND : angle 2.37975 / 1.33 ( 30) hydrogen bonds : bond 0.05711 / 3.69 ( 482) hydrogen bonds : angle 5.28678 / 3.60 ( 1392) link_ALPHA1-3 : bond 0.01037 / 0.55 ( 1) link_ALPHA1-3 : angle 1.59810 / 0.86 ( 3) link_BETA1-4 : bond 0.00867 / 0.46 ( 5) link_BETA1-4 : angle 3.70611 / 2.33 ( 15) link_NAG-ASN : bond 0.00590 / 0.31 ( 13) link_NAG-ASN : angle 3.35944 / 1.93 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.5502 (tt0) cc_final: 0.4536 (tm-30) REVERT: A 78 ARG cc_start: 0.8706 (tpt-90) cc_final: 0.8436 (tpp-160) REVERT: A 93 PHE cc_start: 0.7731 (m-80) cc_final: 0.7157 (m-80) REVERT: A 127 GLU cc_start: 0.5092 (OUTLIER) cc_final: 0.4588 (pm20) REVERT: A 212 PHE cc_start: 0.6029 (m-80) cc_final: 0.5816 (m-80) REVERT: A 376 ASN cc_start: 0.8594 (t0) cc_final: 0.8226 (p0) REVERT: A 550 TYR cc_start: 0.8241 (p90) cc_final: 0.7849 (p90) REVERT: A 584 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8424 (mt-10) REVERT: A 714 ARG cc_start: 0.7479 (ptp90) cc_final: 0.6898 (ptm-80) REVERT: A 751 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7530 (pt) REVERT: A 825 TYR cc_start: 0.8822 (t80) cc_final: 0.7978 (t80) REVERT: A 912 MET cc_start: 0.7001 (mmp) cc_final: 0.6658 (mmt) REVERT: A 1005 ASP cc_start: 0.8976 (t0) cc_final: 0.8699 (t0) REVERT: A 1127 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8266 (tpp) outliers start: 47 outliers final: 30 residues processed: 198 average time/residue: 0.0762 time to fit residues: 22.9743 Evaluate side-chains 190 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1127 MET Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [47, 32, 13, 9, 102, 28, 38, 33, 72, 82, 67] chunk 47 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 GLN A1137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.139825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.109317 restraints weight = 16703.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108585 restraints weight = 9634.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.109539 restraints weight = 8892.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.111515 restraints weight = 6513.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111370 restraints weight = 5168.302| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9787 Z= 0.155 Angle : 0.805 12.472 13383 Z= 0.383 Chirality : 0.048 0.276 1557 Planarity : 0.004 0.040 1664 Dihedral : 7.174 59.476 1297 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.17 % Favored : 93.66 % Rotamer: Outliers : 4.23 % Allowed : 20.26 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.72 (0.24), residues: 1167 helix: 0.67 (0.21), residues: 610 sheet: -2.00 (0.49), residues: 95 loop : -1.69 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 372 TYR 0.012 0.001 TYR A 634 PHE 0.029 0.002 PHE A 503 TRP 0.024 0.001 TRP A1143 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 9753) covalent geometry : angle 0.76713 / 0.37 (13296) SS BOND : bond 0.00411 / 0.23 ( 15) SS BOND : angle 3.17170 / 2.09 ( 30) hydrogen bonds : bond 0.04877 / 3.15 ( 482) hydrogen bonds : angle 5.14664 / 3.52 ( 1392) link_ALPHA1-3 : bond 0.01512 / 0.80 ( 1) link_ALPHA1-3 : angle 1.22833 / 0.67 ( 3) link_BETA1-4 : bond 0.01127 / 0.59 ( 5) link_BETA1-4 : angle 3.23173 / 2.09 ( 15) link_NAG-ASN : bond 0.00662 / 0.34 ( 13) link_NAG-ASN : angle 3.16030 / 1.78 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 0.371 Fit side-chains REVERT: A 43 GLU cc_start: 0.5257 (tt0) cc_final: 0.4440 (tm-30) REVERT: A 56 TYR cc_start: 0.7347 (m-80) cc_final: 0.7071 (m-80) REVERT: A 78 ARG cc_start: 0.8714 (tpt-90) cc_final: 0.8429 (tpp-160) REVERT: A 101 PHE cc_start: 0.8663 (t80) cc_final: 0.8108 (m-80) REVERT: A 272 MET cc_start: 0.8420 (mmt) cc_final: 0.8090 (mmm) REVERT: A 376 ASN cc_start: 0.8590 (t0) cc_final: 0.8287 (p0) REVERT: A 406 GLU cc_start: 0.8549 (mp0) cc_final: 0.8260 (mp0) REVERT: A 550 TYR cc_start: 0.8094 (p90) cc_final: 0.7662 (p90) REVERT: A 584 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8285 (mt-10) REVERT: A 714 ARG cc_start: 0.7412 (ptp90) cc_final: 0.6953 (ptm-80) REVERT: A 751 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7433 (pt) REVERT: A 825 TYR cc_start: 0.8781 (t80) cc_final: 0.8043 (t80) REVERT: A 912 MET cc_start: 0.6983 (mmp) cc_final: 0.6651 (mmt) REVERT: A 958 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7098 (mtm180) REVERT: A 1235 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8246 (mt) outliers start: 43 outliers final: 28 residues processed: 204 average time/residue: 0.0750 time to fit residues: 22.9680 Evaluate side-chains 190 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 958 ARG Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [35, 7, 13, 11, 19, 82, 105, 69, 53, 65, 102] chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 0.0970 chunk 19 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.144128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.114251 restraints weight = 16919.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.114787 restraints weight = 9108.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.116007 restraints weight = 7787.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.116126 restraints weight = 5621.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.116535 restraints weight = 5529.220| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9787 Z= 0.142 Angle : 0.784 12.270 13383 Z= 0.373 Chirality : 0.047 0.268 1557 Planarity : 0.004 0.040 1664 Dihedral : 6.523 55.152 1292 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.60 % Favored : 93.23 % Rotamer: Outliers : 4.62 % Allowed : 21.34 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.24), residues: 1167 helix: 0.77 (0.21), residues: 611 sheet: -2.01 (0.47), residues: 101 loop : -1.59 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 372 TYR 0.023 0.001 TYR A 709 PHE 0.027 0.002 PHE A 503 TRP 0.023 0.001 TRP A1143 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 9753) covalent geometry : angle 0.75111 / 0.36 (13296) SS BOND : bond 0.00488 / 0.26 ( 15) SS BOND : angle 2.26904 / 1.33 ( 30) hydrogen bonds : bond 0.04555 / 2.93 ( 482) hydrogen bonds : angle 5.10549 / 3.49 ( 1392) link_ALPHA1-3 : bond 0.01161 / 0.61 ( 1) link_ALPHA1-3 : angle 1.29915 / 0.70 ( 3) link_BETA1-4 : bond 0.01120 / 0.61 ( 5) link_BETA1-4 : angle 3.01692 / 1.96 ( 15) link_NAG-ASN : bond 0.00670 / 0.35 ( 13) link_NAG-ASN : angle 3.31436 / 1.86 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.5200 (tt0) cc_final: 0.4578 (tm-30) REVERT: A 56 TYR cc_start: 0.7276 (m-80) cc_final: 0.6826 (m-80) REVERT: A 78 ARG cc_start: 0.8696 (tpt-90) cc_final: 0.8422 (tpp-160) REVERT: A 111 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8009 (tt) REVERT: A 272 MET cc_start: 0.8435 (mmt) cc_final: 0.8102 (mmm) REVERT: A 550 TYR cc_start: 0.7957 (p90) cc_final: 0.7501 (p90) REVERT: A 714 ARG cc_start: 0.7373 (ptp90) cc_final: 0.7005 (ptm-80) REVERT: A 825 TYR cc_start: 0.8815 (t80) cc_final: 0.8053 (t80) REVERT: A 912 MET cc_start: 0.6843 (mmp) cc_final: 0.6490 (mmt) REVERT: A 958 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7138 (mtm180) REVERT: A 1013 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6352 (mmmt) REVERT: A 1202 ILE cc_start: 0.8273 (mp) cc_final: 0.8028 (mt) REVERT: A 1235 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8284 (mt) outliers start: 47 outliers final: 31 residues processed: 201 average time/residue: 0.0766 time to fit residues: 23.3276 Evaluate side-chains 189 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 958 ARG Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [58, 73, 57, 78, 93, 24, 22, 74, 109, 8, 100] chunk 58 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.143818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113951 restraints weight = 16848.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.114548 restraints weight = 9136.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.115578 restraints weight = 7881.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.115976 restraints weight = 5687.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.116792 restraints weight = 5177.598| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9787 Z= 0.146 Angle : 0.776 12.075 13383 Z= 0.373 Chirality : 0.047 0.264 1557 Planarity : 0.004 0.041 1664 Dihedral : 6.323 51.408 1292 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.51 % Favored : 93.40 % Rotamer: Outliers : 4.52 % Allowed : 22.42 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.40 (0.25), residues: 1167 helix: 0.90 (0.21), residues: 611 sheet: -1.95 (0.45), residues: 115 loop : -1.40 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 372 TYR 0.013 0.001 TYR A 709 PHE 0.051 0.002 PHE A 93 TRP 0.018 0.001 TRP A 27 HIS 0.003 0.001 HIS A 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 9753) covalent geometry : angle 0.74762 / 0.37 (13296) SS BOND : bond 0.00466 / 0.25 ( 15) SS BOND : angle 2.22092 / 1.22 ( 30) hydrogen bonds : bond 0.04532 / 2.91 ( 482) hydrogen bonds : angle 5.06156 / 3.45 ( 1392) link_ALPHA1-3 : bond 0.01125 / 0.59 ( 1) link_ALPHA1-3 : angle 1.35775 / 0.73 ( 3) link_BETA1-4 : bond 0.01128 / 0.59 ( 5) link_BETA1-4 : angle 2.77372 / 1.79 ( 15) link_NAG-ASN : bond 0.00643 / 0.33 ( 13) link_NAG-ASN : angle 3.03983 / 1.69 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.5244 (tt0) cc_final: 0.4618 (tm-30) REVERT: A 56 TYR cc_start: 0.7246 (m-80) cc_final: 0.6779 (m-80) REVERT: A 78 ARG cc_start: 0.8656 (tpt-90) cc_final: 0.8394 (tpp-160) REVERT: A 101 PHE cc_start: 0.8565 (t80) cc_final: 0.7909 (m-80) REVERT: A 272 MET cc_start: 0.8450 (mmt) cc_final: 0.8141 (mmm) REVERT: A 550 TYR cc_start: 0.8017 (p90) cc_final: 0.7515 (p90) REVERT: A 578 GLN cc_start: 0.8421 (mp10) cc_final: 0.8089 (mp10) REVERT: A 714 ARG cc_start: 0.7381 (ptp90) cc_final: 0.7041 (ptm-80) REVERT: A 819 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.6663 (tpt-90) REVERT: A 825 TYR cc_start: 0.8810 (t80) cc_final: 0.8133 (t80) REVERT: A 958 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7200 (mtm180) REVERT: A 1013 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6358 (mmmt) REVERT: A 1142 MET cc_start: 0.8930 (mtp) cc_final: 0.8650 (mtp) REVERT: A 1235 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8266 (mt) outliers start: 46 outliers final: 33 residues processed: 192 average time/residue: 0.0768 time to fit residues: 22.4271 Evaluate side-chains 190 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 958 ARG Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [49, 112, 45, 100, 96, 103, 18, 24, 94, 102, 12] chunk 49 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.143573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.112709 restraints weight = 16969.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.114228 restraints weight = 9264.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114826 restraints weight = 8084.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.115183 restraints weight = 5999.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.115588 restraints weight = 5634.379| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9787 Z= 0.141 Angle : 0.757 11.932 13383 Z= 0.360 Chirality : 0.046 0.262 1557 Planarity : 0.004 0.042 1664 Dihedral : 6.104 49.024 1292 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.42 % Allowed : 22.81 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.19 (0.25), residues: 1167 helix: 1.01 (0.21), residues: 613 sheet: -1.72 (0.47), residues: 115 loop : -1.25 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 372 TYR 0.023 0.001 TYR A 420 PHE 0.045 0.002 PHE A 93 TRP 0.015 0.001 TRP A1143 HIS 0.003 0.001 HIS A 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 9753) covalent geometry : angle 0.73270 / 0.35 (13296) SS BOND : bond 0.00676 / 0.36 ( 15) SS BOND : angle 1.79830 / 0.99 ( 30) hydrogen bonds : bond 0.04423 / 2.84 ( 482) hydrogen bonds : angle 4.97953 / 3.39 ( 1392) link_ALPHA1-3 : bond 0.01063 / 0.56 ( 1) link_ALPHA1-3 : angle 1.38018 / 0.74 ( 3) link_BETA1-4 : bond 0.01061 / 0.56 ( 5) link_BETA1-4 : angle 2.58182 / 1.65 ( 15) link_NAG-ASN : bond 0.00642 / 0.33 ( 13) link_NAG-ASN : angle 2.91634 / 1.61 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.5182 (tt0) cc_final: 0.4578 (tm-30) REVERT: A 56 TYR cc_start: 0.7213 (m-80) cc_final: 0.6815 (m-80) REVERT: A 78 ARG cc_start: 0.8613 (tpt-90) cc_final: 0.8366 (tpp-160) REVERT: A 101 PHE cc_start: 0.8532 (t80) cc_final: 0.8019 (m-80) REVERT: A 272 MET cc_start: 0.8420 (mmt) cc_final: 0.8129 (mmm) REVERT: A 277 MET cc_start: 0.7637 (mmt) cc_final: 0.7433 (mmm) REVERT: A 293 TYR cc_start: 0.7412 (t80) cc_final: 0.7141 (t80) REVERT: A 550 TYR cc_start: 0.8026 (p90) cc_final: 0.7480 (p90) REVERT: A 578 GLN cc_start: 0.8406 (mp10) cc_final: 0.8089 (mp-120) REVERT: A 714 ARG cc_start: 0.7418 (ptp90) cc_final: 0.7169 (mtp85) REVERT: A 819 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.6909 (tpt-90) REVERT: A 825 TYR cc_start: 0.8799 (t80) cc_final: 0.8067 (t80) REVERT: A 912 MET cc_start: 0.5778 (mmp) cc_final: 0.5530 (mmt) REVERT: A 958 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7151 (mtm180) REVERT: A 1013 LYS cc_start: 0.7017 (OUTLIER) cc_final: 0.6404 (mmmt) REVERT: A 1191 LEU cc_start: 0.8564 (tt) cc_final: 0.8342 (tt) REVERT: A 1235 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8248 (mt) outliers start: 45 outliers final: 31 residues processed: 191 average time/residue: 0.0776 time to fit residues: 22.1664 Evaluate side-chains 195 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 958 ARG Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [53, 27, 20, 50, 94, 24, 107, 29, 103, 84, 66] chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 94 optimal weight: 0.0670 chunk 24 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.142582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.111694 restraints weight = 16899.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.112905 restraints weight = 9346.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.113559 restraints weight = 8353.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113961 restraints weight = 6144.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114236 restraints weight = 5806.703| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9787 Z= 0.152 Angle : 0.767 11.821 13383 Z= 0.368 Chirality : 0.047 0.258 1557 Planarity : 0.004 0.043 1664 Dihedral : 6.061 46.979 1291 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.93 % Allowed : 23.89 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.17 (0.25), residues: 1167 helix: 1.01 (0.21), residues: 613 sheet: -1.54 (0.48), residues: 116 loop : -1.27 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 372 TYR 0.012 0.001 TYR A 709 PHE 0.029 0.002 PHE A 152 TRP 0.029 0.002 TRP A1143 HIS 0.003 0.001 HIS A 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 9753) covalent geometry : angle 0.74223 / 0.36 (13296) SS BOND : bond 0.00365 / 0.20 ( 15) SS BOND : angle 2.05263 / 1.42 ( 30) hydrogen bonds : bond 0.04554 / 2.93 ( 482) hydrogen bonds : angle 5.02089 / 3.41 ( 1392) link_ALPHA1-3 : bond 0.00990 / 0.52 ( 1) link_ALPHA1-3 : angle 1.43044 / 0.76 ( 3) link_BETA1-4 : bond 0.01055 / 0.56 ( 5) link_BETA1-4 : angle 2.46541 / 1.58 ( 15) link_NAG-ASN : bond 0.00601 / 0.30 ( 13) link_NAG-ASN : angle 2.88596 / 1.59 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.5176 (tt0) cc_final: 0.4708 (tm-30) REVERT: A 56 TYR cc_start: 0.7269 (m-80) cc_final: 0.6936 (m-80) REVERT: A 78 ARG cc_start: 0.8588 (tpt-90) cc_final: 0.8363 (tpp-160) REVERT: A 86 ASN cc_start: 0.7575 (m110) cc_final: 0.7359 (m110) REVERT: A 101 PHE cc_start: 0.8352 (t80) cc_final: 0.7973 (m-80) REVERT: A 272 MET cc_start: 0.8500 (mmt) cc_final: 0.8179 (mmm) REVERT: A 277 MET cc_start: 0.7651 (mmt) cc_final: 0.7446 (mmm) REVERT: A 293 TYR cc_start: 0.7449 (t80) cc_final: 0.7154 (t80) REVERT: A 407 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8391 (mp10) REVERT: A 550 TYR cc_start: 0.8049 (p90) cc_final: 0.7481 (p90) REVERT: A 578 GLN cc_start: 0.8382 (mp10) cc_final: 0.8097 (mp10) REVERT: A 656 LEU cc_start: 0.7442 (mm) cc_final: 0.7223 (mm) REVERT: A 714 ARG cc_start: 0.7434 (ptp90) cc_final: 0.7061 (ptm-80) REVERT: A 770 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7835 (tt) REVERT: A 819 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6994 (tpt-90) REVERT: A 825 TYR cc_start: 0.8825 (t80) cc_final: 0.8142 (t80) REVERT: A 912 MET cc_start: 0.5808 (mmp) cc_final: 0.5552 (mmt) REVERT: A 958 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7180 (mtm180) REVERT: A 1191 LEU cc_start: 0.8556 (tt) cc_final: 0.8339 (tt) REVERT: A 1235 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8268 (mt) outliers start: 40 outliers final: 30 residues processed: 186 average time/residue: 0.0804 time to fit residues: 22.5202 Evaluate side-chains 191 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 958 ARG Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [68, 13, 64, 23, 73, 51, 25, 66, 37, 27, 100] chunk 68 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 100 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 897 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.144007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113613 restraints weight = 16912.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.113478 restraints weight = 10165.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.114702 restraints weight = 8978.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.114782 restraints weight = 6533.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.115266 restraints weight = 5847.541| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9787 Z= 0.140 Angle : 0.760 11.833 13383 Z= 0.362 Chirality : 0.046 0.262 1557 Planarity : 0.004 0.042 1664 Dihedral : 5.886 46.790 1287 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.24 % Allowed : 24.78 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.11 (0.25), residues: 1167 helix: 1.04 (0.21), residues: 615 sheet: -1.49 (0.49), residues: 115 loop : -1.22 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 714 TYR 0.013 0.001 TYR A 709 PHE 0.032 0.002 PHE A 152 TRP 0.027 0.001 TRP A1143 HIS 0.003 0.001 HIS A 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 9753) covalent geometry : angle 0.73774 / 0.36 (13296) SS BOND : bond 0.00391 / 0.21 ( 15) SS BOND : angle 1.72797 / 1.18 ( 30) hydrogen bonds : bond 0.04343 / 2.79 ( 482) hydrogen bonds : angle 4.97806 / 3.39 ( 1392) link_ALPHA1-3 : bond 0.00945 / 0.50 ( 1) link_ALPHA1-3 : angle 1.40909 / 0.75 ( 3) link_BETA1-4 : bond 0.01022 / 0.53 ( 5) link_BETA1-4 : angle 2.34451 / 1.49 ( 15) link_NAG-ASN : bond 0.00644 / 0.33 ( 13) link_NAG-ASN : angle 2.81794 / 1.55 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.5377 (tt0) cc_final: 0.4632 (tm-30) REVERT: A 56 TYR cc_start: 0.7336 (m-80) cc_final: 0.7071 (m-80) REVERT: A 78 ARG cc_start: 0.8660 (tpt-90) cc_final: 0.8351 (tpp-160) REVERT: A 86 ASN cc_start: 0.7574 (m110) cc_final: 0.7337 (m110) REVERT: A 101 PHE cc_start: 0.8444 (t80) cc_final: 0.7991 (m-80) REVERT: A 191 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7566 (mt-10) REVERT: A 217 MET cc_start: 0.2665 (mtt) cc_final: 0.2395 (mtp) REVERT: A 272 MET cc_start: 0.8513 (mmt) cc_final: 0.8226 (mmm) REVERT: A 277 MET cc_start: 0.7617 (mmt) cc_final: 0.7410 (mmm) REVERT: A 293 TYR cc_start: 0.7541 (t80) cc_final: 0.7253 (t80) REVERT: A 407 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8255 (mp10) REVERT: A 550 TYR cc_start: 0.8030 (p90) cc_final: 0.7446 (p90) REVERT: A 578 GLN cc_start: 0.8399 (mp10) cc_final: 0.8134 (mp10) REVERT: A 714 ARG cc_start: 0.7434 (ptp90) cc_final: 0.7141 (mtp85) REVERT: A 770 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7912 (tt) REVERT: A 819 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7062 (tpt-90) REVERT: A 825 TYR cc_start: 0.8797 (t80) cc_final: 0.8187 (t80) REVERT: A 912 MET cc_start: 0.5912 (mmp) cc_final: 0.5655 (mmt) REVERT: A 1235 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8299 (mt) outliers start: 33 outliers final: 27 residues processed: 181 average time/residue: 0.0745 time to fit residues: 20.7137 Evaluate side-chains 185 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [96, 100, 107, 111, 77, 109, 13, 47, 54, 106, 31] chunk 96 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 77 optimal weight: 0.2980 chunk 109 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.141551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.110524 restraints weight = 16897.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.112062 restraints weight = 9326.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.112680 restraints weight = 8105.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.112953 restraints weight = 6046.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.113297 restraints weight = 5674.121| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9787 Z= 0.176 Angle : 0.797 11.657 13383 Z= 0.382 Chirality : 0.047 0.260 1557 Planarity : 0.004 0.044 1664 Dihedral : 5.968 46.606 1287 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.44 % Allowed : 25.07 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.14 (0.25), residues: 1167 helix: 0.98 (0.21), residues: 612 sheet: -1.49 (0.48), residues: 116 loop : -1.17 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 372 TYR 0.019 0.001 TYR A 709 PHE 0.030 0.002 PHE A 152 TRP 0.026 0.002 TRP A1143 HIS 0.002 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 ( 9753) covalent geometry : angle 0.77322 / 0.38 (13296) SS BOND : bond 0.00475 / 0.25 ( 15) SS BOND : angle 2.08438 / 1.32 ( 30) hydrogen bonds : bond 0.04745 / 3.04 ( 482) hydrogen bonds : angle 5.03483 / 3.42 ( 1392) link_ALPHA1-3 : bond 0.01008 / 0.53 ( 1) link_ALPHA1-3 : angle 1.53081 / 0.82 ( 3) link_BETA1-4 : bond 0.00974 / 0.51 ( 5) link_BETA1-4 : angle 2.33566 / 1.49 ( 15) link_NAG-ASN : bond 0.00573 / 0.28 ( 13) link_NAG-ASN : angle 2.88497 / 1.60 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.5525 (tt0) cc_final: 0.4807 (tm-30) REVERT: A 56 TYR cc_start: 0.7100 (m-80) cc_final: 0.6831 (m-80) REVERT: A 78 ARG cc_start: 0.8630 (tpt-90) cc_final: 0.8391 (tpp-160) REVERT: A 101 PHE cc_start: 0.8343 (t80) cc_final: 0.7940 (m-80) REVERT: A 217 MET cc_start: 0.2801 (mtt) cc_final: 0.2512 (mtp) REVERT: A 272 MET cc_start: 0.8585 (mmt) cc_final: 0.8294 (mmm) REVERT: A 407 GLN cc_start: 0.9277 (OUTLIER) cc_final: 0.8397 (mp10) REVERT: A 550 TYR cc_start: 0.8092 (p90) cc_final: 0.7505 (p90) REVERT: A 578 GLN cc_start: 0.8431 (mp10) cc_final: 0.8167 (mp10) REVERT: A 714 ARG cc_start: 0.7468 (ptp90) cc_final: 0.7134 (ptm-80) REVERT: A 770 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7895 (tt) REVERT: A 825 TYR cc_start: 0.8812 (t80) cc_final: 0.8133 (t80) REVERT: A 1235 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8296 (mt) outliers start: 35 outliers final: 28 residues processed: 176 average time/residue: 0.0744 time to fit residues: 19.8987 Evaluate side-chains 180 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [105, 3, 41, 112, 44, 98, 97, 108, 7, 34, 19] chunk 105 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 0.0470 chunk 112 optimal weight: 0.0010 chunk 44 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 overall best weight: 0.4484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 HIS A 897 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.142562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.111919 restraints weight = 16841.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.111054 restraints weight = 9983.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.112254 restraints weight = 8280.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.114443 restraints weight = 6456.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114237 restraints weight = 5695.109| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9787 Z= 0.140 Angle : 0.785 11.752 13383 Z= 0.374 Chirality : 0.047 0.260 1557 Planarity : 0.004 0.041 1664 Dihedral : 5.636 46.652 1283 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.05 % Allowed : 26.06 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.11 (0.25), residues: 1167 helix: 1.04 (0.21), residues: 609 sheet: -1.45 (0.48), residues: 115 loop : -1.21 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 372 TYR 0.015 0.001 TYR A 709 PHE 0.032 0.001 PHE A 152 TRP 0.025 0.001 TRP A1143 HIS 0.003 0.001 HIS A 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 9753) covalent geometry : angle 0.76144 / 0.37 (13296) SS BOND : bond 0.00542 / 0.27 ( 15) SS BOND : angle 2.25281 / 1.65 ( 30) hydrogen bonds : bond 0.04327 / 2.77 ( 482) hydrogen bonds : angle 4.96857 / 3.38 ( 1392) link_ALPHA1-3 : bond 0.00936 / 0.49 ( 1) link_ALPHA1-3 : angle 1.38336 / 0.74 ( 3) link_BETA1-4 : bond 0.01023 / 0.54 ( 5) link_BETA1-4 : angle 2.22787 / 1.41 ( 15) link_NAG-ASN : bond 0.00662 / 0.34 ( 13) link_NAG-ASN : angle 2.78549 / 1.53 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1498.44 seconds wall clock time: 26 minutes 37.31 seconds (1597.31 seconds total)