Starting phenix.real_space_refine on Wed May 14 06:47:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dzv_47339/05_2025/9dzv_47339.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dzv_47339/05_2025/9dzv_47339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dzv_47339/05_2025/9dzv_47339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dzv_47339/05_2025/9dzv_47339.map" model { file = "/net/cci-nas-00/data/ceres_data/9dzv_47339/05_2025/9dzv_47339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dzv_47339/05_2025/9dzv_47339.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 45 5.16 5 C 7398 2.51 5 N 1903 2.21 5 O 2155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11502 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2723 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 24, 'TRANS': 324} Chain: "A" Number of atoms: 8636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8636 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 32, 'TRANS': 1049} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.39, per 1000 atoms: 0.64 Number of scatterers: 11502 At special positions: 0 Unit cell: (81.144, 99.36, 173.052, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 Mg 1 11.99 O 2155 8.00 N 1903 7.00 C 7398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 209 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 6 " ALPHA1-4 " MAN E 4 " - " MAN E 5 " ALPHA1-6 " BMA E 3 " - " MAN E 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG B 501 " - " ASN B 235 " " NAG D 1 " - " ASN B 129 " " NAG E 1 " - " ASN B 218 " " NAG G 1 " - " ASN B 239 " Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.6 seconds 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2670 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 10 sheets defined 47.6% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'B' and resid 48 through 76 Proline residue: B 54 - end of helix Proline residue: B 65 - end of helix Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.536A pdb=" N CYS B 87 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP B 88 " --> pdb=" O THR B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 84 through 88' Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.919A pdb=" N SER B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 182 Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 209 through 215 removed outlier: 4.171A pdb=" N ALA B 213 " --> pdb=" O CYS B 209 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 290 through 297 removed outlier: 3.993A pdb=" N GLN B 294 " --> pdb=" O ASP B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 336 Processing helix chain 'B' and resid 354 through 381 removed outlier: 3.746A pdb=" N TRP B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 removed outlier: 3.604A pdb=" N LYS A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.556A pdb=" N PHE A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 154 removed outlier: 3.798A pdb=" N VAL A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 407 through 445 Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 459 through 475 Processing helix chain 'A' and resid 482 through 501 Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.758A pdb=" N ILE A 529 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 633 Processing helix chain 'A' and resid 637 through 653 Processing helix chain 'A' and resid 672 through 685 Processing helix chain 'A' and resid 745 through 752 Processing helix chain 'A' and resid 758 through 776 removed outlier: 3.560A pdb=" N GLU A 776 " --> pdb=" O TYR A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 805 removed outlier: 4.309A pdb=" N VAL A 805 " --> pdb=" O HIS A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 822 Processing helix chain 'A' and resid 840 through 850 Processing helix chain 'A' and resid 863 through 866 Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 891 through 905 Processing helix chain 'A' and resid 907 through 915 removed outlier: 3.727A pdb=" N ARG A 911 " --> pdb=" O ASP A 907 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 912 " --> pdb=" O ALA A 908 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR A 913 " --> pdb=" O GLY A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 966 Processing helix chain 'A' and resid 967 through 979 Processing helix chain 'A' and resid 989 through 1005 Processing helix chain 'A' and resid 1014 through 1023 Processing helix chain 'A' and resid 1036 through 1041 Processing helix chain 'A' and resid 1048 through 1090 Processing helix chain 'A' and resid 1101 through 1107 Processing helix chain 'A' and resid 1114 through 1124 removed outlier: 3.734A pdb=" N ASP A1124 " --> pdb=" O ILE A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1135 Processing helix chain 'A' and resid 1136 through 1138 No H-bonds generated for 'chain 'A' and resid 1136 through 1138' Processing helix chain 'A' and resid 1139 through 1144 Processing helix chain 'A' and resid 1150 through 1176 Processing helix chain 'A' and resid 1188 through 1211 removed outlier: 3.848A pdb=" N MET A1192 " --> pdb=" O TYR A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1225 through 1238 removed outlier: 3.615A pdb=" N SER A1238 " --> pdb=" O THR A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1256 Processing helix chain 'A' and resid 1259 through 1287 Proline residue: A1267 - end of helix Proline residue: A1276 - end of helix Processing helix chain 'A' and resid 1290 through 1302 Processing helix chain 'A' and resid 1306 through 1310 removed outlier: 4.090A pdb=" N HIS A1310 " --> pdb=" O LEU A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1317 Processing sheet with id=AA1, first strand: chain 'B' and resid 105 through 108 removed outlier: 7.088A pdb=" N LEU B 155 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ARG B 311 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU B 157 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'B' and resid 200 through 201 removed outlier: 3.621A pdb=" N ARG B 201 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 161 removed outlier: 3.604A pdb=" N LEU A 161 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N PHE A 268 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 331 through 333 Processing sheet with id=AA7, first strand: chain 'A' and resid 506 through 508 Processing sheet with id=AA8, first strand: chain 'A' and resid 516 through 517 removed outlier: 6.458A pdb=" N CYS A1008 " --> pdb=" O VAL A1026 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL A1028 " --> pdb=" O CYS A1008 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ALA A1010 " --> pdb=" O VAL A1028 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE A1030 " --> pdb=" O ALA A1010 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY A1012 " --> pdb=" O ILE A1030 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE A 532 " --> pdb=" O TRP A 856 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ALA A 858 " --> pdb=" O ILE A 532 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER A 534 " --> pdb=" O ALA A 858 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 855 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N CYS A 985 " --> pdb=" O VAL A 855 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL A 857 " --> pdb=" O CYS A 985 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A 953 " --> pdb=" O ILE A 984 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N CYS A 986 " --> pdb=" O LEU A 953 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 955 " --> pdb=" O CYS A 986 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 546 through 551 removed outlier: 3.541A pdb=" N GLU A 834 " --> pdb=" O ILE A 546 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 548 " --> pdb=" O ALA A 832 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ALA A 832 " --> pdb=" O ARG A 548 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N CYS A 550 " --> pdb=" O ALA A 830 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ALA A 830 " --> pdb=" O CYS A 550 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY A 829 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A 744 " --> pdb=" O CYS A 782 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N CYS A 742 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE A 738 " --> pdb=" O LEU A 788 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ILE A 728 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 711 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 691 " --> pdb=" O ARG A 698 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 657 through 658 removed outlier: 3.772A pdb=" N LEU A 657 " --> pdb=" O LYS A 669 " (cutoff:3.500A) 534 hydrogen bonds defined for protein. 1497 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3664 1.34 - 1.46: 2520 1.46 - 1.58: 5527 1.58 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 11780 Sorted by residual: bond pdb=" CE1 HIS A 155 " pdb=" NE2 HIS A 155 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.68e+01 bond pdb=" N ASN A 154 " pdb=" CA ASN A 154 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.17e-02 7.31e+03 9.30e+00 bond pdb=" N ILE A 157 " pdb=" CA ILE A 157 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.27e-02 6.20e+03 8.58e+00 bond pdb=" N HIS A 155 " pdb=" CA HIS A 155 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.35e-02 5.49e+03 5.16e+00 bond pdb=" N ALA A 156 " pdb=" CA ALA A 156 " ideal model delta sigma weight residual 1.456 1.482 -0.025 1.22e-02 6.72e+03 4.29e+00 ... (remaining 11775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 15487 1.31 - 2.62: 409 2.62 - 3.93: 85 3.93 - 5.23: 33 5.23 - 6.54: 10 Bond angle restraints: 16024 Sorted by residual: angle pdb=" N ARG A 372 " pdb=" CA ARG A 372 " pdb=" C ARG A 372 " ideal model delta sigma weight residual 108.52 113.03 -4.51 1.52e+00 4.33e-01 8.80e+00 angle pdb=" CA LEU A 371 " pdb=" C LEU A 371 " pdb=" O LEU A 371 " ideal model delta sigma weight residual 120.71 117.59 3.12 1.10e+00 8.26e-01 8.07e+00 angle pdb=" CA ASN A 154 " pdb=" C ASN A 154 " pdb=" O ASN A 154 " ideal model delta sigma weight residual 121.50 117.97 3.53 1.25e+00 6.40e-01 7.99e+00 angle pdb=" N HIS A 155 " pdb=" CA HIS A 155 " pdb=" C HIS A 155 " ideal model delta sigma weight residual 113.23 109.98 3.25 1.22e+00 6.72e-01 7.08e+00 angle pdb=" CA ILE A 157 " pdb=" C ILE A 157 " pdb=" O ILE A 157 " ideal model delta sigma weight residual 121.13 118.30 2.83 1.16e+00 7.43e-01 5.96e+00 ... (remaining 16019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.72: 6798 24.72 - 49.43: 194 49.43 - 74.15: 28 74.15 - 98.87: 17 98.87 - 123.59: 16 Dihedral angle restraints: 7053 sinusoidal: 2892 harmonic: 4161 Sorted by residual: dihedral pdb=" C2 MAN E 5 " pdb=" C1 MAN E 5 " pdb=" O5 MAN E 5 " pdb=" C5 MAN E 5 " ideal model delta sinusoidal sigma weight residual -57.62 65.97 -123.59 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" C1 MAN E 4 " pdb=" C5 MAN E 4 " pdb=" O5 MAN E 4 " pdb=" C4 MAN E 4 " ideal model delta sinusoidal sigma weight residual -58.30 56.99 -115.29 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" C1 MAN E 4 " pdb=" C5 MAN E 4 " pdb=" O5 MAN E 4 " pdb=" C6 MAN E 4 " ideal model delta sinusoidal sigma weight residual 179.92 -69.98 -110.10 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 7050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1414 0.050 - 0.099: 340 0.099 - 0.149: 66 0.149 - 0.199: 6 0.199 - 0.248: 2 Chirality restraints: 1828 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 239 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C3 MAN E 4 " pdb=" C2 MAN E 4 " pdb=" C4 MAN E 4 " pdb=" O3 MAN E 4 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 1825 not shown) Planarity restraints: 2026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A1056 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C LEU A1056 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU A1056 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A1057 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 810 " -0.010 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" C ARG A 810 " 0.035 2.00e-02 2.50e+03 pdb=" O ARG A 810 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 811 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 53 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO A 54 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 54 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 54 " -0.025 5.00e-02 4.00e+02 ... (remaining 2023 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2105 2.77 - 3.30: 11755 3.30 - 3.83: 19620 3.83 - 4.37: 22471 4.37 - 4.90: 38481 Nonbonded interactions: 94432 Sorted by model distance: nonbonded pdb=" O VAL A 347 " pdb=" ND1 HIS A 362 " model vdw 2.235 3.120 nonbonded pdb=" OH TYR A1076 " pdb=" OE1 GLN A1163 " model vdw 2.256 3.040 nonbonded pdb=" O GLY B 136 " pdb=" ND2 ASN B 329 " model vdw 2.260 3.120 nonbonded pdb=" OE1 GLU A 711 " pdb=" OH TYR A 793 " model vdw 2.272 3.040 nonbonded pdb=" O ALA A1047 " pdb=" NE2 GLN A1048 " model vdw 2.275 3.120 ... (remaining 94427 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 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.530 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11793 Z= 0.161 Angle : 0.573 7.362 16061 Z= 0.293 Chirality : 0.043 0.248 1828 Planarity : 0.003 0.046 2022 Dihedral : 14.166 123.587 4377 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 4.33 % Allowed : 7.60 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.24), residues: 1419 helix: 1.43 (0.22), residues: 592 sheet: -0.74 (0.39), residues: 196 loop : -2.11 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 72 HIS 0.003 0.001 HIS A 362 PHE 0.013 0.001 PHE A 646 TYR 0.012 0.001 TYR A1262 ARG 0.002 0.000 ARG A 786 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 4) link_NAG-ASN : angle 1.64051 ( 12) link_ALPHA1-4 : bond 0.01629 ( 1) link_ALPHA1-4 : angle 4.63733 ( 3) link_ALPHA1-6 : bond 0.00438 ( 1) link_ALPHA1-6 : angle 2.69431 ( 3) link_BETA1-4 : bond 0.00671 ( 4) link_BETA1-4 : angle 1.68088 ( 12) link_ALPHA1-3 : bond 0.00392 ( 1) link_ALPHA1-3 : angle 1.56136 ( 3) hydrogen bonds : bond 0.15571 ( 522) hydrogen bonds : angle 6.30068 ( 1497) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.75869 ( 4) covalent geometry : bond 0.00303 (11780) covalent geometry : angle 0.56436 (16024) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 288 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7877 (mm-30) REVERT: B 115 VAL cc_start: 0.9138 (t) cc_final: 0.8808 (m) REVERT: B 294 GLN cc_start: 0.7967 (mt0) cc_final: 0.7743 (mt0) REVERT: A 275 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7179 (mt-10) REVERT: A 291 ASP cc_start: 0.5877 (OUTLIER) cc_final: 0.5441 (p0) REVERT: A 298 LYS cc_start: 0.8470 (tptp) cc_final: 0.8109 (tppt) REVERT: A 340 MET cc_start: 0.7831 (tpp) cc_final: 0.7427 (tpp) REVERT: A 372 ARG cc_start: 0.6595 (OUTLIER) cc_final: 0.6030 (tpt90) REVERT: A 406 ARG cc_start: 0.7386 (mtm-85) cc_final: 0.7125 (mtm-85) REVERT: A 450 MET cc_start: 0.8498 (mmm) cc_final: 0.7731 (mmm) REVERT: A 488 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7423 (mm-30) REVERT: A 503 ASP cc_start: 0.7865 (t0) cc_final: 0.7656 (t0) REVERT: A 548 ARG cc_start: 0.7854 (mmt-90) cc_final: 0.7610 (mmt-90) REVERT: A 653 CYS cc_start: 0.8076 (t) cc_final: 0.7834 (t) REVERT: A 717 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6528 (tm-30) REVERT: A 771 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7862 (mm-40) REVERT: A 811 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7718 (pp20) REVERT: A 815 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7779 (tp30) REVERT: A 951 PHE cc_start: 0.6681 (m-80) cc_final: 0.6466 (m-80) REVERT: A 970 GLU cc_start: 0.7417 (tt0) cc_final: 0.7105 (tt0) REVERT: A 1003 ASN cc_start: 0.7711 (t0) cc_final: 0.7492 (t0) REVERT: A 1123 PHE cc_start: 0.8868 (m-80) cc_final: 0.8389 (m-80) REVERT: A 1189 MET cc_start: 0.8184 (ttp) cc_final: 0.7971 (ttp) REVERT: A 1193 SER cc_start: 0.8773 (p) cc_final: 0.8423 (p) REVERT: A 1258 ARG cc_start: 0.8620 (mtt90) cc_final: 0.8413 (mtt90) outliers start: 53 outliers final: 20 residues processed: 328 average time/residue: 0.2664 time to fit residues: 120.7078 Evaluate side-chains 277 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 255 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 963 CYS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1016 ASN Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1112 TRP Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1309 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 0.0030 chunk 111 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 995 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.138961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.115999 restraints weight = 19416.934| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.50 r_work: 0.3448 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11793 Z= 0.162 Angle : 0.680 10.559 16061 Z= 0.342 Chirality : 0.047 0.244 1828 Planarity : 0.004 0.044 2022 Dihedral : 12.866 111.892 1822 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 3.84 % Allowed : 13.81 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.23), residues: 1419 helix: 1.15 (0.21), residues: 604 sheet: -0.69 (0.39), residues: 202 loop : -2.12 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1220 HIS 0.005 0.001 HIS A 654 PHE 0.016 0.001 PHE A1225 TYR 0.020 0.001 TYR B 322 ARG 0.005 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 4) link_NAG-ASN : angle 1.54554 ( 12) link_ALPHA1-4 : bond 0.02391 ( 1) link_ALPHA1-4 : angle 6.52742 ( 3) link_ALPHA1-6 : bond 0.01214 ( 1) link_ALPHA1-6 : angle 4.17079 ( 3) link_BETA1-4 : bond 0.00599 ( 4) link_BETA1-4 : angle 1.57243 ( 12) link_ALPHA1-3 : bond 0.00525 ( 1) link_ALPHA1-3 : angle 3.02425 ( 3) hydrogen bonds : bond 0.05238 ( 522) hydrogen bonds : angle 5.28681 ( 1497) SS BOND : bond 0.00302 ( 2) SS BOND : angle 0.72643 ( 4) covalent geometry : bond 0.00349 (11780) covalent geometry : angle 0.66798 (16024) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 257 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 VAL cc_start: 0.9191 (t) cc_final: 0.8838 (m) REVERT: B 201 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8227 (ttp80) REVERT: A 291 ASP cc_start: 0.6390 (p0) cc_final: 0.5899 (p0) REVERT: A 298 LYS cc_start: 0.8503 (tptp) cc_final: 0.8087 (tppt) REVERT: A 367 GLU cc_start: 0.7654 (pm20) cc_final: 0.7432 (pm20) REVERT: A 406 ARG cc_start: 0.7343 (mtm-85) cc_final: 0.7096 (mtm-85) REVERT: A 488 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7461 (tp30) REVERT: A 503 ASP cc_start: 0.8005 (t0) cc_final: 0.7760 (t0) REVERT: A 653 CYS cc_start: 0.8075 (t) cc_final: 0.7778 (t) REVERT: A 717 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6754 (tm-30) REVERT: A 771 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7929 (mm-40) REVERT: A 811 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8020 (pp20) REVERT: A 1123 PHE cc_start: 0.8882 (m-80) cc_final: 0.8567 (m-80) REVERT: A 1152 ARG cc_start: 0.8341 (mtp180) cc_final: 0.8110 (mtp-110) REVERT: A 1189 MET cc_start: 0.8053 (ttp) cc_final: 0.7847 (ttp) REVERT: A 1193 SER cc_start: 0.8574 (p) cc_final: 0.8228 (p) outliers start: 47 outliers final: 30 residues processed: 287 average time/residue: 0.2587 time to fit residues: 103.4965 Evaluate side-chains 284 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 254 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 502 ARG Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1112 TRP Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain A residue 1210 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 7 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 85 optimal weight: 0.0370 chunk 32 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 ASN ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.141663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.118246 restraints weight = 19627.083| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.54 r_work: 0.3464 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11793 Z= 0.139 Angle : 0.662 11.360 16061 Z= 0.331 Chirality : 0.045 0.181 1828 Planarity : 0.004 0.065 2022 Dihedral : 9.884 103.985 1809 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 3.51 % Allowed : 16.26 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.23), residues: 1419 helix: 1.08 (0.22), residues: 610 sheet: -0.83 (0.38), residues: 205 loop : -2.18 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 381 HIS 0.003 0.001 HIS A 362 PHE 0.021 0.001 PHE B 127 TYR 0.019 0.001 TYR B 105 ARG 0.014 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 4) link_NAG-ASN : angle 1.30136 ( 12) link_ALPHA1-4 : bond 0.03690 ( 1) link_ALPHA1-4 : angle 6.85033 ( 3) link_ALPHA1-6 : bond 0.01690 ( 1) link_ALPHA1-6 : angle 2.84400 ( 3) link_BETA1-4 : bond 0.00562 ( 4) link_BETA1-4 : angle 1.49037 ( 12) link_ALPHA1-3 : bond 0.00695 ( 1) link_ALPHA1-3 : angle 2.35447 ( 3) hydrogen bonds : bond 0.04797 ( 522) hydrogen bonds : angle 5.04451 ( 1497) SS BOND : bond 0.00156 ( 2) SS BOND : angle 0.44765 ( 4) covalent geometry : bond 0.00294 (11780) covalent geometry : angle 0.65155 (16024) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 257 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 VAL cc_start: 0.9201 (t) cc_final: 0.8860 (m) REVERT: B 142 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7654 (mt-10) REVERT: B 201 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8214 (ttp80) REVERT: B 289 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: A 291 ASP cc_start: 0.6393 (p0) cc_final: 0.5857 (p0) REVERT: A 298 LYS cc_start: 0.8456 (tptp) cc_final: 0.8084 (tppt) REVERT: A 319 ASN cc_start: 0.6617 (OUTLIER) cc_final: 0.6099 (p0) REVERT: A 367 GLU cc_start: 0.7626 (pm20) cc_final: 0.7323 (pm20) REVERT: A 406 ARG cc_start: 0.7324 (mtm-85) cc_final: 0.7081 (mtm-85) REVERT: A 488 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7423 (tp30) REVERT: A 503 ASP cc_start: 0.8011 (t0) cc_final: 0.7744 (t0) REVERT: A 552 VAL cc_start: 0.8331 (t) cc_final: 0.7921 (m) REVERT: A 653 CYS cc_start: 0.7987 (t) cc_final: 0.7745 (t) REVERT: A 717 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6675 (tm-30) REVERT: A 725 MET cc_start: 0.8516 (tmm) cc_final: 0.8278 (tmm) REVERT: A 780 THR cc_start: 0.8313 (p) cc_final: 0.8051 (t) REVERT: A 811 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8015 (pp20) REVERT: A 970 GLU cc_start: 0.7669 (tt0) cc_final: 0.7259 (tt0) REVERT: A 1003 ASN cc_start: 0.7821 (t0) cc_final: 0.7614 (t0) REVERT: A 1104 TYR cc_start: 0.8105 (m-80) cc_final: 0.7788 (m-80) REVERT: A 1152 ARG cc_start: 0.8359 (mtp180) cc_final: 0.8107 (mtp180) REVERT: A 1189 MET cc_start: 0.8024 (ttp) cc_final: 0.7819 (ttp) REVERT: A 1193 SER cc_start: 0.8552 (p) cc_final: 0.8246 (p) outliers start: 43 outliers final: 27 residues processed: 285 average time/residue: 0.2625 time to fit residues: 104.0383 Evaluate side-chains 278 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 249 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 502 ARG Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 635 HIS Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 963 CYS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1112 TRP Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1210 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 140 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 30 optimal weight: 0.0980 chunk 34 optimal weight: 0.2980 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 0.0020 chunk 124 optimal weight: 0.0980 chunk 51 optimal weight: 0.9980 chunk 134 optimal weight: 0.0970 overall best weight: 0.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 ASN ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A1205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.143358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.120176 restraints weight = 19435.422| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.53 r_work: 0.3490 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11793 Z= 0.125 Angle : 0.651 10.383 16061 Z= 0.325 Chirality : 0.045 0.237 1828 Planarity : 0.004 0.058 2022 Dihedral : 8.972 95.637 1805 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 3.68 % Allowed : 17.48 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.23), residues: 1419 helix: 1.11 (0.22), residues: 619 sheet: -0.57 (0.40), residues: 188 loop : -2.26 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 381 HIS 0.003 0.000 HIS A 362 PHE 0.011 0.001 PHE A 50 TYR 0.018 0.001 TYR B 105 ARG 0.010 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 4) link_NAG-ASN : angle 1.13101 ( 12) link_ALPHA1-4 : bond 0.02824 ( 1) link_ALPHA1-4 : angle 6.40805 ( 3) link_ALPHA1-6 : bond 0.00884 ( 1) link_ALPHA1-6 : angle 0.50226 ( 3) link_BETA1-4 : bond 0.00660 ( 4) link_BETA1-4 : angle 1.38664 ( 12) link_ALPHA1-3 : bond 0.01005 ( 1) link_ALPHA1-3 : angle 1.79636 ( 3) hydrogen bonds : bond 0.04374 ( 522) hydrogen bonds : angle 4.83499 ( 1497) SS BOND : bond 0.00172 ( 2) SS BOND : angle 0.42420 ( 4) covalent geometry : bond 0.00258 (11780) covalent geometry : angle 0.64303 (16024) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 VAL cc_start: 0.9174 (t) cc_final: 0.8813 (m) REVERT: B 142 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7550 (mt-10) REVERT: B 201 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8157 (ttp80) REVERT: B 288 ARG cc_start: 0.8564 (ttm170) cc_final: 0.8296 (ttm-80) REVERT: B 289 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: A 291 ASP cc_start: 0.6384 (p0) cc_final: 0.5817 (p0) REVERT: A 298 LYS cc_start: 0.8461 (tptp) cc_final: 0.8083 (tppt) REVERT: A 318 LEU cc_start: 0.8318 (mt) cc_final: 0.7994 (mt) REVERT: A 319 ASN cc_start: 0.6800 (OUTLIER) cc_final: 0.6466 (p0) REVERT: A 343 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6695 (tt) REVERT: A 367 GLU cc_start: 0.7677 (pm20) cc_final: 0.7342 (pm20) REVERT: A 406 ARG cc_start: 0.7284 (mtm-85) cc_final: 0.7059 (mtm-85) REVERT: A 450 MET cc_start: 0.8177 (mmm) cc_final: 0.7906 (mmm) REVERT: A 488 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7375 (tp30) REVERT: A 503 ASP cc_start: 0.7971 (t0) cc_final: 0.7707 (t0) REVERT: A 552 VAL cc_start: 0.8241 (t) cc_final: 0.7882 (m) REVERT: A 653 CYS cc_start: 0.7895 (t) cc_final: 0.7586 (t) REVERT: A 717 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6503 (tm-30) REVERT: A 725 MET cc_start: 0.8394 (tmm) cc_final: 0.7993 (tmm) REVERT: A 811 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8014 (pp20) REVERT: A 880 THR cc_start: 0.6160 (OUTLIER) cc_final: 0.5895 (p) REVERT: A 1003 ASN cc_start: 0.7819 (t0) cc_final: 0.7608 (t0) REVERT: A 1104 TYR cc_start: 0.8091 (m-80) cc_final: 0.7825 (m-80) REVERT: A 1152 ARG cc_start: 0.8337 (mtp180) cc_final: 0.8104 (mtp180) REVERT: A 1189 MET cc_start: 0.7979 (ttp) cc_final: 0.7772 (ttp) REVERT: A 1193 SER cc_start: 0.8513 (p) cc_final: 0.8218 (p) REVERT: A 1293 ASP cc_start: 0.7458 (m-30) cc_final: 0.7221 (m-30) outliers start: 45 outliers final: 31 residues processed: 291 average time/residue: 0.2570 time to fit residues: 103.1243 Evaluate side-chains 282 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 247 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 502 ARG Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 635 HIS Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 963 CYS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1112 TRP Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1245 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1205 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 = 0.3915 r_free = 0.3915 target = 0.140623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.117192 restraints weight = 19430.626| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.57 r_work: 0.3444 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11793 Z= 0.168 Angle : 0.658 9.427 16061 Z= 0.333 Chirality : 0.046 0.233 1828 Planarity : 0.004 0.060 2022 Dihedral : 8.582 89.944 1801 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 3.68 % Allowed : 18.46 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.23), residues: 1419 helix: 1.02 (0.21), residues: 616 sheet: -0.56 (0.40), residues: 188 loop : -2.31 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 381 HIS 0.004 0.001 HIS A1059 PHE 0.020 0.001 PHE A 50 TYR 0.017 0.002 TYR B 105 ARG 0.007 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 4) link_NAG-ASN : angle 1.22996 ( 12) link_ALPHA1-4 : bond 0.02387 ( 1) link_ALPHA1-4 : angle 6.00138 ( 3) link_ALPHA1-6 : bond 0.00677 ( 1) link_ALPHA1-6 : angle 0.74415 ( 3) link_BETA1-4 : bond 0.00619 ( 4) link_BETA1-4 : angle 1.40001 ( 12) link_ALPHA1-3 : bond 0.00873 ( 1) link_ALPHA1-3 : angle 2.18707 ( 3) hydrogen bonds : bond 0.04789 ( 522) hydrogen bonds : angle 4.87122 ( 1497) SS BOND : bond 0.00234 ( 2) SS BOND : angle 0.55029 ( 4) covalent geometry : bond 0.00374 (11780) covalent geometry : angle 0.65116 (16024) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 TYR cc_start: 0.8020 (m-80) cc_final: 0.7806 (m-10) REVERT: B 115 VAL cc_start: 0.9180 (t) cc_final: 0.8823 (m) REVERT: B 142 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7571 (mt-10) REVERT: B 144 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7513 (mt-10) REVERT: B 201 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8245 (ttp80) REVERT: B 288 ARG cc_start: 0.8583 (ttm170) cc_final: 0.8305 (ttm-80) REVERT: B 289 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: A 291 ASP cc_start: 0.6459 (p0) cc_final: 0.5886 (p0) REVERT: A 298 LYS cc_start: 0.8502 (tptp) cc_final: 0.8159 (tppt) REVERT: A 318 LEU cc_start: 0.8428 (mt) cc_final: 0.8131 (mt) REVERT: A 319 ASN cc_start: 0.7146 (p0) cc_final: 0.6802 (p0) REVERT: A 367 GLU cc_start: 0.7692 (pm20) cc_final: 0.7363 (pm20) REVERT: A 372 ARG cc_start: 0.6530 (OUTLIER) cc_final: 0.5844 (tpt90) REVERT: A 406 ARG cc_start: 0.7337 (mtm-85) cc_final: 0.7111 (mtm-85) REVERT: A 488 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7620 (mm-30) REVERT: A 503 ASP cc_start: 0.7972 (t0) cc_final: 0.7712 (t0) REVERT: A 653 CYS cc_start: 0.7959 (t) cc_final: 0.7611 (t) REVERT: A 717 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6781 (tm-30) REVERT: A 725 MET cc_start: 0.8513 (tmm) cc_final: 0.8122 (tmm) REVERT: A 771 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7994 (mm-40) REVERT: A 791 GLN cc_start: 0.8599 (mp10) cc_final: 0.8324 (mp10) REVERT: A 1003 ASN cc_start: 0.7856 (t0) cc_final: 0.7599 (t0) REVERT: A 1089 MET cc_start: 0.8012 (ttm) cc_final: 0.7771 (ttm) REVERT: A 1104 TYR cc_start: 0.8109 (m-80) cc_final: 0.7801 (m-80) REVERT: A 1152 ARG cc_start: 0.8394 (mtp180) cc_final: 0.8089 (mtp180) REVERT: A 1189 MET cc_start: 0.8078 (ttp) cc_final: 0.7858 (ttp) REVERT: A 1193 SER cc_start: 0.8569 (p) cc_final: 0.8230 (p) outliers start: 45 outliers final: 32 residues processed: 290 average time/residue: 0.2678 time to fit residues: 106.9987 Evaluate side-chains 293 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 259 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 502 ARG Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 635 HIS Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 963 CYS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1112 TRP Chi-restraints excluded: chain A residue 1117 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 8 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 74 optimal weight: 0.0970 chunk 76 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 4 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 HIS A 714 HIS ** A 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.141154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.117834 restraints weight = 19548.945| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.54 r_work: 0.3454 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11793 Z= 0.146 Angle : 0.649 9.591 16061 Z= 0.326 Chirality : 0.045 0.214 1828 Planarity : 0.004 0.062 2022 Dihedral : 8.254 82.235 1801 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 3.59 % Allowed : 19.53 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.23), residues: 1419 helix: 1.04 (0.21), residues: 616 sheet: -0.61 (0.40), residues: 188 loop : -2.31 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 381 HIS 0.003 0.001 HIS A 362 PHE 0.016 0.001 PHE A 50 TYR 0.017 0.001 TYR B 105 ARG 0.006 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 4) link_NAG-ASN : angle 1.22900 ( 12) link_ALPHA1-4 : bond 0.02346 ( 1) link_ALPHA1-4 : angle 5.90133 ( 3) link_ALPHA1-6 : bond 0.00573 ( 1) link_ALPHA1-6 : angle 1.12827 ( 3) link_BETA1-4 : bond 0.00621 ( 4) link_BETA1-4 : angle 1.37598 ( 12) link_ALPHA1-3 : bond 0.01074 ( 1) link_ALPHA1-3 : angle 2.17857 ( 3) hydrogen bonds : bond 0.04670 ( 522) hydrogen bonds : angle 4.79445 ( 1497) SS BOND : bond 0.00148 ( 2) SS BOND : angle 0.38638 ( 4) covalent geometry : bond 0.00318 (11780) covalent geometry : angle 0.64176 (16024) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 256 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 TYR cc_start: 0.8038 (m-80) cc_final: 0.7753 (m-10) REVERT: B 115 VAL cc_start: 0.9187 (t) cc_final: 0.8832 (m) REVERT: B 176 ASP cc_start: 0.7804 (t70) cc_final: 0.7571 (t0) REVERT: B 286 ASN cc_start: 0.7751 (t0) cc_final: 0.7535 (t0) REVERT: A 291 ASP cc_start: 0.6458 (p0) cc_final: 0.5914 (p0) REVERT: A 298 LYS cc_start: 0.8503 (tptp) cc_final: 0.8122 (tppt) REVERT: A 318 LEU cc_start: 0.8526 (mt) cc_final: 0.8281 (mt) REVERT: A 343 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6731 (tt) REVERT: A 367 GLU cc_start: 0.7729 (pm20) cc_final: 0.7472 (pm20) REVERT: A 372 ARG cc_start: 0.6482 (OUTLIER) cc_final: 0.4379 (tmt170) REVERT: A 406 ARG cc_start: 0.7356 (mtm-85) cc_final: 0.7120 (mtm-85) REVERT: A 450 MET cc_start: 0.8203 (mmm) cc_final: 0.7925 (mmm) REVERT: A 488 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7436 (tp30) REVERT: A 503 ASP cc_start: 0.7942 (t0) cc_final: 0.7683 (t0) REVERT: A 552 VAL cc_start: 0.8335 (t) cc_final: 0.8064 (m) REVERT: A 653 CYS cc_start: 0.7857 (t) cc_final: 0.7468 (t) REVERT: A 717 GLU cc_start: 0.7216 (tm-30) cc_final: 0.6668 (tm-30) REVERT: A 725 MET cc_start: 0.8467 (tmm) cc_final: 0.8135 (tmm) REVERT: A 771 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7961 (mm-40) REVERT: A 798 LYS cc_start: 0.8178 (pttm) cc_final: 0.7879 (ptpp) REVERT: A 1104 TYR cc_start: 0.8107 (m-80) cc_final: 0.7822 (m-80) REVERT: A 1152 ARG cc_start: 0.8392 (mtp180) cc_final: 0.8078 (mtp180) REVERT: A 1189 MET cc_start: 0.8071 (ttp) cc_final: 0.7848 (ttp) REVERT: A 1193 SER cc_start: 0.8564 (p) cc_final: 0.8227 (p) outliers start: 44 outliers final: 31 residues processed: 282 average time/residue: 0.2699 time to fit residues: 105.3793 Evaluate side-chains 274 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 502 ARG Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 635 HIS Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 963 CYS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1112 TRP Chi-restraints excluded: chain A residue 1117 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 50 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1205 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 = 0.3916 r_free = 0.3916 target = 0.140804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.117240 restraints weight = 19642.502| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.60 r_work: 0.3438 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11793 Z= 0.153 Angle : 0.656 9.219 16061 Z= 0.332 Chirality : 0.045 0.197 1828 Planarity : 0.004 0.064 2022 Dihedral : 7.993 78.570 1801 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 3.68 % Allowed : 20.18 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.23), residues: 1419 helix: 1.03 (0.21), residues: 613 sheet: -0.80 (0.39), residues: 195 loop : -2.29 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1220 HIS 0.003 0.001 HIS A 362 PHE 0.016 0.001 PHE A 277 TYR 0.019 0.001 TYR B 149 ARG 0.006 0.000 ARG A 779 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 4) link_NAG-ASN : angle 1.25506 ( 12) link_ALPHA1-4 : bond 0.02297 ( 1) link_ALPHA1-4 : angle 5.90806 ( 3) link_ALPHA1-6 : bond 0.00683 ( 1) link_ALPHA1-6 : angle 1.47897 ( 3) link_BETA1-4 : bond 0.00611 ( 4) link_BETA1-4 : angle 1.39189 ( 12) link_ALPHA1-3 : bond 0.01040 ( 1) link_ALPHA1-3 : angle 2.21820 ( 3) hydrogen bonds : bond 0.04730 ( 522) hydrogen bonds : angle 4.78448 ( 1497) SS BOND : bond 0.00184 ( 2) SS BOND : angle 0.49263 ( 4) covalent geometry : bond 0.00334 (11780) covalent geometry : angle 0.64882 (16024) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 254 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 TYR cc_start: 0.8095 (m-80) cc_final: 0.7838 (m-10) REVERT: B 191 ASN cc_start: 0.8335 (m-40) cc_final: 0.8057 (m-40) REVERT: B 286 ASN cc_start: 0.7755 (t0) cc_final: 0.7555 (t0) REVERT: A 291 ASP cc_start: 0.6482 (p0) cc_final: 0.5930 (p0) REVERT: A 298 LYS cc_start: 0.8507 (tptp) cc_final: 0.8148 (tppt) REVERT: A 318 LEU cc_start: 0.8595 (mt) cc_final: 0.8337 (mt) REVERT: A 343 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6739 (tt) REVERT: A 372 ARG cc_start: 0.6627 (OUTLIER) cc_final: 0.4179 (tmt170) REVERT: A 406 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.7120 (mtm-85) REVERT: A 488 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 503 ASP cc_start: 0.7959 (t0) cc_final: 0.7700 (t0) REVERT: A 552 VAL cc_start: 0.8345 (t) cc_final: 0.8062 (m) REVERT: A 641 ARG cc_start: 0.7808 (mmp80) cc_final: 0.7339 (mmp80) REVERT: A 653 CYS cc_start: 0.7889 (t) cc_final: 0.7463 (t) REVERT: A 717 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6667 (tm-30) REVERT: A 725 MET cc_start: 0.8488 (tmm) cc_final: 0.8260 (tmm) REVERT: A 771 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7976 (mm-40) REVERT: A 881 ASN cc_start: 0.7996 (m-40) cc_final: 0.7698 (p0) REVERT: A 1104 TYR cc_start: 0.8112 (m-80) cc_final: 0.7818 (m-80) REVERT: A 1152 ARG cc_start: 0.8410 (mtp180) cc_final: 0.8084 (mtp180) REVERT: A 1189 MET cc_start: 0.8086 (ttp) cc_final: 0.7869 (ttp) REVERT: A 1193 SER cc_start: 0.8625 (p) cc_final: 0.8265 (p) REVERT: A 1258 ARG cc_start: 0.8740 (mtt180) cc_final: 0.8537 (mtt180) outliers start: 45 outliers final: 36 residues processed: 283 average time/residue: 0.2625 time to fit residues: 103.3239 Evaluate side-chains 289 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 502 ARG Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 635 HIS Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 963 CYS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1112 TRP Chi-restraints excluded: chain A residue 1117 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 111 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 106 optimal weight: 0.1980 chunk 76 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1205 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 = 0.3907 r_free = 0.3907 target = 0.139798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.116802 restraints weight = 19569.553| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.52 r_work: 0.3449 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11793 Z= 0.152 Angle : 0.673 9.197 16061 Z= 0.340 Chirality : 0.045 0.186 1828 Planarity : 0.004 0.066 2022 Dihedral : 7.829 77.921 1801 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 3.68 % Allowed : 20.42 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.23), residues: 1419 helix: 1.01 (0.21), residues: 614 sheet: -0.73 (0.40), residues: 189 loop : -2.30 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1220 HIS 0.004 0.001 HIS A 644 PHE 0.016 0.001 PHE A 277 TYR 0.016 0.001 TYR B 105 ARG 0.010 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 4) link_NAG-ASN : angle 1.25045 ( 12) link_ALPHA1-4 : bond 0.02231 ( 1) link_ALPHA1-4 : angle 5.88195 ( 3) link_ALPHA1-6 : bond 0.00643 ( 1) link_ALPHA1-6 : angle 1.70108 ( 3) link_BETA1-4 : bond 0.00640 ( 4) link_BETA1-4 : angle 1.40886 ( 12) link_ALPHA1-3 : bond 0.01069 ( 1) link_ALPHA1-3 : angle 2.11464 ( 3) hydrogen bonds : bond 0.04729 ( 522) hydrogen bonds : angle 4.74333 ( 1497) SS BOND : bond 0.00139 ( 2) SS BOND : angle 0.37877 ( 4) covalent geometry : bond 0.00333 (11780) covalent geometry : angle 0.66581 (16024) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 251 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 TYR cc_start: 0.8113 (m-80) cc_final: 0.7847 (m-10) REVERT: A 291 ASP cc_start: 0.6422 (p0) cc_final: 0.5864 (p0) REVERT: A 298 LYS cc_start: 0.8509 (tptp) cc_final: 0.8148 (tppt) REVERT: A 318 LEU cc_start: 0.8632 (mt) cc_final: 0.8366 (mt) REVERT: A 343 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6671 (tt) REVERT: A 372 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.4192 (tmt170) REVERT: A 406 ARG cc_start: 0.7330 (mtm-85) cc_final: 0.7098 (mtm-85) REVERT: A 450 MET cc_start: 0.8203 (mmm) cc_final: 0.7913 (mmm) REVERT: A 488 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7554 (mm-30) REVERT: A 503 ASP cc_start: 0.7969 (t0) cc_final: 0.7705 (t0) REVERT: A 552 VAL cc_start: 0.8360 (t) cc_final: 0.8078 (m) REVERT: A 641 ARG cc_start: 0.7803 (mmp80) cc_final: 0.7359 (mmp80) REVERT: A 653 CYS cc_start: 0.7901 (t) cc_final: 0.7444 (t) REVERT: A 717 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6683 (tm-30) REVERT: A 725 MET cc_start: 0.8480 (tmm) cc_final: 0.8238 (tmm) REVERT: A 771 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7928 (mm-40) REVERT: A 798 LYS cc_start: 0.8210 (pttm) cc_final: 0.7999 (ptpp) REVERT: A 881 ASN cc_start: 0.8005 (m-40) cc_final: 0.7708 (p0) REVERT: A 1104 TYR cc_start: 0.8106 (m-80) cc_final: 0.7785 (m-80) REVERT: A 1152 ARG cc_start: 0.8394 (mtp180) cc_final: 0.8059 (mtp180) REVERT: A 1189 MET cc_start: 0.8078 (ttp) cc_final: 0.7856 (ttp) REVERT: A 1193 SER cc_start: 0.8632 (p) cc_final: 0.8262 (p) REVERT: A 1258 ARG cc_start: 0.8729 (mtt180) cc_final: 0.8519 (mtt180) outliers start: 45 outliers final: 37 residues processed: 277 average time/residue: 0.2566 time to fit residues: 99.5564 Evaluate side-chains 281 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 502 ARG Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 635 HIS Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 963 CYS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1112 TRP Chi-restraints excluded: chain A residue 1117 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 136 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.139198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.116177 restraints weight = 19578.820| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.51 r_work: 0.3439 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11793 Z= 0.171 Angle : 0.692 9.354 16061 Z= 0.352 Chirality : 0.046 0.188 1828 Planarity : 0.004 0.069 2022 Dihedral : 7.802 82.418 1801 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 3.43 % Allowed : 20.59 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.23), residues: 1419 helix: 0.98 (0.21), residues: 615 sheet: -0.94 (0.39), residues: 196 loop : -2.30 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1220 HIS 0.006 0.001 HIS B 168 PHE 0.016 0.001 PHE B 284 TYR 0.016 0.002 TYR B 105 ARG 0.013 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 4) link_NAG-ASN : angle 1.26567 ( 12) link_ALPHA1-4 : bond 0.02236 ( 1) link_ALPHA1-4 : angle 5.87233 ( 3) link_ALPHA1-6 : bond 0.00610 ( 1) link_ALPHA1-6 : angle 1.83444 ( 3) link_BETA1-4 : bond 0.00679 ( 4) link_BETA1-4 : angle 1.43926 ( 12) link_ALPHA1-3 : bond 0.01027 ( 1) link_ALPHA1-3 : angle 2.16515 ( 3) hydrogen bonds : bond 0.04911 ( 522) hydrogen bonds : angle 4.76718 ( 1497) SS BOND : bond 0.00204 ( 2) SS BOND : angle 0.54645 ( 4) covalent geometry : bond 0.00377 (11780) covalent geometry : angle 0.68547 (16024) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 TYR cc_start: 0.8165 (m-80) cc_final: 0.7850 (m-10) REVERT: B 191 ASN cc_start: 0.8432 (m-40) cc_final: 0.8143 (m-40) REVERT: A 253 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8224 (mp) REVERT: A 291 ASP cc_start: 0.6468 (p0) cc_final: 0.5917 (p0) REVERT: A 298 LYS cc_start: 0.8521 (tptp) cc_final: 0.8153 (tppt) REVERT: A 318 LEU cc_start: 0.8668 (mt) cc_final: 0.8380 (mt) REVERT: A 343 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6710 (tt) REVERT: A 372 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.4295 (tmt170) REVERT: A 406 ARG cc_start: 0.7327 (mtm-85) cc_final: 0.7104 (mtm-85) REVERT: A 488 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7570 (mm-30) REVERT: A 503 ASP cc_start: 0.7942 (t0) cc_final: 0.7703 (t0) REVERT: A 552 VAL cc_start: 0.8378 (t) cc_final: 0.8090 (m) REVERT: A 641 ARG cc_start: 0.7797 (mmp80) cc_final: 0.7424 (mmp80) REVERT: A 653 CYS cc_start: 0.7879 (t) cc_final: 0.7443 (t) REVERT: A 717 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6664 (tm-30) REVERT: A 725 MET cc_start: 0.8485 (tmm) cc_final: 0.8265 (tmm) REVERT: A 771 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7907 (mm-40) REVERT: A 795 GLN cc_start: 0.8378 (pp30) cc_final: 0.8157 (pp30) REVERT: A 881 ASN cc_start: 0.8009 (m-40) cc_final: 0.7737 (p0) REVERT: A 1104 TYR cc_start: 0.8065 (m-80) cc_final: 0.7745 (m-80) REVERT: A 1152 ARG cc_start: 0.8404 (mtp180) cc_final: 0.8141 (mtp180) REVERT: A 1189 MET cc_start: 0.8080 (ttp) cc_final: 0.7850 (ttp) REVERT: A 1193 SER cc_start: 0.8617 (p) cc_final: 0.8260 (p) outliers start: 42 outliers final: 37 residues processed: 275 average time/residue: 0.2686 time to fit residues: 102.5361 Evaluate side-chains 285 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 502 ARG Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 635 HIS Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 963 CYS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1112 TRP Chi-restraints excluded: chain A residue 1117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 111 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 139 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 995 GLN ** A1205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.139335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.116368 restraints weight = 19397.614| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.50 r_work: 0.3442 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11793 Z= 0.165 Angle : 0.713 9.705 16061 Z= 0.364 Chirality : 0.046 0.188 1828 Planarity : 0.004 0.070 2022 Dihedral : 7.695 84.004 1799 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 3.59 % Allowed : 20.59 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.23), residues: 1419 helix: 0.95 (0.21), residues: 613 sheet: -0.82 (0.39), residues: 189 loop : -2.33 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1220 HIS 0.006 0.001 HIS B 168 PHE 0.028 0.001 PHE A 277 TYR 0.016 0.001 TYR B 105 ARG 0.007 0.000 ARG A 779 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 4) link_NAG-ASN : angle 1.32166 ( 12) link_ALPHA1-4 : bond 0.02312 ( 1) link_ALPHA1-4 : angle 5.86198 ( 3) link_ALPHA1-6 : bond 0.00651 ( 1) link_ALPHA1-6 : angle 1.90539 ( 3) link_BETA1-4 : bond 0.00657 ( 4) link_BETA1-4 : angle 1.37815 ( 12) link_ALPHA1-3 : bond 0.00983 ( 1) link_ALPHA1-3 : angle 2.05403 ( 3) hydrogen bonds : bond 0.04900 ( 522) hydrogen bonds : angle 4.81542 ( 1497) SS BOND : bond 0.00180 ( 2) SS BOND : angle 0.46865 ( 4) covalent geometry : bond 0.00365 (11780) covalent geometry : angle 0.70628 (16024) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 246 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 ARG cc_start: 0.7274 (ttm170) cc_final: 0.7040 (ptm160) REVERT: B 191 ASN cc_start: 0.8396 (m-40) cc_final: 0.8082 (m-40) REVERT: A 253 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8243 (mp) REVERT: A 283 ILE cc_start: 0.6241 (OUTLIER) cc_final: 0.6037 (tt) REVERT: A 291 ASP cc_start: 0.6513 (p0) cc_final: 0.5964 (p0) REVERT: A 298 LYS cc_start: 0.8509 (tptp) cc_final: 0.8147 (tppt) REVERT: A 343 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6633 (tt) REVERT: A 372 ARG cc_start: 0.6579 (OUTLIER) cc_final: 0.5679 (tpt90) REVERT: A 406 ARG cc_start: 0.7344 (mtm-85) cc_final: 0.7113 (mtm-85) REVERT: A 448 TYR cc_start: 0.8638 (m-80) cc_final: 0.8335 (m-80) REVERT: A 450 MET cc_start: 0.8218 (mmm) cc_final: 0.7925 (mmm) REVERT: A 488 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7578 (mm-30) REVERT: A 503 ASP cc_start: 0.7944 (t0) cc_final: 0.7665 (t0) REVERT: A 552 VAL cc_start: 0.8423 (t) cc_final: 0.8126 (m) REVERT: A 641 ARG cc_start: 0.7823 (mmp80) cc_final: 0.7428 (mmp80) REVERT: A 653 CYS cc_start: 0.7914 (t) cc_final: 0.7451 (t) REVERT: A 717 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6670 (tm-30) REVERT: A 725 MET cc_start: 0.8480 (tmm) cc_final: 0.8232 (tmm) REVERT: A 771 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7945 (mm-40) REVERT: A 795 GLN cc_start: 0.8402 (pp30) cc_final: 0.8131 (pp30) REVERT: A 881 ASN cc_start: 0.8012 (m-40) cc_final: 0.7644 (p0) REVERT: A 1104 TYR cc_start: 0.8089 (m-80) cc_final: 0.7771 (m-80) REVERT: A 1110 VAL cc_start: 0.8542 (t) cc_final: 0.8307 (p) REVERT: A 1152 ARG cc_start: 0.8391 (mtp180) cc_final: 0.8130 (mtp180) REVERT: A 1189 MET cc_start: 0.8075 (ttp) cc_final: 0.7851 (ttp) REVERT: A 1193 SER cc_start: 0.8643 (p) cc_final: 0.8263 (p) outliers start: 44 outliers final: 35 residues processed: 271 average time/residue: 0.2730 time to fit residues: 104.0831 Evaluate side-chains 282 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 243 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 502 ARG Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 635 HIS Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 963 CYS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1112 TRP Chi-restraints excluded: chain A residue 1117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 37 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 136 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1205 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 = 0.3900 r_free = 0.3900 target = 0.139309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.116189 restraints weight = 19586.998| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.52 r_work: 0.3440 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11793 Z= 0.164 Angle : 0.707 9.899 16061 Z= 0.362 Chirality : 0.046 0.201 1828 Planarity : 0.005 0.071 2022 Dihedral : 7.675 87.008 1799 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 3.51 % Allowed : 21.00 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.23), residues: 1419 helix: 0.94 (0.21), residues: 613 sheet: -0.83 (0.39), residues: 189 loop : -2.33 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1220 HIS 0.005 0.001 HIS B 168 PHE 0.022 0.001 PHE A 277 TYR 0.017 0.001 TYR B 105 ARG 0.013 0.000 ARG A 752 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 4) link_NAG-ASN : angle 1.28832 ( 12) link_ALPHA1-4 : bond 0.02258 ( 1) link_ALPHA1-4 : angle 5.83370 ( 3) link_ALPHA1-6 : bond 0.00666 ( 1) link_ALPHA1-6 : angle 2.02827 ( 3) link_BETA1-4 : bond 0.00659 ( 4) link_BETA1-4 : angle 1.34976 ( 12) link_ALPHA1-3 : bond 0.00920 ( 1) link_ALPHA1-3 : angle 1.93840 ( 3) hydrogen bonds : bond 0.04883 ( 522) hydrogen bonds : angle 4.77050 ( 1497) SS BOND : bond 0.00151 ( 2) SS BOND : angle 0.45369 ( 4) covalent geometry : bond 0.00361 (11780) covalent geometry : angle 0.70043 (16024) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5466.08 seconds wall clock time: 95 minutes 48.53 seconds (5748.53 seconds total)