Starting phenix.real_space_refine on Tue Jun 10 08:45:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dzv_47339/06_2025/9dzv_47339.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dzv_47339/06_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_47339/06_2025/9dzv_47339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dzv_47339/06_2025/9dzv_47339.map" model { file = "/net/cci-nas-00/data/ceres_data/9dzv_47339/06_2025/9dzv_47339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dzv_47339/06_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-5710/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: 7.64, per 1000 atoms: 0.66 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: 3.19 Conformation dependent library (CDL) restraints added in 1.8 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: 1.53 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: 4.57 Time building geometry restraints manager: 3.66 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: 1.990 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: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.540 Find NCS groups from input model: 0.160 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.630 ------------------------------------------------------------------------------- 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 : 1.531 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: 0.2606 time to fit residues: 118.3057 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 : 1.251 ------------------------------------------------------------------------------- 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: 2.94 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 : 1.310 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: 0.8837 (m) REVERT: B 201 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8233 (ttp80) REVERT: A 291 ASP cc_start: 0.6392 (p0) cc_final: 0.5900 (p0) REVERT: A 298 LYS cc_start: 0.8500 (tptp) cc_final: 0.8085 (tppt) REVERT: A 367 GLU cc_start: 0.7659 (pm20) cc_final: 0.7436 (pm20) REVERT: A 406 ARG cc_start: 0.7344 (mtm-85) cc_final: 0.7099 (mtm-85) REVERT: A 488 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7464 (tp30) REVERT: A 503 ASP cc_start: 0.7998 (t0) cc_final: 0.7755 (t0) REVERT: A 653 CYS cc_start: 0.8073 (t) cc_final: 0.7778 (t) REVERT: A 717 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6755 (tm-30) REVERT: A 771 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7933 (mm-40) REVERT: A 811 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8025 (pp20) REVERT: A 1123 PHE cc_start: 0.8883 (m-80) cc_final: 0.8569 (m-80) REVERT: A 1152 ARG cc_start: 0.8343 (mtp180) cc_final: 0.8112 (mtp-110) REVERT: A 1189 MET cc_start: 0.8058 (ttp) cc_final: 0.7852 (ttp) REVERT: A 1193 SER cc_start: 0.8574 (p) cc_final: 0.8229 (p) outliers start: 47 outliers final: 30 residues processed: 287 average time/residue: 0.2614 time to fit residues: 104.6231 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 : 1.216 ------------------------------------------------------------------------------- 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: 0.8980 chunk 23 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.140484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.116983 restraints weight = 19610.927| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.54 r_work: 0.3444 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1570 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= 0.157 Angle : 0.669 11.311 16061 Z= 0.336 Chirality : 0.046 0.184 1828 Planarity : 0.004 0.063 2022 Dihedral : 10.003 104.566 1809 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 3.68 % Allowed : 16.18 % Favored : 80.15 % 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: 0.97 (0.21), residues: 617 sheet: -0.83 (0.38), residues: 205 loop : -2.25 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 381 HIS 0.004 0.001 HIS A 654 PHE 0.021 0.001 PHE B 127 TYR 0.020 0.001 TYR B 105 ARG 0.013 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 4) link_NAG-ASN : angle 1.38999 ( 12) link_ALPHA1-4 : bond 0.03590 ( 1) link_ALPHA1-4 : angle 6.84649 ( 3) link_ALPHA1-6 : bond 0.01532 ( 1) link_ALPHA1-6 : angle 2.87773 ( 3) link_BETA1-4 : bond 0.00624 ( 4) link_BETA1-4 : angle 1.47453 ( 12) link_ALPHA1-3 : bond 0.00584 ( 1) link_ALPHA1-3 : angle 2.48400 ( 3) hydrogen bonds : bond 0.05013 ( 522) hydrogen bonds : angle 5.11072 ( 1497) SS BOND : bond 0.00238 ( 2) SS BOND : angle 0.56281 ( 4) covalent geometry : bond 0.00339 (11780) covalent geometry : angle 0.65872 (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 298 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 VAL cc_start: 0.9200 (t) cc_final: 0.8857 (m) REVERT: B 142 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7667 (mt-10) REVERT: B 144 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7741 (mt-10) REVERT: B 201 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8222 (ttp80) REVERT: B 286 ASN cc_start: 0.7756 (t0) cc_final: 0.6765 (t0) REVERT: B 289 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: A 291 ASP cc_start: 0.6412 (p0) cc_final: 0.5868 (p0) REVERT: A 298 LYS cc_start: 0.8476 (tptp) cc_final: 0.8110 (tppt) REVERT: A 319 ASN cc_start: 0.6619 (OUTLIER) cc_final: 0.6117 (p0) REVERT: A 406 ARG cc_start: 0.7337 (mtm-85) cc_final: 0.7090 (mtm-85) REVERT: A 488 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7453 (tp30) REVERT: A 503 ASP cc_start: 0.8011 (t0) cc_final: 0.7752 (t0) REVERT: A 653 CYS cc_start: 0.8046 (t) cc_final: 0.7805 (t) REVERT: A 717 GLU cc_start: 0.7390 (tm-30) cc_final: 0.6782 (tm-30) REVERT: A 725 MET cc_start: 0.8556 (tmm) cc_final: 0.8272 (tmm) REVERT: A 811 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8020 (pp20) REVERT: A 970 GLU cc_start: 0.7715 (tt0) cc_final: 0.7323 (tt0) REVERT: A 1123 PHE cc_start: 0.8891 (m-80) cc_final: 0.8671 (m-80) REVERT: A 1152 ARG cc_start: 0.8374 (mtp180) cc_final: 0.8082 (mtp180) REVERT: A 1189 MET cc_start: 0.8059 (ttp) cc_final: 0.7844 (ttp) REVERT: A 1193 SER cc_start: 0.8578 (p) cc_final: 0.8228 (p) outliers start: 45 outliers final: 31 residues processed: 282 average time/residue: 0.2739 time to fit residues: 107.9033 Evaluate side-chains 283 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 250 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 334 GLN 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 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 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: 0.9980 chunk 74 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 34 optimal weight: 0.0070 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 124 optimal weight: 0.0770 chunk 51 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.141211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.117712 restraints weight = 19383.981| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.52 r_work: 0.3455 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1803 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= 0.140 Angle : 0.664 10.375 16061 Z= 0.334 Chirality : 0.045 0.237 1828 Planarity : 0.004 0.058 2022 Dihedral : 9.224 96.658 1805 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.58 % Favored : 90.35 % Rotamer: Outliers : 3.59 % Allowed : 17.73 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.23), residues: 1419 helix: 1.06 (0.22), residues: 610 sheet: -0.75 (0.39), residues: 195 loop : -2.23 (0.25), residues: 614 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 0.010 0.001 PHE A 904 TYR 0.019 0.001 TYR B 105 ARG 0.008 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 4) link_NAG-ASN : angle 1.25880 ( 12) link_ALPHA1-4 : bond 0.02587 ( 1) link_ALPHA1-4 : angle 6.39127 ( 3) link_ALPHA1-6 : bond 0.00807 ( 1) link_ALPHA1-6 : angle 0.78829 ( 3) link_BETA1-4 : bond 0.00617 ( 4) link_BETA1-4 : angle 1.38474 ( 12) link_ALPHA1-3 : bond 0.00946 ( 1) link_ALPHA1-3 : angle 2.00487 ( 3) hydrogen bonds : bond 0.04734 ( 522) hydrogen bonds : angle 4.98646 ( 1497) SS BOND : bond 0.00167 ( 2) SS BOND : angle 0.44417 ( 4) covalent geometry : bond 0.00300 (11780) covalent geometry : angle 0.65650 (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 299 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 255 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 VAL cc_start: 0.9187 (t) cc_final: 0.8824 (m) REVERT: B 140 ARG cc_start: 0.7628 (mtm110) cc_final: 0.7321 (mtm-85) REVERT: B 142 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7599 (mt-10) REVERT: B 144 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7710 (mt-10) REVERT: B 169 ARG cc_start: 0.7298 (ttm170) cc_final: 0.7041 (ttm170) REVERT: B 201 ARG cc_start: 0.8420 (ttp80) cc_final: 0.8187 (ttp80) REVERT: B 289 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: A 291 ASP cc_start: 0.6416 (p0) cc_final: 0.5860 (p0) REVERT: A 298 LYS cc_start: 0.8479 (tptp) cc_final: 0.8097 (tppt) REVERT: A 318 LEU cc_start: 0.8372 (mt) cc_final: 0.8058 (mt) REVERT: A 319 ASN cc_start: 0.6799 (OUTLIER) cc_final: 0.6441 (p0) REVERT: A 406 ARG cc_start: 0.7329 (mtm-85) cc_final: 0.7090 (mtm-85) REVERT: A 450 MET cc_start: 0.8226 (mmm) cc_final: 0.7958 (mmm) REVERT: A 488 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7406 (tp30) REVERT: A 503 ASP cc_start: 0.7998 (t0) cc_final: 0.7766 (t0) REVERT: A 552 VAL cc_start: 0.8301 (t) cc_final: 0.7956 (m) REVERT: A 653 CYS cc_start: 0.7987 (t) cc_final: 0.7707 (t) REVERT: A 717 GLU cc_start: 0.7334 (tm-30) cc_final: 0.6741 (tm-30) REVERT: A 725 MET cc_start: 0.8498 (tmm) cc_final: 0.8141 (tmm) REVERT: A 795 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7786 (mm-40) REVERT: A 811 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7977 (pp20) REVERT: A 970 GLU cc_start: 0.7727 (tt0) cc_final: 0.7434 (tt0) REVERT: A 1003 ASN cc_start: 0.7840 (t0) cc_final: 0.7596 (t0) REVERT: A 1104 TYR cc_start: 0.8109 (m-80) cc_final: 0.7809 (m-80) REVERT: A 1152 ARG cc_start: 0.8370 (mtp180) cc_final: 0.8114 (mtp180) REVERT: A 1189 MET cc_start: 0.8033 (ttp) cc_final: 0.7821 (ttp) REVERT: A 1193 SER cc_start: 0.8552 (p) cc_final: 0.8207 (p) outliers start: 44 outliers final: 33 residues processed: 283 average time/residue: 0.2624 time to fit residues: 103.7153 Evaluate side-chains 281 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 246 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 290 ASP Chi-restraints excluded: chain B residue 297 MET 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 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 371 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 21 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 44 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** A 644 HIS ** A 995 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 = 0.3915 r_free = 0.3915 target = 0.140632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.117131 restraints weight = 19327.088| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.51 r_work: 0.3443 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11793 Z= 0.157 Angle : 0.648 9.676 16061 Z= 0.328 Chirality : 0.046 0.233 1828 Planarity : 0.004 0.060 2022 Dihedral : 8.758 90.902 1803 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.08 % Favored : 89.85 % Rotamer: Outliers : 4.00 % Allowed : 17.65 % Favored : 78.35 % 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: -0.89 (0.23), residues: 1419 helix: 1.03 (0.21), residues: 609 sheet: -0.77 (0.39), residues: 195 loop : -2.27 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 381 HIS 0.003 0.001 HIS A1059 PHE 0.022 0.001 PHE A 50 TYR 0.017 0.001 TYR B 105 ARG 0.007 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 4) link_NAG-ASN : angle 1.27392 ( 12) link_ALPHA1-4 : bond 0.02401 ( 1) link_ALPHA1-4 : angle 6.12975 ( 3) link_ALPHA1-6 : bond 0.00435 ( 1) link_ALPHA1-6 : angle 0.51573 ( 3) link_BETA1-4 : bond 0.00637 ( 4) link_BETA1-4 : angle 1.38097 ( 12) link_ALPHA1-3 : bond 0.01096 ( 1) link_ALPHA1-3 : angle 2.24825 ( 3) hydrogen bonds : bond 0.04823 ( 522) hydrogen bonds : angle 4.94309 ( 1497) SS BOND : bond 0.00217 ( 2) SS BOND : angle 0.45811 ( 4) covalent geometry : bond 0.00346 (11780) covalent geometry : angle 0.64075 (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 301 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 252 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 VAL cc_start: 0.9171 (t) cc_final: 0.8813 (m) REVERT: B 140 ARG cc_start: 0.7633 (mtm110) cc_final: 0.7369 (mtm-85) REVERT: B 142 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7628 (mt-10) REVERT: B 144 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7697 (mt-10) REVERT: B 169 ARG cc_start: 0.7257 (ttm170) cc_final: 0.7006 (ttm170) REVERT: B 201 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8191 (ttp80) REVERT: B 289 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: A 291 ASP cc_start: 0.6479 (p0) cc_final: 0.5887 (p0) REVERT: A 298 LYS cc_start: 0.8488 (tptp) cc_final: 0.8140 (tppt) REVERT: A 318 LEU cc_start: 0.8428 (mt) cc_final: 0.8124 (mt) REVERT: A 319 ASN cc_start: 0.7051 (p0) cc_final: 0.6711 (p0) REVERT: A 343 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6732 (tt) REVERT: A 372 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.5987 (tpt-90) REVERT: A 406 ARG cc_start: 0.7286 (mtm-85) cc_final: 0.7053 (mtm-85) REVERT: A 488 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7445 (tp30) REVERT: A 503 ASP cc_start: 0.8005 (t0) cc_final: 0.7769 (t0) REVERT: A 653 CYS cc_start: 0.7959 (t) cc_final: 0.7720 (t) REVERT: A 717 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6778 (tm-30) REVERT: A 725 MET cc_start: 0.8550 (tmm) cc_final: 0.8197 (tmm) REVERT: A 970 GLU cc_start: 0.7736 (tt0) cc_final: 0.7489 (tt0) REVERT: A 1003 ASN cc_start: 0.7879 (t0) cc_final: 0.7651 (t0) REVERT: A 1104 TYR cc_start: 0.8107 (m-80) cc_final: 0.7806 (m-80) REVERT: A 1152 ARG cc_start: 0.8371 (mtp180) cc_final: 0.8071 (mtp180) REVERT: A 1189 MET cc_start: 0.8075 (ttp) cc_final: 0.7850 (ttp) REVERT: A 1193 SER cc_start: 0.8555 (p) cc_final: 0.8211 (p) outliers start: 49 outliers final: 36 residues processed: 282 average time/residue: 0.2657 time to fit residues: 104.7282 Evaluate side-chains 285 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 246 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 290 ASP 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 268 PHE 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 393 THR Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 504 ILE 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 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 1097 THR Chi-restraints excluded: chain A residue 1112 TRP Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1187 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: 0.6980 chunk 74 optimal weight: 0.0030 chunk 76 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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** ** 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 = 0.3912 r_free = 0.3912 target = 0.140480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.117472 restraints weight = 19582.373| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.50 r_work: 0.3444 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2038 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= 0.153 Angle : 0.651 9.414 16061 Z= 0.328 Chirality : 0.045 0.222 1828 Planarity : 0.004 0.061 2022 Dihedral : 8.467 84.358 1803 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.94 % Favored : 89.99 % Rotamer: Outliers : 3.84 % Allowed : 18.71 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 609 sheet: -0.74 (0.39), residues: 193 loop : -2.29 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 381 HIS 0.003 0.001 HIS A 654 PHE 0.019 0.001 PHE A 50 TYR 0.016 0.001 TYR B 105 ARG 0.006 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 4) link_NAG-ASN : angle 1.26058 ( 12) link_ALPHA1-4 : bond 0.02354 ( 1) link_ALPHA1-4 : angle 6.02037 ( 3) link_ALPHA1-6 : bond 0.00567 ( 1) link_ALPHA1-6 : angle 1.02487 ( 3) link_BETA1-4 : bond 0.00614 ( 4) link_BETA1-4 : angle 1.38790 ( 12) link_ALPHA1-3 : bond 0.01006 ( 1) link_ALPHA1-3 : angle 2.20488 ( 3) hydrogen bonds : bond 0.04778 ( 522) hydrogen bonds : angle 4.89061 ( 1497) SS BOND : bond 0.00193 ( 2) SS BOND : angle 0.41624 ( 4) covalent geometry : bond 0.00333 (11780) covalent geometry : angle 0.64327 (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: 47 poor density : 253 time to evaluate : 1.210 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 142 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7637 (mt-10) REVERT: B 169 ARG cc_start: 0.7253 (ttm170) cc_final: 0.7036 (ttm170) REVERT: B 176 ASP cc_start: 0.7864 (t70) cc_final: 0.7638 (t0) REVERT: B 201 ARG cc_start: 0.8435 (ttp80) cc_final: 0.8200 (ttp80) REVERT: B 289 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: A 291 ASP cc_start: 0.6495 (p0) cc_final: 0.5894 (p0) REVERT: A 298 LYS cc_start: 0.8470 (tptp) cc_final: 0.8110 (tppt) REVERT: A 318 LEU cc_start: 0.8542 (mt) cc_final: 0.8278 (mt) REVERT: A 343 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6665 (tt) REVERT: A 372 ARG cc_start: 0.6479 (OUTLIER) cc_final: 0.6006 (tpt-90) REVERT: A 406 ARG cc_start: 0.7332 (mtm-85) cc_final: 0.7103 (mtm-85) REVERT: A 488 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7583 (mm-30) REVERT: A 503 ASP cc_start: 0.7999 (t0) cc_final: 0.7775 (t0) REVERT: A 552 VAL cc_start: 0.8345 (t) cc_final: 0.8070 (m) REVERT: A 653 CYS cc_start: 0.7877 (t) cc_final: 0.7542 (t) REVERT: A 717 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6723 (tm-30) REVERT: A 725 MET cc_start: 0.8492 (tmm) cc_final: 0.8268 (tmm) REVERT: A 771 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7969 (mm-40) REVERT: A 970 GLU cc_start: 0.7719 (tt0) cc_final: 0.7512 (tt0) REVERT: A 1089 MET cc_start: 0.8083 (ttm) cc_final: 0.7881 (ttm) REVERT: A 1104 TYR cc_start: 0.8116 (m-80) cc_final: 0.7820 (m-80) REVERT: A 1152 ARG cc_start: 0.8383 (mtp180) cc_final: 0.8069 (mtp180) REVERT: A 1189 MET cc_start: 0.8085 (ttp) cc_final: 0.7857 (ttp) REVERT: A 1193 SER cc_start: 0.8569 (p) cc_final: 0.8227 (p) outliers start: 47 outliers final: 35 residues processed: 282 average time/residue: 0.2616 time to fit residues: 102.8025 Evaluate side-chains 284 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 246 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 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 268 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 317 HIS 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 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 504 ILE 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 737 ARG Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 833 ILE 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 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: 0.6980 chunk 37 optimal weight: 10.0000 chunk 136 optimal weight: 0.2980 chunk 107 optimal weight: 0.7980 chunk 30 optimal weight: 0.0170 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.141482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.118099 restraints weight = 19547.450| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.58 r_work: 0.3443 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11793 Z= 0.140 Angle : 0.658 9.498 16061 Z= 0.329 Chirality : 0.045 0.205 1828 Planarity : 0.004 0.064 2022 Dihedral : 8.174 78.823 1803 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 3.68 % Allowed : 19.53 % Favored : 76.80 % 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: 1.03 (0.21), residues: 610 sheet: -0.74 (0.40), residues: 189 loop : -2.30 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1220 HIS 0.005 0.001 HIS A 644 PHE 0.014 0.001 PHE A 277 TYR 0.015 0.001 TYR B 105 ARG 0.006 0.000 ARG A 779 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 4) link_NAG-ASN : angle 1.08238 ( 12) link_ALPHA1-4 : bond 0.02414 ( 1) link_ALPHA1-4 : angle 6.02468 ( 3) link_ALPHA1-6 : bond 0.00636 ( 1) link_ALPHA1-6 : angle 1.29144 ( 3) link_BETA1-4 : bond 0.00712 ( 4) link_BETA1-4 : angle 1.47376 ( 12) link_ALPHA1-3 : bond 0.01113 ( 1) link_ALPHA1-3 : angle 2.10263 ( 3) hydrogen bonds : bond 0.04629 ( 522) hydrogen bonds : angle 4.82035 ( 1497) SS BOND : bond 0.00130 ( 2) SS BOND : angle 0.35155 ( 4) covalent geometry : bond 0.00302 (11780) covalent geometry : angle 0.65079 (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 297 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 ARG cc_start: 0.7671 (mtm110) cc_final: 0.7393 (mtm-85) REVERT: B 142 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7552 (mt-10) REVERT: B 169 ARG cc_start: 0.7292 (ttm170) cc_final: 0.7048 (ttm170) REVERT: B 191 ASN cc_start: 0.8395 (m-40) cc_final: 0.8078 (m-40) REVERT: B 201 ARG cc_start: 0.8401 (ttp80) cc_final: 0.8152 (ttp80) REVERT: B 289 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: A 291 ASP cc_start: 0.6506 (p0) cc_final: 0.5931 (p0) REVERT: A 298 LYS cc_start: 0.8484 (tptp) cc_final: 0.8127 (tppt) REVERT: A 318 LEU cc_start: 0.8604 (mt) cc_final: 0.8335 (mt) REVERT: A 343 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6559 (tt) REVERT: A 372 ARG cc_start: 0.6529 (OUTLIER) cc_final: 0.5952 (tpt-90) REVERT: A 406 ARG cc_start: 0.7353 (mtm-85) cc_final: 0.7123 (mtm-85) REVERT: A 450 MET cc_start: 0.8176 (mmm) cc_final: 0.7896 (mmm) REVERT: A 488 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7579 (mm-30) REVERT: A 503 ASP cc_start: 0.8003 (t0) cc_final: 0.7783 (t0) REVERT: A 552 VAL cc_start: 0.8388 (t) cc_final: 0.8112 (m) REVERT: A 641 ARG cc_start: 0.7799 (mmp80) cc_final: 0.7348 (mmp80) REVERT: A 653 CYS cc_start: 0.7843 (t) cc_final: 0.7580 (t) REVERT: A 717 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6709 (tm-30) REVERT: A 771 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7978 (mm-40) REVERT: A 791 GLN cc_start: 0.8595 (mp10) cc_final: 0.7845 (mp10) REVERT: A 795 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7806 (mm-40) REVERT: A 798 LYS cc_start: 0.8330 (ptpp) cc_final: 0.8091 (ptpp) REVERT: A 811 GLU cc_start: 0.8401 (tp30) cc_final: 0.7961 (tp30) REVERT: A 970 GLU cc_start: 0.7672 (tt0) cc_final: 0.7463 (tt0) REVERT: A 1104 TYR cc_start: 0.8113 (m-80) cc_final: 0.7832 (m-80) REVERT: A 1152 ARG cc_start: 0.8390 (mtp180) cc_final: 0.8075 (mtp180) REVERT: A 1189 MET cc_start: 0.8054 (ttp) cc_final: 0.7843 (ttp) REVERT: A 1193 SER cc_start: 0.8628 (p) cc_final: 0.8267 (p) REVERT: A 1258 ARG cc_start: 0.8756 (mtt180) cc_final: 0.8551 (mtt180) outliers start: 45 outliers final: 34 residues processed: 281 average time/residue: 0.2567 time to fit residues: 100.0795 Evaluate side-chains 284 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 247 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 268 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 317 HIS 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 393 THR Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 502 ARG Chi-restraints excluded: chain A residue 504 ILE 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 111 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 106 optimal weight: 0.0970 chunk 76 optimal weight: 0.0670 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- 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 714 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 = 0.3921 r_free = 0.3921 target = 0.140884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.117852 restraints weight = 19545.770| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.50 r_work: 0.3466 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2235 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= 0.136 Angle : 0.676 10.201 16061 Z= 0.338 Chirality : 0.045 0.189 1828 Planarity : 0.004 0.067 2022 Dihedral : 7.836 78.999 1801 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.87 % Favored : 90.06 % Rotamer: Outliers : 3.51 % Allowed : 20.26 % Favored : 76.23 % 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: -0.90 (0.23), residues: 1419 helix: 0.99 (0.21), residues: 617 sheet: -0.74 (0.40), residues: 189 loop : -2.28 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1220 HIS 0.004 0.001 HIS A 644 PHE 0.016 0.001 PHE A 277 TYR 0.014 0.001 TYR B 105 ARG 0.007 0.000 ARG A 779 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 4) link_NAG-ASN : angle 1.16733 ( 12) link_ALPHA1-4 : bond 0.02414 ( 1) link_ALPHA1-4 : angle 5.99580 ( 3) link_ALPHA1-6 : bond 0.00682 ( 1) link_ALPHA1-6 : angle 1.58442 ( 3) link_BETA1-4 : bond 0.00675 ( 4) link_BETA1-4 : angle 1.40726 ( 12) link_ALPHA1-3 : bond 0.01133 ( 1) link_ALPHA1-3 : angle 2.02520 ( 3) hydrogen bonds : bond 0.04554 ( 522) hydrogen bonds : angle 4.74364 ( 1497) SS BOND : bond 0.00087 ( 2) SS BOND : angle 0.28314 ( 4) covalent geometry : bond 0.00292 (11780) covalent geometry : angle 0.66904 (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 295 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 252 time to evaluate : 1.280 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 140 ARG cc_start: 0.7642 (mtm110) cc_final: 0.7377 (mtm-85) REVERT: B 142 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7518 (mt-10) REVERT: B 169 ARG cc_start: 0.7279 (ttm170) cc_final: 0.7028 (ttm170) REVERT: A 291 ASP cc_start: 0.6486 (p0) cc_final: 0.5894 (p0) REVERT: A 298 LYS cc_start: 0.8497 (tptp) cc_final: 0.8133 (tppt) REVERT: A 318 LEU cc_start: 0.8623 (mt) cc_final: 0.8360 (mt) REVERT: A 343 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6457 (tt) REVERT: A 372 ARG cc_start: 0.6562 (OUTLIER) cc_final: 0.6104 (tpt-90) REVERT: A 406 ARG cc_start: 0.7312 (mtm-85) cc_final: 0.7086 (mtm-85) REVERT: A 450 MET cc_start: 0.8158 (mmm) cc_final: 0.7888 (mmm) REVERT: A 488 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7555 (mm-30) REVERT: A 503 ASP cc_start: 0.7991 (t0) cc_final: 0.7761 (t0) REVERT: A 552 VAL cc_start: 0.8396 (t) cc_final: 0.8088 (m) REVERT: A 641 ARG cc_start: 0.7795 (mmp80) cc_final: 0.7318 (mmp80) REVERT: A 717 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6654 (tm-30) REVERT: A 771 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7931 (mm-40) REVERT: A 881 ASN cc_start: 0.7978 (m-40) cc_final: 0.7649 (p0) REVERT: A 970 GLU cc_start: 0.7714 (tt0) cc_final: 0.7444 (tt0) REVERT: A 1104 TYR cc_start: 0.8102 (m-80) cc_final: 0.7820 (m-80) REVERT: A 1152 ARG cc_start: 0.8377 (mtp180) cc_final: 0.8080 (mtp180) REVERT: A 1189 MET cc_start: 0.8037 (ttp) cc_final: 0.7828 (ttp) REVERT: A 1193 SER cc_start: 0.8613 (p) cc_final: 0.8248 (p) REVERT: A 1258 ARG cc_start: 0.8767 (mtt180) cc_final: 0.8557 (mtt180) outliers start: 43 outliers final: 33 residues processed: 280 average time/residue: 0.2622 time to fit residues: 102.3271 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 : 1.228 ------------------------------------------------------------------------------- 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 390 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 317 HIS 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 465 LEU Chi-restraints excluded: chain A residue 502 ARG Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 511 VAL 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 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 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: 0.5980 chunk 27 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 137 optimal weight: 0.0170 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.7220 ------------------------------------------------------------------------------- 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 714 HIS ** A 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1003 ASN ** 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 = 0.3912 r_free = 0.3912 target = 0.140195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.116920 restraints weight = 19609.335| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.52 r_work: 0.3446 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2326 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= 0.156 Angle : 0.697 10.607 16061 Z= 0.349 Chirality : 0.046 0.207 1828 Planarity : 0.005 0.079 2022 Dihedral : 7.755 83.623 1801 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 3.68 % Allowed : 20.34 % 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: -0.93 (0.23), residues: 1419 helix: 0.96 (0.21), residues: 617 sheet: -0.72 (0.40), residues: 190 loop : -2.30 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1220 HIS 0.005 0.001 HIS A 644 PHE 0.011 0.001 PHE A 904 TYR 0.017 0.001 TYR B 105 ARG 0.008 0.000 ARG A 752 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 4) link_NAG-ASN : angle 1.23399 ( 12) link_ALPHA1-4 : bond 0.02314 ( 1) link_ALPHA1-4 : angle 5.93634 ( 3) link_ALPHA1-6 : bond 0.00671 ( 1) link_ALPHA1-6 : angle 1.80896 ( 3) link_BETA1-4 : bond 0.00659 ( 4) link_BETA1-4 : angle 1.43778 ( 12) link_ALPHA1-3 : bond 0.01062 ( 1) link_ALPHA1-3 : angle 2.12239 ( 3) hydrogen bonds : bond 0.04708 ( 522) hydrogen bonds : angle 4.77766 ( 1497) SS BOND : bond 0.00157 ( 2) SS BOND : angle 0.49327 ( 4) covalent geometry : bond 0.00343 (11780) covalent geometry : angle 0.69020 (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 296 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 251 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 ARG cc_start: 0.7664 (mtm110) cc_final: 0.7408 (mtm-85) REVERT: A 291 ASP cc_start: 0.6508 (p0) cc_final: 0.5906 (p0) REVERT: A 298 LYS cc_start: 0.8500 (tptp) cc_final: 0.8133 (tppt) REVERT: A 318 LEU cc_start: 0.8669 (mt) cc_final: 0.8385 (mt) REVERT: A 343 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6488 (tt) REVERT: A 372 ARG cc_start: 0.6565 (OUTLIER) cc_final: 0.4546 (tmt170) REVERT: A 406 ARG cc_start: 0.7314 (mtm-85) cc_final: 0.7085 (mtm-85) REVERT: A 450 MET cc_start: 0.8206 (mmm) cc_final: 0.7938 (mmm) REVERT: A 488 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7568 (mm-30) REVERT: A 503 ASP cc_start: 0.8005 (t0) cc_final: 0.7787 (t0) REVERT: A 552 VAL cc_start: 0.8402 (t) cc_final: 0.8094 (m) REVERT: A 641 ARG cc_start: 0.7778 (mmp80) cc_final: 0.7379 (mmp80) REVERT: A 717 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6628 (tm-30) REVERT: A 752 ARG cc_start: 0.7286 (mmm160) cc_final: 0.6690 (mmm160) REVERT: A 771 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7944 (mm-40) REVERT: A 881 ASN cc_start: 0.8010 (m-40) cc_final: 0.7659 (p0) REVERT: A 1104 TYR cc_start: 0.8079 (m-80) cc_final: 0.7747 (m-80) REVERT: A 1152 ARG cc_start: 0.8397 (mtp180) cc_final: 0.8087 (mtp180) REVERT: A 1189 MET cc_start: 0.8061 (ttp) cc_final: 0.7850 (ttp) REVERT: A 1193 SER cc_start: 0.8619 (p) cc_final: 0.8251 (p) REVERT: A 1258 ARG cc_start: 0.8764 (mtt180) cc_final: 0.8540 (mtt180) outliers start: 45 outliers final: 37 residues processed: 276 average time/residue: 0.2713 time to fit residues: 104.1201 Evaluate side-chains 284 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 49 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 317 HIS 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 465 LEU Chi-restraints excluded: chain A residue 502 ARG Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 511 VAL 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 737 ARG Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 750 PHE 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 999 LEU Chi-restraints excluded: chain A residue 1003 ASN 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: 0.9990 chunk 25 optimal weight: 0.0000 chunk 139 optimal weight: 0.1980 chunk 32 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.140645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.117498 restraints weight = 19401.788| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.57 r_work: 0.3455 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11793 Z= 0.149 Angle : 0.722 11.201 16061 Z= 0.362 Chirality : 0.045 0.187 1828 Planarity : 0.005 0.073 2022 Dihedral : 7.604 85.637 1799 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 3.27 % Allowed : 21.24 % 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: -0.93 (0.23), residues: 1419 helix: 0.96 (0.21), residues: 615 sheet: -0.78 (0.40), residues: 189 loop : -2.27 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1220 HIS 0.005 0.001 HIS A 644 PHE 0.014 0.001 PHE B 284 TYR 0.023 0.001 TYR B 149 ARG 0.009 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 4) link_NAG-ASN : angle 1.27934 ( 12) link_ALPHA1-4 : bond 0.02373 ( 1) link_ALPHA1-4 : angle 5.94269 ( 3) link_ALPHA1-6 : bond 0.00661 ( 1) link_ALPHA1-6 : angle 1.88280 ( 3) link_BETA1-4 : bond 0.00654 ( 4) link_BETA1-4 : angle 1.36215 ( 12) link_ALPHA1-3 : bond 0.01092 ( 1) link_ALPHA1-3 : angle 1.99369 ( 3) hydrogen bonds : bond 0.04691 ( 522) hydrogen bonds : angle 4.75208 ( 1497) SS BOND : bond 0.00093 ( 2) SS BOND : angle 0.38776 ( 4) covalent geometry : bond 0.00327 (11780) covalent geometry : angle 0.71499 (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 287 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 247 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 ARG cc_start: 0.7675 (mtm110) cc_final: 0.7390 (mtm110) REVERT: A 291 ASP cc_start: 0.6502 (p0) cc_final: 0.5938 (p0) REVERT: A 298 LYS cc_start: 0.8512 (tptp) cc_final: 0.8142 (tppt) REVERT: A 318 LEU cc_start: 0.8673 (mt) cc_final: 0.8385 (mt) REVERT: A 343 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6404 (tt) REVERT: A 372 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.4570 (tmt170) REVERT: A 406 ARG cc_start: 0.7342 (mtm-85) cc_final: 0.7121 (mtm-85) REVERT: A 450 MET cc_start: 0.8199 (mmm) cc_final: 0.7941 (mmm) REVERT: A 488 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7564 (mm-30) REVERT: A 503 ASP cc_start: 0.8012 (t0) cc_final: 0.7792 (t0) REVERT: A 552 VAL cc_start: 0.8405 (t) cc_final: 0.8112 (m) REVERT: A 641 ARG cc_start: 0.7789 (mmp80) cc_final: 0.7324 (mmp80) REVERT: A 717 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6628 (tm-30) REVERT: A 752 ARG cc_start: 0.7287 (mmm160) cc_final: 0.6965 (mmm160) REVERT: A 771 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7950 (mm-40) REVERT: A 791 GLN cc_start: 0.8559 (mp10) cc_final: 0.8321 (mp10) REVERT: A 822 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7445 (mt-10) REVERT: A 881 ASN cc_start: 0.8020 (m-40) cc_final: 0.7671 (p0) REVERT: A 1104 TYR cc_start: 0.8084 (m-80) cc_final: 0.7771 (m-80) REVERT: A 1110 VAL cc_start: 0.8533 (t) cc_final: 0.8286 (p) REVERT: A 1152 ARG cc_start: 0.8400 (mtp180) cc_final: 0.8094 (mtp180) REVERT: A 1189 MET cc_start: 0.8085 (ttp) cc_final: 0.7865 (ttp) REVERT: A 1193 SER cc_start: 0.8634 (p) cc_final: 0.8278 (p) outliers start: 40 outliers final: 33 residues processed: 270 average time/residue: 0.2711 time to fit residues: 101.1019 Evaluate side-chains 280 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 245 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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 390 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 317 HIS 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 465 LEU Chi-restraints excluded: chain A residue 502 ARG Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 511 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 37 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 65 optimal weight: 0.4980 chunk 109 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.139950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.116691 restraints weight = 19633.266| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.53 r_work: 0.3453 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2429 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= 0.154 Angle : 0.720 11.259 16061 Z= 0.363 Chirality : 0.045 0.189 1828 Planarity : 0.004 0.069 2022 Dihedral : 7.538 88.204 1799 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 3.43 % Allowed : 21.41 % Favored : 75.16 % 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: 0.95 (0.21), residues: 617 sheet: -0.77 (0.39), residues: 190 loop : -2.33 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1220 HIS 0.004 0.001 HIS A 644 PHE 0.012 0.001 PHE B 127 TYR 0.016 0.001 TYR B 105 ARG 0.007 0.000 ARG A 752 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 4) link_NAG-ASN : angle 1.24149 ( 12) link_ALPHA1-4 : bond 0.02355 ( 1) link_ALPHA1-4 : angle 5.90411 ( 3) link_ALPHA1-6 : bond 0.00628 ( 1) link_ALPHA1-6 : angle 2.00094 ( 3) link_BETA1-4 : bond 0.00651 ( 4) link_BETA1-4 : angle 1.37043 ( 12) link_ALPHA1-3 : bond 0.01021 ( 1) link_ALPHA1-3 : angle 1.91697 ( 3) hydrogen bonds : bond 0.04736 ( 522) hydrogen bonds : angle 4.75590 ( 1497) SS BOND : bond 0.00117 ( 2) SS BOND : angle 0.40603 ( 4) covalent geometry : bond 0.00338 (11780) covalent geometry : angle 0.71391 (16024) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5670.25 seconds wall clock time: 98 minutes 15.05 seconds (5895.05 seconds total)