Starting phenix.real_space_refine on Sat Jun 14 18:42:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xq7_38568/06_2025/8xq7_38568.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xq7_38568/06_2025/8xq7_38568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xq7_38568/06_2025/8xq7_38568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xq7_38568/06_2025/8xq7_38568.map" model { file = "/net/cci-nas-00/data/ceres_data/8xq7_38568/06_2025/8xq7_38568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xq7_38568/06_2025/8xq7_38568.cif" } resolution = 3.15 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 88 5.16 5 C 10694 2.51 5 N 2724 2.21 5 O 2922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16430 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8193 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 33, 'TRANS': 1007} Chain breaks: 7 Chain: "B" Number of atoms: 8193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8193 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 33, 'TRANS': 1007} Chain breaks: 7 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 10.49, per 1000 atoms: 0.64 Number of scatterers: 16430 At special positions: 0 Unit cell: (106.92, 135, 122.04, 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 88 16.00 P 2 15.00 O 2922 8.00 N 2724 7.00 C 10694 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 3.89 Conformation dependent library (CDL) restraints added in 2.0 seconds 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3924 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 10 sheets defined 74.0% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 75 through 95 removed outlier: 4.281A pdb=" N VAL A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.813A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.822A pdb=" N HIS A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 removed outlier: 3.534A pdb=" N SER A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 207 removed outlier: 3.797A pdb=" N ALA A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 253 Processing helix chain 'A' and resid 260 through 292 Proline residue: A 276 - end of helix removed outlier: 3.850A pdb=" N HIS A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 317 removed outlier: 3.892A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 removed outlier: 3.686A pdb=" N ALA A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 376 through 379 removed outlier: 3.982A pdb=" N ALA A 379 " --> pdb=" O ALA A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 379' Processing helix chain 'A' and resid 381 through 412 Proline residue: A 408 - end of helix removed outlier: 4.041A pdb=" N ARG A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.672A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 481 removed outlier: 4.309A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 removed outlier: 4.012A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 Processing helix chain 'A' and resid 548 through 558 Processing helix chain 'A' and resid 571 through 601 Processing helix chain 'A' and resid 604 through 621 Processing helix chain 'A' and resid 627 through 633 removed outlier: 3.882A pdb=" N LEU A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 652 removed outlier: 3.854A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 699 Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 727 through 753 Processing helix chain 'A' and resid 762 through 777 Processing helix chain 'A' and resid 799 through 853 removed outlier: 4.120A pdb=" N LEU A 805 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A 806 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET A 810 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 811 " --> pdb=" O GLY A 807 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Proline residue: A 819 - end of helix Processing helix chain 'A' and resid 853 through 858 removed outlier: 3.865A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.702A pdb=" N HIS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.691A pdb=" N ASN A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 959 removed outlier: 3.683A pdb=" N LEU A 957 " --> pdb=" O PRO A 953 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 958 " --> pdb=" O GLU A 954 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 976 Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1069 through 1080 Processing helix chain 'A' and resid 1085 through 1107 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1123 removed outlier: 3.700A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1133 removed outlier: 4.044A pdb=" N SER A1132 " --> pdb=" O ASP A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1210 removed outlier: 4.144A pdb=" N SER A1210 " --> pdb=" O SER A1207 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 95 removed outlier: 4.273A pdb=" N VAL B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 120 removed outlier: 3.813A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.748A pdb=" N HIS B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 153 Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.529A pdb=" N SER B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 189 Processing helix chain 'B' and resid 194 through 207 removed outlier: 3.755A pdb=" N ALA B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 220 Processing helix chain 'B' and resid 223 through 253 Processing helix chain 'B' and resid 260 through 292 Proline residue: B 276 - end of helix removed outlier: 3.819A pdb=" N HIS B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 317 removed outlier: 3.901A pdb=" N GLU B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.673A pdb=" N ALA B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 375 Processing helix chain 'B' and resid 381 through 412 Proline residue: B 408 - end of helix removed outlier: 4.081A pdb=" N ARG B 412 " --> pdb=" O PRO B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.658A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 481 removed outlier: 4.347A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 513 Processing helix chain 'B' and resid 522 through 530 Processing helix chain 'B' and resid 548 through 558 Processing helix chain 'B' and resid 571 through 600 Processing helix chain 'B' and resid 604 through 621 removed outlier: 3.621A pdb=" N GLU B 621 " --> pdb=" O VAL B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 633 removed outlier: 3.878A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 652 removed outlier: 3.865A pdb=" N TRP B 643 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 699 Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 727 through 753 Processing helix chain 'B' and resid 762 through 777 Processing helix chain 'B' and resid 799 through 853 removed outlier: 4.215A pdb=" N LEU B 805 " --> pdb=" O LEU B 801 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 806 " --> pdb=" O PHE B 802 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET B 810 " --> pdb=" O ARG B 806 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 811 " --> pdb=" O GLY B 807 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS B 815 " --> pdb=" O LEU B 811 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA B 816 " --> pdb=" O ARG B 812 " (cutoff:3.500A) Proline residue: B 819 - end of helix Processing helix chain 'B' and resid 853 through 858 removed outlier: 3.873A pdb=" N MET B 857 " --> pdb=" O ILE B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 3.716A pdb=" N HIS B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.684A pdb=" N ASN B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 959 removed outlier: 3.679A pdb=" N LEU B 957 " --> pdb=" O PRO B 953 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 958 " --> pdb=" O GLU B 954 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 976 Processing helix chain 'B' and resid 1043 through 1050 Processing helix chain 'B' and resid 1069 through 1080 Processing helix chain 'B' and resid 1085 through 1107 Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1113 through 1122 Processing helix chain 'B' and resid 1128 through 1133 removed outlier: 3.872A pdb=" N SER B1132 " --> pdb=" O ASP B1128 " (cutoff:3.500A) Processing helix chain 'B' and resid 1206 through 1210 removed outlier: 4.183A pdb=" N SER B1210 " --> pdb=" O SER B1207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1041 through 1042 removed outlier: 6.412A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1032 through 1034 Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 3.680A pdb=" N VAL A1188 " --> pdb=" O TYR A1125 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP A1144 " --> pdb=" O VAL A1189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137 Processing sheet with id=AA5, first strand: chain 'A' and resid 1203 through 1204 removed outlier: 3.583A pdb=" N ASP A1204 " --> pdb=" O SER A1213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A1213 " --> pdb=" O ASP A1204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 1041 through 1042 removed outlier: 6.413A pdb=" N GLN B1064 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1032 through 1034 Processing sheet with id=AA8, first strand: chain 'B' and resid 1125 through 1126 removed outlier: 3.652A pdb=" N VAL B1188 " --> pdb=" O TYR B1125 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP B1144 " --> pdb=" O VAL B1189 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL B1145 " --> pdb=" O ILE B1167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1136 through 1137 Processing sheet with id=AB1, first strand: chain 'B' and resid 1203 through 1204 removed outlier: 3.570A pdb=" N ASP B1204 " --> pdb=" O SER B1213 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B1213 " --> pdb=" O ASP B1204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 1163 hydrogen bonds defined for protein. 3459 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: 5.46 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5145 1.34 - 1.46: 2580 1.46 - 1.58: 8851 1.58 - 1.69: 6 1.69 - 1.81: 158 Bond restraints: 16740 Sorted by residual: bond pdb=" O2P CMP A2001 " pdb=" P CMP A2001 " ideal model delta sigma weight residual 1.510 1.649 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" O2P CMP B2001 " pdb=" P CMP B2001 " ideal model delta sigma weight residual 1.510 1.648 -0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" C4 CMP B2001 " pdb=" C5 CMP B2001 " ideal model delta sigma weight residual 1.490 1.370 0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C4 CMP A2001 " pdb=" C5 CMP A2001 " ideal model delta sigma weight residual 1.490 1.371 0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C6 CMP A2001 " pdb=" N6 CMP A2001 " ideal model delta sigma weight residual 1.355 1.451 -0.096 2.00e-02 2.50e+03 2.32e+01 ... (remaining 16735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 22481 3.07 - 6.15: 192 6.15 - 9.22: 25 9.22 - 12.29: 4 12.29 - 15.37: 4 Bond angle restraints: 22706 Sorted by residual: angle pdb=" C3' CMP B2001 " pdb=" O3' CMP B2001 " pdb=" P CMP B2001 " ideal model delta sigma weight residual 120.50 105.13 15.37 3.00e+00 1.11e-01 2.62e+01 angle pdb=" C3' CMP A2001 " pdb=" O3' CMP A2001 " pdb=" P CMP A2001 " ideal model delta sigma weight residual 120.50 105.70 14.80 3.00e+00 1.11e-01 2.43e+01 angle pdb=" C ASP B 129 " pdb=" N VAL B 130 " pdb=" CA VAL B 130 " ideal model delta sigma weight residual 122.97 118.37 4.60 9.80e-01 1.04e+00 2.20e+01 angle pdb=" C ASP A 129 " pdb=" N VAL A 130 " pdb=" CA VAL A 130 " ideal model delta sigma weight residual 123.08 118.44 4.64 1.01e+00 9.80e-01 2.11e+01 angle pdb=" C THR A1061 " pdb=" N THR A1062 " pdb=" CA THR A1062 " ideal model delta sigma weight residual 122.82 128.93 -6.11 1.42e+00 4.96e-01 1.85e+01 ... (remaining 22701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.43: 9698 27.43 - 54.87: 293 54.87 - 82.30: 33 82.30 - 109.73: 0 109.73 - 137.17: 2 Dihedral angle restraints: 10026 sinusoidal: 3982 harmonic: 6044 Sorted by residual: dihedral pdb=" CA GLU A 621 " pdb=" C GLU A 621 " pdb=" N LYS A 622 " pdb=" CA LYS A 622 " ideal model delta harmonic sigma weight residual 180.00 147.83 32.17 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA TYR A1083 " pdb=" C TYR A1083 " pdb=" N PRO A1084 " pdb=" CA PRO A1084 " ideal model delta harmonic sigma weight residual 180.00 153.63 26.37 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ALA A1180 " pdb=" C ALA A1180 " pdb=" N THR A1181 " pdb=" CA THR A1181 " ideal model delta harmonic sigma weight residual -180.00 -153.78 -26.22 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 10023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2422 0.072 - 0.144: 272 0.144 - 0.216: 35 0.216 - 0.288: 1 0.288 - 0.360: 4 Chirality restraints: 2734 Sorted by residual: chirality pdb=" CB ILE B 742 " pdb=" CA ILE B 742 " pdb=" CG1 ILE B 742 " pdb=" CG2 ILE B 742 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CB ILE A 742 " pdb=" CA ILE A 742 " pdb=" CG1 ILE A 742 " pdb=" CG2 ILE A 742 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CB ILE B 751 " pdb=" CA ILE B 751 " pdb=" CG1 ILE B 751 " pdb=" CG2 ILE B 751 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 2731 not shown) Planarity restraints: 2796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 693 " -0.063 5.00e-02 4.00e+02 9.49e-02 1.44e+01 pdb=" N PRO A 694 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO A 694 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 694 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 693 " 0.063 5.00e-02 4.00e+02 9.47e-02 1.44e+01 pdb=" N PRO B 694 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 694 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 694 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A1083 " -0.049 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO A1084 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A1084 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A1084 " -0.040 5.00e-02 4.00e+02 ... (remaining 2793 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3672 2.79 - 3.32: 15591 3.32 - 3.84: 27753 3.84 - 4.37: 30681 4.37 - 4.90: 55050 Nonbonded interactions: 132747 Sorted by model distance: nonbonded pdb=" O MET A1045 " pdb=" OG1 THR A1049 " model vdw 2.261 3.040 nonbonded pdb=" O ILE A 469 " pdb=" OG1 THR A 473 " model vdw 2.271 3.040 nonbonded pdb=" O ILE B 469 " pdb=" OG1 THR B 473 " model vdw 2.272 3.040 nonbonded pdb=" O ALA A 307 " pdb=" OG1 THR A 311 " model vdw 2.297 3.040 nonbonded pdb=" O ALA B 307 " pdb=" OG1 THR B 311 " model vdw 2.301 3.040 ... (remaining 132742 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.290 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: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 38.030 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 16740 Z= 0.239 Angle : 0.793 15.366 22706 Z= 0.438 Chirality : 0.049 0.360 2734 Planarity : 0.007 0.095 2796 Dihedral : 13.363 137.168 6102 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.64 % Allowed : 9.10 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.16), residues: 2050 helix: -0.41 (0.12), residues: 1454 sheet: -1.45 (0.72), residues: 50 loop : -2.03 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 962 HIS 0.002 0.001 HIS B1133 PHE 0.031 0.002 PHE B 766 TYR 0.012 0.001 TYR A1153 ARG 0.002 0.000 ARG A 431 Details of bonding type rmsd hydrogen bonds : bond 0.10702 ( 1163) hydrogen bonds : angle 5.79532 ( 3459) covalent geometry : bond 0.00453 (16740) covalent geometry : angle 0.79273 (22706) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 641 time to evaluate : 1.855 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8548 (mm) cc_final: 0.8158 (mt) REVERT: A 116 VAL cc_start: 0.8685 (t) cc_final: 0.8434 (t) REVERT: A 174 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8129 (tt) REVERT: A 195 PHE cc_start: 0.8027 (t80) cc_final: 0.7772 (t80) REVERT: A 196 SER cc_start: 0.8164 (p) cc_final: 0.7946 (p) REVERT: A 233 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7533 (tm-30) REVERT: A 237 ASN cc_start: 0.8352 (t0) cc_final: 0.8114 (t0) REVERT: A 269 LEU cc_start: 0.8440 (tp) cc_final: 0.8020 (tt) REVERT: A 280 TYR cc_start: 0.8508 (t80) cc_final: 0.8178 (t80) REVERT: A 300 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7753 (mt-10) REVERT: A 337 GLU cc_start: 0.7859 (tp30) cc_final: 0.7515 (tp30) REVERT: A 346 GLU cc_start: 0.7810 (tt0) cc_final: 0.7570 (tt0) REVERT: A 354 GLU cc_start: 0.8365 (tt0) cc_final: 0.8049 (tt0) REVERT: A 366 MET cc_start: 0.8634 (mmm) cc_final: 0.8237 (mmt) REVERT: A 375 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8489 (ttpp) REVERT: A 377 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8111 (mp) REVERT: A 383 MET cc_start: 0.7130 (mmm) cc_final: 0.6550 (mmm) REVERT: A 385 TRP cc_start: 0.8545 (m100) cc_final: 0.8299 (m100) REVERT: A 387 TYR cc_start: 0.8505 (m-10) cc_final: 0.8206 (m-10) REVERT: A 443 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7819 (tm-30) REVERT: A 486 ILE cc_start: 0.8745 (mp) cc_final: 0.8514 (mm) REVERT: A 487 SER cc_start: 0.8314 (t) cc_final: 0.8005 (p) REVERT: A 511 MET cc_start: 0.8838 (tmm) cc_final: 0.8281 (tmm) REVERT: A 531 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6956 (tm-30) REVERT: A 554 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7700 (tp30) REVERT: A 578 MET cc_start: 0.8583 (mtp) cc_final: 0.8375 (mtp) REVERT: A 579 MET cc_start: 0.8146 (tmm) cc_final: 0.7900 (tpp) REVERT: A 581 GLU cc_start: 0.8381 (tp30) cc_final: 0.7910 (tp30) REVERT: A 588 LYS cc_start: 0.8632 (tppt) cc_final: 0.8208 (tppt) REVERT: A 602 MET cc_start: 0.7830 (mpp) cc_final: 0.7513 (mpp) REVERT: A 613 GLN cc_start: 0.8161 (tt0) cc_final: 0.7959 (tt0) REVERT: A 632 LYS cc_start: 0.8288 (ttpt) cc_final: 0.7807 (ttmm) REVERT: A 637 ILE cc_start: 0.8689 (tp) cc_final: 0.8473 (tp) REVERT: A 645 LYS cc_start: 0.8512 (tttp) cc_final: 0.8227 (tttm) REVERT: A 647 LYS cc_start: 0.8690 (mmtp) cc_final: 0.8413 (mmtm) REVERT: A 697 MET cc_start: 0.6212 (mmm) cc_final: 0.5610 (mmm) REVERT: A 736 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8365 (p0) REVERT: A 810 MET cc_start: 0.6702 (ptt) cc_final: 0.6469 (ptt) REVERT: A 815 LYS cc_start: 0.8997 (tttt) cc_final: 0.8730 (tppp) REVERT: A 820 LYS cc_start: 0.8276 (mmmt) cc_final: 0.8008 (mmmt) REVERT: A 841 LYS cc_start: 0.8558 (mtpt) cc_final: 0.8334 (mtpt) REVERT: A 864 LEU cc_start: 0.8487 (tp) cc_final: 0.8185 (tp) REVERT: A 878 VAL cc_start: 0.8796 (t) cc_final: 0.8571 (t) REVERT: A 881 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7929 (tp30) REVERT: A 923 ASP cc_start: 0.7690 (p0) cc_final: 0.7367 (p0) REVERT: A 942 MET cc_start: 0.8604 (tpp) cc_final: 0.8373 (tpt) REVERT: A 958 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8670 (ttpt) REVERT: A 969 LEU cc_start: 0.9015 (tp) cc_final: 0.8801 (tt) REVERT: A 983 ASP cc_start: 0.7981 (t0) cc_final: 0.7630 (p0) REVERT: A 994 GLU cc_start: 0.7968 (pm20) cc_final: 0.7671 (pm20) REVERT: A 1003 SER cc_start: 0.8567 (t) cc_final: 0.8358 (m) REVERT: A 1041 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8168 (p) REVERT: A 1060 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7386 (mm-30) REVERT: A 1063 VAL cc_start: 0.8648 (t) cc_final: 0.8397 (p) REVERT: A 1098 ILE cc_start: 0.8952 (tt) cc_final: 0.8624 (tp) REVERT: A 1104 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7519 (tpt) REVERT: A 1121 LEU cc_start: 0.8818 (mm) cc_final: 0.8579 (mt) REVERT: A 1122 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7614 (tp30) REVERT: A 1125 TYR cc_start: 0.8329 (p90) cc_final: 0.8075 (p90) REVERT: A 1167 ILE cc_start: 0.8205 (mm) cc_final: 0.7968 (mt) REVERT: A 1212 ILE cc_start: 0.5567 (OUTLIER) cc_final: 0.5083 (mp) REVERT: B 112 ILE cc_start: 0.8445 (mm) cc_final: 0.8102 (mt) REVERT: B 154 MET cc_start: 0.8619 (tpp) cc_final: 0.8361 (tpp) REVERT: B 174 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8264 (tt) REVERT: B 196 SER cc_start: 0.8313 (p) cc_final: 0.8086 (p) REVERT: B 250 LYS cc_start: 0.8477 (mttt) cc_final: 0.8223 (mttm) REVERT: B 263 GLN cc_start: 0.8384 (mt0) cc_final: 0.8079 (mt0) REVERT: B 266 LEU cc_start: 0.8479 (tp) cc_final: 0.8243 (tt) REVERT: B 267 TYR cc_start: 0.8510 (t80) cc_final: 0.8054 (t80) REVERT: B 300 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7889 (mt-10) REVERT: B 321 VAL cc_start: 0.7524 (OUTLIER) cc_final: 0.7252 (m) REVERT: B 337 GLU cc_start: 0.7909 (tp30) cc_final: 0.7571 (tp30) REVERT: B 375 LYS cc_start: 0.8644 (tppp) cc_final: 0.8173 (mtpp) REVERT: B 385 TRP cc_start: 0.8468 (m100) cc_final: 0.8259 (m100) REVERT: B 419 TRP cc_start: 0.8107 (p-90) cc_final: 0.7806 (p-90) REVERT: B 486 ILE cc_start: 0.8816 (mp) cc_final: 0.8573 (mm) REVERT: B 487 SER cc_start: 0.8439 (t) cc_final: 0.8126 (p) REVERT: B 511 MET cc_start: 0.8885 (tmm) cc_final: 0.8326 (tmm) REVERT: B 515 ASP cc_start: 0.8642 (t0) cc_final: 0.8374 (t70) REVERT: B 531 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6958 (tm-30) REVERT: B 579 MET cc_start: 0.8082 (tmm) cc_final: 0.7734 (tpp) REVERT: B 588 LYS cc_start: 0.8638 (tppt) cc_final: 0.8310 (tttm) REVERT: B 637 ILE cc_start: 0.8845 (tp) cc_final: 0.8636 (tp) REVERT: B 697 MET cc_start: 0.5687 (mmm) cc_final: 0.5073 (mmm) REVERT: B 736 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8214 (p0) REVERT: B 808 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7848 (pt) REVERT: B 810 MET cc_start: 0.6738 (ptt) cc_final: 0.6503 (ptt) REVERT: B 820 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7939 (mmmt) REVERT: B 825 VAL cc_start: 0.8758 (t) cc_final: 0.8499 (p) REVERT: B 852 LYS cc_start: 0.8359 (mttp) cc_final: 0.7895 (ttmm) REVERT: B 931 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7613 (mt-10) REVERT: B 942 MET cc_start: 0.8568 (tpp) cc_final: 0.8346 (tpt) REVERT: B 954 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7619 (mm-30) REVERT: B 958 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8505 (ttmm) REVERT: B 968 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8334 (mmmm) REVERT: B 972 PHE cc_start: 0.8730 (t80) cc_final: 0.8302 (t80) REVERT: B 994 GLU cc_start: 0.7893 (pm20) cc_final: 0.7551 (pm20) REVERT: B 1003 SER cc_start: 0.8594 (t) cc_final: 0.8283 (m) REVERT: B 1005 LEU cc_start: 0.8453 (tp) cc_final: 0.8219 (tt) REVERT: B 1041 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8208 (p) REVERT: B 1051 LYS cc_start: 0.8297 (pttt) cc_final: 0.7963 (pttt) REVERT: B 1060 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7583 (mm-30) REVERT: B 1098 ILE cc_start: 0.8925 (tt) cc_final: 0.8592 (tp) REVERT: B 1104 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7343 (tpp) REVERT: B 1105 GLU cc_start: 0.7634 (tp30) cc_final: 0.7410 (tp30) REVERT: B 1118 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8258 (mtmm) REVERT: B 1121 LEU cc_start: 0.8978 (mm) cc_final: 0.8758 (mt) REVERT: B 1122 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7538 (mm-30) REVERT: B 1125 TYR cc_start: 0.8278 (p90) cc_final: 0.8049 (p90) REVERT: B 1162 ARG cc_start: 0.5414 (OUTLIER) cc_final: 0.5070 (tpm-80) REVERT: B 1179 THR cc_start: 0.5317 (OUTLIER) cc_final: 0.5027 (p) REVERT: B 1212 ILE cc_start: 0.5617 (OUTLIER) cc_final: 0.5323 (mp) outliers start: 101 outliers final: 37 residues processed: 709 average time/residue: 0.3157 time to fit residues: 322.9169 Evaluate side-chains 595 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 540 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 MET Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1158 ARG Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1041 VAL Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1156 HIS Chi-restraints excluded: chain B residue 1158 ARG Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.5980 chunk 157 optimal weight: 0.1980 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 163 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 121 optimal weight: 0.7980 chunk 188 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN A 295 ASN A 421 ASN A 600 HIS A 736 ASN A 831 ASN A 943 ASN A 959 ASN A 981 HIS B 421 ASN ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN B1191 ASN B1220 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.144322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.120340 restraints weight = 25355.039| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.10 r_work: 0.3384 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16740 Z= 0.151 Angle : 0.638 17.165 22706 Z= 0.321 Chirality : 0.041 0.200 2734 Planarity : 0.005 0.072 2796 Dihedral : 8.896 132.734 2343 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.02 % Allowed : 17.24 % Favored : 77.73 % 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: 0.16 (0.18), residues: 2050 helix: 0.99 (0.13), residues: 1466 sheet: -3.08 (0.47), residues: 102 loop : -1.76 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1112 HIS 0.007 0.001 HIS A 981 PHE 0.021 0.001 PHE A 972 TYR 0.017 0.001 TYR B 415 ARG 0.009 0.001 ARG A 609 Details of bonding type rmsd hydrogen bonds : bond 0.04938 ( 1163) hydrogen bonds : angle 4.48901 ( 3459) covalent geometry : bond 0.00311 (16740) covalent geometry : angle 0.63816 (22706) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 563 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8687 (mm) cc_final: 0.8255 (mt) REVERT: A 116 VAL cc_start: 0.8799 (t) cc_final: 0.8535 (t) REVERT: A 149 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7605 (tm-30) REVERT: A 176 VAL cc_start: 0.8831 (p) cc_final: 0.8578 (t) REVERT: A 225 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7671 (tp40) REVERT: A 233 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7674 (tm-30) REVERT: A 266 LEU cc_start: 0.8425 (tp) cc_final: 0.8190 (tt) REVERT: A 269 LEU cc_start: 0.8497 (tp) cc_final: 0.8191 (tt) REVERT: A 300 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7941 (mt-10) REVERT: A 316 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7879 (m-30) REVERT: A 337 GLU cc_start: 0.7708 (tp30) cc_final: 0.7377 (tp30) REVERT: A 346 GLU cc_start: 0.7791 (tt0) cc_final: 0.7523 (tt0) REVERT: A 354 GLU cc_start: 0.8259 (tt0) cc_final: 0.7949 (tt0) REVERT: A 366 MET cc_start: 0.8585 (mmm) cc_final: 0.8151 (mmt) REVERT: A 375 LYS cc_start: 0.8764 (tppp) cc_final: 0.8470 (ttpp) REVERT: A 383 MET cc_start: 0.7193 (mmm) cc_final: 0.6623 (mmm) REVERT: A 385 TRP cc_start: 0.8520 (m100) cc_final: 0.8066 (m100) REVERT: A 387 TYR cc_start: 0.8634 (m-10) cc_final: 0.8198 (m-10) REVERT: A 443 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8061 (tm-30) REVERT: A 486 ILE cc_start: 0.8691 (mp) cc_final: 0.8457 (mm) REVERT: A 487 SER cc_start: 0.8271 (t) cc_final: 0.7963 (p) REVERT: A 511 MET cc_start: 0.8911 (tmm) cc_final: 0.8662 (tmm) REVERT: A 516 ARG cc_start: 0.8557 (ttp-110) cc_final: 0.8289 (ttp-110) REVERT: A 531 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: A 578 MET cc_start: 0.8681 (mtp) cc_final: 0.8425 (mtp) REVERT: A 579 MET cc_start: 0.7935 (tmm) cc_final: 0.7722 (tpp) REVERT: A 580 GLU cc_start: 0.8136 (tp30) cc_final: 0.7732 (tp30) REVERT: A 602 MET cc_start: 0.7514 (mpp) cc_final: 0.7216 (mpp) REVERT: A 609 ARG cc_start: 0.8372 (ttm-80) cc_final: 0.8163 (ttp-110) REVERT: A 632 LYS cc_start: 0.8341 (ttpt) cc_final: 0.8090 (ttmm) REVERT: A 647 LYS cc_start: 0.8689 (mmtp) cc_final: 0.8405 (mmtm) REVERT: A 697 MET cc_start: 0.6451 (mmm) cc_final: 0.5854 (mmm) REVERT: A 815 LYS cc_start: 0.9005 (tttt) cc_final: 0.8636 (tppp) REVERT: A 820 LYS cc_start: 0.8350 (mmmt) cc_final: 0.8042 (mmmt) REVERT: A 841 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8487 (mtpt) REVERT: A 853 ILE cc_start: 0.8799 (tp) cc_final: 0.8506 (tt) REVERT: A 864 LEU cc_start: 0.8543 (tp) cc_final: 0.8322 (tp) REVERT: A 897 LYS cc_start: 0.8953 (mttp) cc_final: 0.8686 (mmtp) REVERT: A 911 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8167 (mm-30) REVERT: A 926 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7815 (mm-30) REVERT: A 942 MET cc_start: 0.8505 (tpp) cc_final: 0.8286 (tpt) REVERT: A 972 PHE cc_start: 0.8552 (t80) cc_final: 0.8339 (t80) REVERT: A 983 ASP cc_start: 0.7956 (t0) cc_final: 0.7749 (p0) REVERT: A 994 GLU cc_start: 0.7911 (pm20) cc_final: 0.7585 (pm20) REVERT: A 1008 LEU cc_start: 0.8193 (mp) cc_final: 0.7785 (tp) REVERT: A 1033 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7618 (mp0) REVERT: A 1044 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7736 (mt-10) REVERT: A 1060 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7672 (mm-30) REVERT: A 1066 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: A 1080 PHE cc_start: 0.8020 (m-80) cc_final: 0.7394 (m-80) REVERT: A 1104 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7527 (tpp) REVERT: A 1121 LEU cc_start: 0.8875 (mm) cc_final: 0.8625 (mt) REVERT: A 1122 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7769 (tp30) REVERT: A 1190 ARG cc_start: 0.8166 (mmm-85) cc_final: 0.7702 (mmm-85) REVERT: A 1212 ILE cc_start: 0.5534 (OUTLIER) cc_final: 0.4994 (mp) REVERT: A 1220 ASN cc_start: 0.7938 (m-40) cc_final: 0.7729 (m-40) REVERT: B 149 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7574 (tm-30) REVERT: B 250 LYS cc_start: 0.8439 (mttt) cc_final: 0.8118 (mttm) REVERT: B 300 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7862 (mt-10) REVERT: B 337 GLU cc_start: 0.7822 (tp30) cc_final: 0.7479 (tp30) REVERT: B 375 LYS cc_start: 0.8789 (tppp) cc_final: 0.8263 (mtpp) REVERT: B 383 MET cc_start: 0.7285 (tpp) cc_final: 0.6749 (mmm) REVERT: B 385 TRP cc_start: 0.8427 (m100) cc_final: 0.8117 (m100) REVERT: B 419 TRP cc_start: 0.8097 (p-90) cc_final: 0.7733 (p-90) REVERT: B 443 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7826 (tm-30) REVERT: B 487 SER cc_start: 0.8416 (t) cc_final: 0.8148 (p) REVERT: B 511 MET cc_start: 0.8927 (tmm) cc_final: 0.8702 (tmm) REVERT: B 531 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6975 (tm-30) REVERT: B 578 MET cc_start: 0.8620 (mtp) cc_final: 0.8269 (mtp) REVERT: B 579 MET cc_start: 0.7807 (tmm) cc_final: 0.7508 (tpp) REVERT: B 588 LYS cc_start: 0.8657 (tppt) cc_final: 0.8370 (tttm) REVERT: B 647 LYS cc_start: 0.8531 (mmtm) cc_final: 0.8276 (mmtp) REVERT: B 697 MET cc_start: 0.5799 (mmm) cc_final: 0.5207 (mmm) REVERT: B 736 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8051 (t0) REVERT: B 808 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7973 (pt) REVERT: B 810 MET cc_start: 0.7007 (ptt) cc_final: 0.6798 (ptt) REVERT: B 820 LYS cc_start: 0.8251 (mmmt) cc_final: 0.7987 (mmmt) REVERT: B 825 VAL cc_start: 0.8754 (t) cc_final: 0.8465 (p) REVERT: B 852 LYS cc_start: 0.8444 (mttp) cc_final: 0.8052 (ttmm) REVERT: B 926 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7761 (mm-30) REVERT: B 931 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7665 (mt-10) REVERT: B 954 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7590 (mm-30) REVERT: B 958 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8493 (ttmm) REVERT: B 968 LYS cc_start: 0.8704 (mtpp) cc_final: 0.8394 (mmmm) REVERT: B 993 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6644 (m-30) REVERT: B 994 GLU cc_start: 0.7806 (pm20) cc_final: 0.7538 (pm20) REVERT: B 996 ASP cc_start: 0.7353 (p0) cc_final: 0.7078 (p0) REVERT: B 1003 SER cc_start: 0.8539 (t) cc_final: 0.8248 (m) REVERT: B 1005 LEU cc_start: 0.8489 (tp) cc_final: 0.8222 (tp) REVERT: B 1060 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7755 (mm-30) REVERT: B 1073 MET cc_start: 0.8597 (tpp) cc_final: 0.8094 (tpp) REVERT: B 1098 ILE cc_start: 0.8908 (tt) cc_final: 0.8561 (tp) REVERT: B 1104 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7363 (tpt) REVERT: B 1118 LYS cc_start: 0.8612 (mtpp) cc_final: 0.8288 (mtmm) REVERT: B 1121 LEU cc_start: 0.8999 (mm) cc_final: 0.8705 (mt) REVERT: B 1122 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7736 (tp30) REVERT: B 1125 TYR cc_start: 0.8378 (p90) cc_final: 0.8139 (p90) REVERT: B 1126 LEU cc_start: 0.8437 (mt) cc_final: 0.8005 (pt) REVERT: B 1143 GLU cc_start: 0.7747 (tt0) cc_final: 0.7033 (tt0) REVERT: B 1162 ARG cc_start: 0.5717 (OUTLIER) cc_final: 0.5124 (tpm-80) REVERT: B 1179 THR cc_start: 0.5620 (OUTLIER) cc_final: 0.5324 (p) REVERT: B 1190 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7616 (mmm-85) REVERT: B 1212 ILE cc_start: 0.5499 (OUTLIER) cc_final: 0.5194 (mp) outliers start: 90 outliers final: 42 residues processed: 617 average time/residue: 0.3217 time to fit residues: 283.9860 Evaluate side-chains 586 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 530 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 981 HIS Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1104 MET Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1158 ARG Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 865 ARG Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1154 ASN Chi-restraints excluded: chain B residue 1156 HIS Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1199 LEU Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 137 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS A 600 HIS A 981 HIS A1120 HIS B 292 HIS B 597 GLN B1220 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.140689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.117290 restraints weight = 25141.222| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.05 r_work: 0.3333 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 16740 Z= 0.260 Angle : 0.674 17.249 22706 Z= 0.342 Chirality : 0.045 0.194 2734 Planarity : 0.005 0.066 2796 Dihedral : 7.910 134.264 2297 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.97 % Allowed : 18.19 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2050 helix: 1.33 (0.13), residues: 1450 sheet: -2.85 (0.48), residues: 92 loop : -1.75 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1112 HIS 0.010 0.001 HIS A 981 PHE 0.019 0.002 PHE B 625 TYR 0.016 0.002 TYR B1035 ARG 0.011 0.001 ARG A1185 Details of bonding type rmsd hydrogen bonds : bond 0.05755 ( 1163) hydrogen bonds : angle 4.51287 ( 3459) covalent geometry : bond 0.00563 (16740) covalent geometry : angle 0.67403 (22706) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 551 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8740 (mm) cc_final: 0.8382 (mt) REVERT: A 116 VAL cc_start: 0.8892 (t) cc_final: 0.8651 (t) REVERT: A 149 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7436 (tm-30) REVERT: A 163 PHE cc_start: 0.8416 (t80) cc_final: 0.8143 (t80) REVERT: A 199 MET cc_start: 0.8451 (mmm) cc_final: 0.8177 (mmm) REVERT: A 233 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7617 (tm-30) REVERT: A 266 LEU cc_start: 0.8399 (tp) cc_final: 0.8156 (tt) REVERT: A 269 LEU cc_start: 0.8692 (tp) cc_final: 0.8439 (tt) REVERT: A 280 TYR cc_start: 0.8479 (t80) cc_final: 0.8151 (t80) REVERT: A 337 GLU cc_start: 0.7734 (tp30) cc_final: 0.7409 (tp30) REVERT: A 346 GLU cc_start: 0.7880 (tt0) cc_final: 0.7648 (tt0) REVERT: A 354 GLU cc_start: 0.8213 (tt0) cc_final: 0.7890 (tt0) REVERT: A 366 MET cc_start: 0.8655 (mmm) cc_final: 0.8223 (mmt) REVERT: A 375 LYS cc_start: 0.8752 (tppp) cc_final: 0.8538 (ttpp) REVERT: A 377 LEU cc_start: 0.8603 (tp) cc_final: 0.8318 (mp) REVERT: A 383 MET cc_start: 0.7275 (mmm) cc_final: 0.6712 (mmm) REVERT: A 385 TRP cc_start: 0.8511 (m100) cc_final: 0.8058 (m100) REVERT: A 443 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8030 (tm-30) REVERT: A 486 ILE cc_start: 0.8772 (mp) cc_final: 0.8479 (mm) REVERT: A 487 SER cc_start: 0.8217 (t) cc_final: 0.7884 (p) REVERT: A 511 MET cc_start: 0.8881 (tmm) cc_final: 0.8457 (ttp) REVERT: A 531 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7178 (tm-30) REVERT: A 554 GLU cc_start: 0.8128 (tp30) cc_final: 0.7882 (tp30) REVERT: A 565 MET cc_start: 0.6372 (pmm) cc_final: 0.6050 (pmm) REVERT: A 579 MET cc_start: 0.7998 (tmm) cc_final: 0.7792 (tpp) REVERT: A 580 GLU cc_start: 0.8204 (tp30) cc_final: 0.7806 (tp30) REVERT: A 599 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: A 602 MET cc_start: 0.7678 (mpp) cc_final: 0.7351 (mpp) REVERT: A 626 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.8000 (mt) REVERT: A 632 LYS cc_start: 0.8324 (ttpt) cc_final: 0.8015 (ttmm) REVERT: A 634 SER cc_start: 0.8878 (m) cc_final: 0.8615 (t) REVERT: A 637 ILE cc_start: 0.8572 (tp) cc_final: 0.8327 (tp) REVERT: A 647 LYS cc_start: 0.8718 (mmtp) cc_final: 0.8455 (mmtm) REVERT: A 697 MET cc_start: 0.6505 (mmm) cc_final: 0.5918 (mmm) REVERT: A 815 LYS cc_start: 0.9016 (tttt) cc_final: 0.8706 (ttmm) REVERT: A 820 LYS cc_start: 0.8332 (mmmt) cc_final: 0.8061 (mmmt) REVERT: A 828 LYS cc_start: 0.8560 (mmmm) cc_final: 0.8265 (mmmm) REVERT: A 841 LYS cc_start: 0.8724 (mtpt) cc_final: 0.8514 (mtpt) REVERT: A 884 LEU cc_start: 0.8497 (mm) cc_final: 0.8244 (mt) REVERT: A 911 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8119 (mm-30) REVERT: A 937 LYS cc_start: 0.8732 (mttm) cc_final: 0.8365 (mmtp) REVERT: A 942 MET cc_start: 0.8589 (tpp) cc_final: 0.8230 (tpt) REVERT: A 972 PHE cc_start: 0.8692 (t80) cc_final: 0.8431 (t80) REVERT: A 983 ASP cc_start: 0.8059 (t0) cc_final: 0.7731 (p0) REVERT: A 994 GLU cc_start: 0.7898 (pm20) cc_final: 0.7545 (pm20) REVERT: A 1008 LEU cc_start: 0.8200 (mp) cc_final: 0.7845 (tp) REVERT: A 1044 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7661 (mt-10) REVERT: A 1060 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7842 (mm-30) REVERT: A 1061 THR cc_start: 0.7941 (OUTLIER) cc_final: 0.7435 (p) REVERT: A 1066 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: A 1072 ASP cc_start: 0.7507 (m-30) cc_final: 0.7271 (m-30) REVERT: A 1080 PHE cc_start: 0.8054 (m-80) cc_final: 0.7540 (m-80) REVERT: A 1116 LYS cc_start: 0.8553 (mttt) cc_final: 0.7916 (mttt) REVERT: A 1121 LEU cc_start: 0.8969 (mm) cc_final: 0.8694 (mt) REVERT: A 1122 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7909 (tp30) REVERT: A 1167 ILE cc_start: 0.8561 (mt) cc_final: 0.8189 (tt) REVERT: A 1173 LYS cc_start: 0.7511 (ttpp) cc_final: 0.7098 (ptmm) REVERT: A 1185 ARG cc_start: 0.7150 (mmt-90) cc_final: 0.6922 (mmt180) REVERT: A 1190 ARG cc_start: 0.8140 (mmm-85) cc_final: 0.7789 (mmm-85) REVERT: A 1212 ILE cc_start: 0.5694 (OUTLIER) cc_final: 0.5132 (mp) REVERT: A 1217 ILE cc_start: 0.8357 (mm) cc_final: 0.8108 (mm) REVERT: A 1220 ASN cc_start: 0.7934 (m-40) cc_final: 0.7671 (m-40) REVERT: B 116 VAL cc_start: 0.8723 (t) cc_final: 0.8392 (m) REVERT: B 134 ASP cc_start: 0.8159 (t0) cc_final: 0.7817 (t70) REVERT: B 149 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7447 (tm-30) REVERT: B 163 PHE cc_start: 0.8448 (t80) cc_final: 0.8185 (t80) REVERT: B 250 LYS cc_start: 0.8474 (mttt) cc_final: 0.8205 (mttm) REVERT: B 263 GLN cc_start: 0.8420 (mt0) cc_final: 0.8104 (mt0) REVERT: B 266 LEU cc_start: 0.8499 (tp) cc_final: 0.8295 (tt) REVERT: B 337 GLU cc_start: 0.7751 (tp30) cc_final: 0.7399 (tp30) REVERT: B 375 LYS cc_start: 0.8790 (tppp) cc_final: 0.8337 (mtpp) REVERT: B 383 MET cc_start: 0.7352 (tpp) cc_final: 0.6857 (mmm) REVERT: B 385 TRP cc_start: 0.8444 (m100) cc_final: 0.8084 (m100) REVERT: B 407 SER cc_start: 0.8750 (t) cc_final: 0.8510 (p) REVERT: B 487 SER cc_start: 0.8402 (t) cc_final: 0.8100 (p) REVERT: B 511 MET cc_start: 0.8953 (tmm) cc_final: 0.8570 (ttp) REVERT: B 520 ASP cc_start: 0.8443 (p0) cc_final: 0.8159 (p0) REVERT: B 531 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7243 (tm-30) REVERT: B 578 MET cc_start: 0.8655 (mtp) cc_final: 0.8309 (mtp) REVERT: B 579 MET cc_start: 0.7815 (tmm) cc_final: 0.7603 (tpp) REVERT: B 588 LYS cc_start: 0.8617 (tppt) cc_final: 0.8402 (tttp) REVERT: B 697 MET cc_start: 0.5799 (mmm) cc_final: 0.5139 (mmm) REVERT: B 736 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8024 (t0) REVERT: B 808 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.8020 (pp) REVERT: B 810 MET cc_start: 0.7129 (ptt) cc_final: 0.6912 (ptt) REVERT: B 815 LYS cc_start: 0.9091 (tttt) cc_final: 0.8690 (tttm) REVERT: B 820 LYS cc_start: 0.8219 (mmmt) cc_final: 0.7953 (mmmt) REVERT: B 825 VAL cc_start: 0.8831 (t) cc_final: 0.8526 (p) REVERT: B 852 LYS cc_start: 0.8523 (mttp) cc_final: 0.8074 (mtpt) REVERT: B 859 ASP cc_start: 0.8020 (p0) cc_final: 0.7688 (p0) REVERT: B 877 GLN cc_start: 0.8655 (tt0) cc_final: 0.8394 (tt0) REVERT: B 926 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7847 (mm-30) REVERT: B 931 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7766 (mt-10) REVERT: B 954 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7670 (mm-30) REVERT: B 958 LYS cc_start: 0.8900 (ttpt) cc_final: 0.8557 (ttmm) REVERT: B 968 LYS cc_start: 0.8725 (mtpp) cc_final: 0.8423 (mmmm) REVERT: B 993 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.6961 (m-30) REVERT: B 994 GLU cc_start: 0.7809 (pm20) cc_final: 0.7413 (pm20) REVERT: B 1003 SER cc_start: 0.8321 (t) cc_final: 0.7862 (m) REVERT: B 1005 LEU cc_start: 0.8475 (tp) cc_final: 0.8266 (tt) REVERT: B 1060 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7744 (mm-30) REVERT: B 1066 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: B 1098 ILE cc_start: 0.8963 (tt) cc_final: 0.8609 (tp) REVERT: B 1118 LYS cc_start: 0.8636 (mtpp) cc_final: 0.8347 (mtmm) REVERT: B 1121 LEU cc_start: 0.9035 (mm) cc_final: 0.8731 (mt) REVERT: B 1143 GLU cc_start: 0.7719 (tt0) cc_final: 0.7395 (tt0) REVERT: B 1144 ASP cc_start: 0.7215 (m-30) cc_final: 0.7015 (m-30) REVERT: B 1162 ARG cc_start: 0.5761 (OUTLIER) cc_final: 0.5173 (tpm-80) REVERT: B 1179 THR cc_start: 0.5477 (OUTLIER) cc_final: 0.5205 (p) REVERT: B 1190 ARG cc_start: 0.7907 (mmm-85) cc_final: 0.7632 (mmm-85) REVERT: B 1212 ILE cc_start: 0.5567 (OUTLIER) cc_final: 0.5226 (mp) outliers start: 107 outliers final: 68 residues processed: 609 average time/residue: 0.4024 time to fit residues: 351.5442 Evaluate side-chains 617 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 537 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 981 HIS Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1104 MET Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1158 ARG Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1154 ASN Chi-restraints excluded: chain B residue 1156 HIS Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1199 LEU Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 181 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 190 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 195 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN A 943 ASN A 981 HIS B 165 GLN B 256 GLN B1220 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.142362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.119288 restraints weight = 25027.210| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.04 r_work: 0.3372 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16740 Z= 0.159 Angle : 0.633 16.456 22706 Z= 0.315 Chirality : 0.042 0.178 2734 Planarity : 0.005 0.063 2796 Dihedral : 7.503 135.207 2287 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.52 % Allowed : 19.87 % Favored : 74.61 % 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: 0.97 (0.19), residues: 2050 helix: 1.67 (0.14), residues: 1452 sheet: -2.62 (0.48), residues: 92 loop : -1.78 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A1112 HIS 0.005 0.001 HIS A 600 PHE 0.016 0.001 PHE A1136 TYR 0.010 0.001 TYR B 191 ARG 0.008 0.001 ARG B1185 Details of bonding type rmsd hydrogen bonds : bond 0.05054 ( 1163) hydrogen bonds : angle 4.37205 ( 3459) covalent geometry : bond 0.00335 (16740) covalent geometry : angle 0.63257 (22706) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 545 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8721 (mm) cc_final: 0.8361 (mt) REVERT: A 116 VAL cc_start: 0.8796 (t) cc_final: 0.8533 (t) REVERT: A 149 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7446 (tm-30) REVERT: A 163 PHE cc_start: 0.8389 (t80) cc_final: 0.8118 (t80) REVERT: A 199 MET cc_start: 0.8448 (mmm) cc_final: 0.8144 (mmm) REVERT: A 233 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7499 (tm-30) REVERT: A 269 LEU cc_start: 0.8614 (tp) cc_final: 0.8388 (tt) REVERT: A 280 TYR cc_start: 0.8458 (t80) cc_final: 0.8143 (t80) REVERT: A 337 GLU cc_start: 0.7710 (tp30) cc_final: 0.7393 (tp30) REVERT: A 346 GLU cc_start: 0.7827 (tt0) cc_final: 0.7582 (tt0) REVERT: A 354 GLU cc_start: 0.8208 (tt0) cc_final: 0.7876 (tt0) REVERT: A 375 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8527 (ttpp) REVERT: A 377 LEU cc_start: 0.8657 (tp) cc_final: 0.8351 (mp) REVERT: A 383 MET cc_start: 0.7151 (mmm) cc_final: 0.6599 (mmm) REVERT: A 443 GLU cc_start: 0.8287 (tm-30) cc_final: 0.8000 (tm-30) REVERT: A 487 SER cc_start: 0.8200 (t) cc_final: 0.7849 (p) REVERT: A 511 MET cc_start: 0.8871 (tmm) cc_final: 0.8498 (tmm) REVERT: A 531 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7039 (tm-30) REVERT: A 554 GLU cc_start: 0.8131 (tp30) cc_final: 0.7844 (tp30) REVERT: A 565 MET cc_start: 0.6418 (pmm) cc_final: 0.6072 (pmm) REVERT: A 578 MET cc_start: 0.8664 (mtp) cc_final: 0.8396 (mmm) REVERT: A 580 GLU cc_start: 0.8115 (tp30) cc_final: 0.7696 (tp30) REVERT: A 602 MET cc_start: 0.7693 (mpp) cc_final: 0.7347 (mpp) REVERT: A 609 ARG cc_start: 0.8426 (ttm170) cc_final: 0.8099 (ttm-80) REVERT: A 632 LYS cc_start: 0.8270 (ttpt) cc_final: 0.7947 (ttmm) REVERT: A 634 SER cc_start: 0.8865 (m) cc_final: 0.8620 (t) REVERT: A 647 LYS cc_start: 0.8712 (mmtp) cc_final: 0.8505 (mmtp) REVERT: A 697 MET cc_start: 0.6505 (mmm) cc_final: 0.5881 (mmm) REVERT: A 820 LYS cc_start: 0.8308 (mmmt) cc_final: 0.8022 (mmmt) REVERT: A 841 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8501 (mtpt) REVERT: A 884 LEU cc_start: 0.8459 (mm) cc_final: 0.8165 (mt) REVERT: A 937 LYS cc_start: 0.8699 (mttm) cc_final: 0.8286 (mmtp) REVERT: A 942 MET cc_start: 0.8627 (tpp) cc_final: 0.8255 (tpt) REVERT: A 982 PHE cc_start: 0.8127 (m-80) cc_final: 0.7769 (m-80) REVERT: A 983 ASP cc_start: 0.8062 (t0) cc_final: 0.7724 (p0) REVERT: A 994 GLU cc_start: 0.7867 (pm20) cc_final: 0.7537 (pm20) REVERT: A 1005 LEU cc_start: 0.8390 (tp) cc_final: 0.8180 (tp) REVERT: A 1006 VAL cc_start: 0.8529 (m) cc_final: 0.8212 (t) REVERT: A 1008 LEU cc_start: 0.8175 (mp) cc_final: 0.7839 (tp) REVERT: A 1044 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7588 (mt-10) REVERT: A 1060 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7811 (mm-30) REVERT: A 1061 THR cc_start: 0.7869 (OUTLIER) cc_final: 0.7405 (p) REVERT: A 1066 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7554 (m-80) REVERT: A 1072 ASP cc_start: 0.7579 (m-30) cc_final: 0.7362 (m-30) REVERT: A 1073 MET cc_start: 0.8722 (tpp) cc_final: 0.8515 (tpp) REVERT: A 1080 PHE cc_start: 0.8012 (m-80) cc_final: 0.7562 (m-80) REVERT: A 1104 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7670 (tpp) REVERT: A 1121 LEU cc_start: 0.8962 (mm) cc_final: 0.8736 (mt) REVERT: A 1190 ARG cc_start: 0.8091 (mmm-85) cc_final: 0.7704 (mmm-85) REVERT: A 1212 ILE cc_start: 0.5695 (OUTLIER) cc_final: 0.5105 (mp) REVERT: A 1220 ASN cc_start: 0.7823 (m-40) cc_final: 0.7618 (m-40) REVERT: B 125 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6585 (mt-10) REVERT: B 128 ARG cc_start: 0.7750 (tmm-80) cc_final: 0.7346 (ttp80) REVERT: B 134 ASP cc_start: 0.8140 (t0) cc_final: 0.7778 (t70) REVERT: B 149 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7442 (tm-30) REVERT: B 155 ASP cc_start: 0.8175 (t0) cc_final: 0.7934 (t0) REVERT: B 163 PHE cc_start: 0.8406 (t80) cc_final: 0.8153 (t80) REVERT: B 225 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7470 (tt0) REVERT: B 250 LYS cc_start: 0.8396 (mttt) cc_final: 0.8128 (mttm) REVERT: B 263 GLN cc_start: 0.8336 (mt0) cc_final: 0.8022 (mt0) REVERT: B 265 VAL cc_start: 0.8648 (t) cc_final: 0.8369 (p) REVERT: B 337 GLU cc_start: 0.7740 (tp30) cc_final: 0.7399 (tp30) REVERT: B 375 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8306 (mtpp) REVERT: B 383 MET cc_start: 0.7240 (tpp) cc_final: 0.6738 (mmm) REVERT: B 385 TRP cc_start: 0.8433 (m100) cc_final: 0.8155 (m100) REVERT: B 407 SER cc_start: 0.8777 (t) cc_final: 0.8540 (p) REVERT: B 415 TYR cc_start: 0.5799 (t80) cc_final: 0.5531 (m-80) REVERT: B 419 TRP cc_start: 0.8088 (p-90) cc_final: 0.7769 (p-90) REVERT: B 487 SER cc_start: 0.8334 (t) cc_final: 0.8053 (p) REVERT: B 511 MET cc_start: 0.8911 (tmm) cc_final: 0.8538 (ttp) REVERT: B 588 LYS cc_start: 0.8602 (tppt) cc_final: 0.8365 (tttp) REVERT: B 621 GLU cc_start: 0.7624 (pp20) cc_final: 0.7343 (pm20) REVERT: B 697 MET cc_start: 0.5797 (mmm) cc_final: 0.5154 (mmm) REVERT: B 736 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.7970 (t0) REVERT: B 810 MET cc_start: 0.7073 (ptt) cc_final: 0.6869 (ptt) REVERT: B 815 LYS cc_start: 0.9102 (tttt) cc_final: 0.8701 (tttm) REVERT: B 820 LYS cc_start: 0.8171 (mmmt) cc_final: 0.7921 (mmmt) REVERT: B 852 LYS cc_start: 0.8533 (mttp) cc_final: 0.8105 (mtpt) REVERT: B 853 ILE cc_start: 0.8953 (tp) cc_final: 0.8617 (tt) REVERT: B 859 ASP cc_start: 0.8006 (p0) cc_final: 0.7760 (p0) REVERT: B 954 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7642 (mm-30) REVERT: B 958 LYS cc_start: 0.8907 (ttpt) cc_final: 0.8557 (ttmm) REVERT: B 968 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8384 (mmmm) REVERT: B 993 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.6936 (m-30) REVERT: B 994 GLU cc_start: 0.7798 (pm20) cc_final: 0.7390 (pm20) REVERT: B 998 LEU cc_start: 0.8629 (mm) cc_final: 0.8423 (mt) REVERT: B 1003 SER cc_start: 0.8349 (t) cc_final: 0.7875 (m) REVERT: B 1005 LEU cc_start: 0.8518 (tp) cc_final: 0.8269 (tt) REVERT: B 1066 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: B 1067 PHE cc_start: 0.8590 (t80) cc_final: 0.8362 (t80) REVERT: B 1098 ILE cc_start: 0.8946 (tt) cc_final: 0.8593 (tp) REVERT: B 1118 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8336 (mtmm) REVERT: B 1121 LEU cc_start: 0.8997 (mm) cc_final: 0.8725 (mt) REVERT: B 1136 PHE cc_start: 0.6967 (t80) cc_final: 0.6579 (t80) REVERT: B 1143 GLU cc_start: 0.7715 (tt0) cc_final: 0.7399 (tt0) REVERT: B 1162 ARG cc_start: 0.5736 (OUTLIER) cc_final: 0.5149 (tpm-80) REVERT: B 1179 THR cc_start: 0.5421 (OUTLIER) cc_final: 0.5144 (p) REVERT: B 1212 ILE cc_start: 0.5476 (OUTLIER) cc_final: 0.5116 (mp) outliers start: 99 outliers final: 55 residues processed: 596 average time/residue: 0.3447 time to fit residues: 295.5304 Evaluate side-chains 608 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 540 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 981 HIS Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 MET Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1158 ARG Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1154 ASN Chi-restraints excluded: chain B residue 1156 HIS Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1199 LEU Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 95 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 107 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 600 HIS A 981 HIS B 165 GLN B 914 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.142333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119034 restraints weight = 25232.720| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.06 r_work: 0.3381 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16740 Z= 0.174 Angle : 0.641 16.405 22706 Z= 0.318 Chirality : 0.042 0.179 2734 Planarity : 0.005 0.062 2796 Dihedral : 7.405 135.349 2282 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.91 % Allowed : 20.54 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.19), residues: 2050 helix: 1.79 (0.14), residues: 1452 sheet: -2.18 (0.56), residues: 72 loop : -1.78 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1112 HIS 0.005 0.001 HIS A 981 PHE 0.021 0.001 PHE A 972 TYR 0.010 0.001 TYR B 191 ARG 0.009 0.001 ARG B1185 Details of bonding type rmsd hydrogen bonds : bond 0.05119 ( 1163) hydrogen bonds : angle 4.32346 ( 3459) covalent geometry : bond 0.00373 (16740) covalent geometry : angle 0.64060 (22706) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 547 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8737 (mm) cc_final: 0.8370 (mt) REVERT: A 116 VAL cc_start: 0.8780 (t) cc_final: 0.8522 (t) REVERT: A 149 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7416 (tm-30) REVERT: A 163 PHE cc_start: 0.8339 (t80) cc_final: 0.8120 (t80) REVERT: A 199 MET cc_start: 0.8474 (mmm) cc_final: 0.8151 (mmm) REVERT: A 233 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7502 (tm-30) REVERT: A 280 TYR cc_start: 0.8440 (t80) cc_final: 0.8137 (t80) REVERT: A 337 GLU cc_start: 0.7728 (tp30) cc_final: 0.7405 (tp30) REVERT: A 346 GLU cc_start: 0.7787 (tt0) cc_final: 0.7573 (tt0) REVERT: A 354 GLU cc_start: 0.8191 (tt0) cc_final: 0.7849 (tt0) REVERT: A 377 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8362 (mp) REVERT: A 383 MET cc_start: 0.7123 (mmm) cc_final: 0.6584 (mmm) REVERT: A 443 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8038 (tm-30) REVERT: A 487 SER cc_start: 0.8177 (t) cc_final: 0.7825 (p) REVERT: A 511 MET cc_start: 0.8869 (tmm) cc_final: 0.8538 (tmm) REVERT: A 531 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7080 (tm-30) REVERT: A 554 GLU cc_start: 0.8143 (tp30) cc_final: 0.7838 (tp30) REVERT: A 580 GLU cc_start: 0.8088 (tp30) cc_final: 0.7673 (tp30) REVERT: A 609 ARG cc_start: 0.8423 (ttm170) cc_final: 0.8109 (ttm-80) REVERT: A 632 LYS cc_start: 0.8238 (ttpt) cc_final: 0.7922 (ttmm) REVERT: A 634 SER cc_start: 0.8868 (m) cc_final: 0.8618 (t) REVERT: A 697 MET cc_start: 0.6519 (mmm) cc_final: 0.5910 (mmm) REVERT: A 815 LYS cc_start: 0.9028 (tttt) cc_final: 0.8640 (tppp) REVERT: A 820 LYS cc_start: 0.8296 (mmmt) cc_final: 0.8012 (mmmt) REVERT: A 828 LYS cc_start: 0.8492 (mmmm) cc_final: 0.8220 (mmmm) REVERT: A 841 LYS cc_start: 0.8721 (mtpt) cc_final: 0.8500 (mtpt) REVERT: A 853 ILE cc_start: 0.8676 (tp) cc_final: 0.8414 (tp) REVERT: A 884 LEU cc_start: 0.8478 (mm) cc_final: 0.8174 (mt) REVERT: A 937 LYS cc_start: 0.8730 (mttm) cc_final: 0.8299 (mmtp) REVERT: A 942 MET cc_start: 0.8604 (tpp) cc_final: 0.8237 (tpt) REVERT: A 983 ASP cc_start: 0.7912 (t0) cc_final: 0.7701 (p0) REVERT: A 989 VAL cc_start: 0.7985 (t) cc_final: 0.7714 (t) REVERT: A 994 GLU cc_start: 0.7860 (pm20) cc_final: 0.7507 (pm20) REVERT: A 1006 VAL cc_start: 0.8523 (m) cc_final: 0.8223 (t) REVERT: A 1008 LEU cc_start: 0.8179 (mp) cc_final: 0.7842 (tp) REVERT: A 1044 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7545 (mt-10) REVERT: A 1060 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7748 (mm-30) REVERT: A 1061 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7370 (p) REVERT: A 1066 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7681 (m-80) REVERT: A 1072 ASP cc_start: 0.7678 (m-30) cc_final: 0.7449 (m-30) REVERT: A 1073 MET cc_start: 0.8739 (tpp) cc_final: 0.8515 (tpp) REVERT: A 1080 PHE cc_start: 0.7998 (m-80) cc_final: 0.7559 (m-80) REVERT: A 1087 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7119 (tm-30) REVERT: A 1104 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7663 (tpp) REVERT: A 1185 ARG cc_start: 0.7050 (mmt180) cc_final: 0.6788 (mmm-85) REVERT: A 1190 ARG cc_start: 0.8094 (mmm-85) cc_final: 0.7721 (mmm-85) REVERT: A 1212 ILE cc_start: 0.5620 (OUTLIER) cc_final: 0.5027 (mp) REVERT: A 1220 ASN cc_start: 0.7846 (m-40) cc_final: 0.7607 (m-40) REVERT: B 116 VAL cc_start: 0.8674 (t) cc_final: 0.8367 (m) REVERT: B 128 ARG cc_start: 0.7756 (tmm-80) cc_final: 0.7392 (ttp80) REVERT: B 134 ASP cc_start: 0.8154 (t0) cc_final: 0.7837 (t70) REVERT: B 149 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7427 (tm-30) REVERT: B 155 ASP cc_start: 0.8199 (t0) cc_final: 0.7738 (t0) REVERT: B 163 PHE cc_start: 0.8404 (t80) cc_final: 0.8140 (t80) REVERT: B 231 GLU cc_start: 0.8106 (tt0) cc_final: 0.7905 (tt0) REVERT: B 233 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7659 (tm-30) REVERT: B 250 LYS cc_start: 0.8408 (mttt) cc_final: 0.8166 (mttm) REVERT: B 265 VAL cc_start: 0.8665 (t) cc_final: 0.8377 (p) REVERT: B 337 GLU cc_start: 0.7739 (tp30) cc_final: 0.7406 (tp30) REVERT: B 375 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8484 (mtpp) REVERT: B 383 MET cc_start: 0.7298 (tpp) cc_final: 0.6832 (mmm) REVERT: B 385 TRP cc_start: 0.8436 (m100) cc_final: 0.8167 (m100) REVERT: B 407 SER cc_start: 0.8811 (t) cc_final: 0.8579 (p) REVERT: B 419 TRP cc_start: 0.8098 (p-90) cc_final: 0.7801 (p-90) REVERT: B 483 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8146 (mtp) REVERT: B 487 SER cc_start: 0.8356 (t) cc_final: 0.8089 (p) REVERT: B 511 MET cc_start: 0.8874 (tmm) cc_final: 0.8547 (ttp) REVERT: B 579 MET cc_start: 0.7994 (tpp) cc_final: 0.7712 (tpp) REVERT: B 584 LEU cc_start: 0.8811 (mm) cc_final: 0.8607 (mm) REVERT: B 588 LYS cc_start: 0.8617 (tppt) cc_final: 0.8385 (tttp) REVERT: B 621 GLU cc_start: 0.7690 (pp20) cc_final: 0.7353 (pm20) REVERT: B 634 SER cc_start: 0.8949 (m) cc_final: 0.8722 (t) REVERT: B 697 MET cc_start: 0.5844 (mmm) cc_final: 0.5203 (mmm) REVERT: B 736 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.7991 (t0) REVERT: B 810 MET cc_start: 0.7047 (ptt) cc_final: 0.6840 (ptt) REVERT: B 820 LYS cc_start: 0.8168 (mmmt) cc_final: 0.7927 (mmmt) REVERT: B 852 LYS cc_start: 0.8535 (mttp) cc_final: 0.8096 (mtpt) REVERT: B 853 ILE cc_start: 0.8995 (tp) cc_final: 0.8646 (tt) REVERT: B 859 ASP cc_start: 0.8022 (p0) cc_final: 0.7769 (p0) REVERT: B 954 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7587 (mm-30) REVERT: B 958 LYS cc_start: 0.8895 (ttpt) cc_final: 0.8502 (ttmm) REVERT: B 968 LYS cc_start: 0.8691 (mtpp) cc_final: 0.8383 (mmmm) REVERT: B 972 PHE cc_start: 0.8781 (t80) cc_final: 0.8380 (t80) REVERT: B 993 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.6973 (m-30) REVERT: B 994 GLU cc_start: 0.7796 (pm20) cc_final: 0.7395 (pm20) REVERT: B 1003 SER cc_start: 0.8309 (t) cc_final: 0.7844 (m) REVERT: B 1005 LEU cc_start: 0.8529 (tp) cc_final: 0.8294 (tt) REVERT: B 1066 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8000 (m-80) REVERT: B 1075 ILE cc_start: 0.8986 (mt) cc_final: 0.8671 (tt) REVERT: B 1098 ILE cc_start: 0.8938 (tt) cc_final: 0.8586 (tp) REVERT: B 1118 LYS cc_start: 0.8605 (mtpp) cc_final: 0.8328 (mtmm) REVERT: B 1121 LEU cc_start: 0.9001 (mm) cc_final: 0.8750 (mt) REVERT: B 1143 GLU cc_start: 0.7792 (tt0) cc_final: 0.7478 (tt0) REVERT: B 1162 ARG cc_start: 0.5737 (OUTLIER) cc_final: 0.5130 (tpm-80) REVERT: B 1179 THR cc_start: 0.5179 (OUTLIER) cc_final: 0.4915 (p) REVERT: B 1212 ILE cc_start: 0.5470 (OUTLIER) cc_final: 0.5111 (mp) outliers start: 88 outliers final: 61 residues processed: 591 average time/residue: 0.3296 time to fit residues: 278.5108 Evaluate side-chains 614 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 539 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 981 HIS Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 MET Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1158 ARG Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1154 ASN Chi-restraints excluded: chain B residue 1156 HIS Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1212 ILE Chi-restraints excluded: chain B residue 1220 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 192 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.142684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.119544 restraints weight = 25128.314| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.05 r_work: 0.3377 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16740 Z= 0.168 Angle : 0.640 16.387 22706 Z= 0.318 Chirality : 0.042 0.172 2734 Planarity : 0.005 0.062 2796 Dihedral : 7.353 134.335 2282 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.13 % Allowed : 21.26 % Favored : 73.60 % 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: 1.25 (0.19), residues: 2050 helix: 1.87 (0.14), residues: 1452 sheet: -2.20 (0.51), residues: 92 loop : -1.70 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1112 HIS 0.007 0.001 HIS A 981 PHE 0.018 0.001 PHE A 575 TYR 0.010 0.001 TYR B 415 ARG 0.007 0.000 ARG B1185 Details of bonding type rmsd hydrogen bonds : bond 0.05048 ( 1163) hydrogen bonds : angle 4.29959 ( 3459) covalent geometry : bond 0.00356 (16740) covalent geometry : angle 0.64038 (22706) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 550 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8180 (mt) REVERT: A 112 ILE cc_start: 0.8746 (mm) cc_final: 0.8380 (mt) REVERT: A 116 VAL cc_start: 0.8769 (t) cc_final: 0.8526 (t) REVERT: A 149 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7490 (tm-30) REVERT: A 163 PHE cc_start: 0.8414 (t80) cc_final: 0.8186 (t80) REVERT: A 165 GLN cc_start: 0.8705 (tt0) cc_final: 0.8475 (tt0) REVERT: A 199 MET cc_start: 0.8482 (mmm) cc_final: 0.8177 (mmm) REVERT: A 280 TYR cc_start: 0.8415 (t80) cc_final: 0.8114 (t80) REVERT: A 337 GLU cc_start: 0.7748 (tp30) cc_final: 0.7425 (tp30) REVERT: A 346 GLU cc_start: 0.7792 (tt0) cc_final: 0.7577 (tt0) REVERT: A 354 GLU cc_start: 0.8191 (tt0) cc_final: 0.7839 (tt0) REVERT: A 375 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8493 (ttpp) REVERT: A 377 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8380 (mp) REVERT: A 383 MET cc_start: 0.7094 (mmm) cc_final: 0.6565 (mmm) REVERT: A 411 SER cc_start: 0.8519 (p) cc_final: 0.8229 (p) REVERT: A 454 LYS cc_start: 0.8765 (mmtp) cc_final: 0.8383 (mmtt) REVERT: A 486 ILE cc_start: 0.8805 (mm) cc_final: 0.8559 (mp) REVERT: A 487 SER cc_start: 0.8187 (t) cc_final: 0.7835 (p) REVERT: A 492 LEU cc_start: 0.8660 (tp) cc_final: 0.8433 (tp) REVERT: A 511 MET cc_start: 0.8856 (tmm) cc_final: 0.8523 (tmm) REVERT: A 531 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7071 (tm-30) REVERT: A 554 GLU cc_start: 0.8145 (tp30) cc_final: 0.7817 (tp30) REVERT: A 569 GLU cc_start: 0.8533 (tp30) cc_final: 0.8264 (tp30) REVERT: A 578 MET cc_start: 0.8612 (mtp) cc_final: 0.8385 (mmm) REVERT: A 579 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8014 (mmm) REVERT: A 580 GLU cc_start: 0.8192 (tp30) cc_final: 0.7654 (tp30) REVERT: A 609 ARG cc_start: 0.8442 (ttm170) cc_final: 0.8147 (ttm-80) REVERT: A 632 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7937 (ttmm) REVERT: A 634 SER cc_start: 0.8863 (m) cc_final: 0.8625 (t) REVERT: A 697 MET cc_start: 0.6581 (mmm) cc_final: 0.5954 (mmm) REVERT: A 815 LYS cc_start: 0.9010 (tttt) cc_final: 0.8637 (tppp) REVERT: A 820 LYS cc_start: 0.8288 (mmmt) cc_final: 0.7996 (mmmt) REVERT: A 828 LYS cc_start: 0.8469 (mmmm) cc_final: 0.8198 (mmmm) REVERT: A 841 LYS cc_start: 0.8731 (mtpt) cc_final: 0.8507 (mtpt) REVERT: A 853 ILE cc_start: 0.8668 (tp) cc_final: 0.8365 (tp) REVERT: A 884 LEU cc_start: 0.8492 (mm) cc_final: 0.8172 (mt) REVERT: A 917 GLN cc_start: 0.8696 (tt0) cc_final: 0.8300 (tt0) REVERT: A 942 MET cc_start: 0.8590 (tpp) cc_final: 0.8221 (tpt) REVERT: A 983 ASP cc_start: 0.7934 (t0) cc_final: 0.7725 (p0) REVERT: A 989 VAL cc_start: 0.7427 (t) cc_final: 0.7208 (t) REVERT: A 994 GLU cc_start: 0.7818 (pm20) cc_final: 0.7424 (pm20) REVERT: A 1006 VAL cc_start: 0.8505 (m) cc_final: 0.8231 (p) REVERT: A 1008 LEU cc_start: 0.8199 (mp) cc_final: 0.7821 (tp) REVERT: A 1035 TYR cc_start: 0.8226 (m-80) cc_final: 0.7688 (m-80) REVERT: A 1041 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8037 (p) REVERT: A 1060 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7643 (mm-30) REVERT: A 1061 THR cc_start: 0.7739 (OUTLIER) cc_final: 0.7496 (p) REVERT: A 1072 ASP cc_start: 0.7682 (m-30) cc_final: 0.7475 (m-30) REVERT: A 1073 MET cc_start: 0.8739 (tpp) cc_final: 0.8534 (tpp) REVERT: A 1080 PHE cc_start: 0.7985 (m-80) cc_final: 0.7543 (m-80) REVERT: A 1104 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7672 (tpp) REVERT: A 1113 THR cc_start: 0.8208 (p) cc_final: 0.7983 (t) REVERT: A 1139 ASP cc_start: 0.7654 (m-30) cc_final: 0.7262 (m-30) REVERT: A 1143 GLU cc_start: 0.7917 (tt0) cc_final: 0.7616 (tp30) REVERT: A 1173 LYS cc_start: 0.7697 (pttp) cc_final: 0.7459 (pttp) REVERT: A 1190 ARG cc_start: 0.8081 (mmm-85) cc_final: 0.7721 (mmm-85) REVERT: A 1220 ASN cc_start: 0.7862 (m-40) cc_final: 0.7596 (m-40) REVERT: B 96 LYS cc_start: 0.8417 (mmmm) cc_final: 0.7984 (tppp) REVERT: B 103 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8203 (p) REVERT: B 116 VAL cc_start: 0.8675 (t) cc_final: 0.8332 (m) REVERT: B 128 ARG cc_start: 0.7738 (tmm-80) cc_final: 0.7376 (ttp80) REVERT: B 149 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7428 (tm-30) REVERT: B 155 ASP cc_start: 0.8166 (t0) cc_final: 0.7687 (t0) REVERT: B 163 PHE cc_start: 0.8387 (t80) cc_final: 0.8145 (t80) REVERT: B 205 MET cc_start: 0.8445 (mmp) cc_final: 0.8025 (mmp) REVERT: B 250 LYS cc_start: 0.8411 (mttt) cc_final: 0.8129 (mttm) REVERT: B 263 GLN cc_start: 0.8267 (mt0) cc_final: 0.7947 (mt0) REVERT: B 265 VAL cc_start: 0.8642 (t) cc_final: 0.8363 (p) REVERT: B 337 GLU cc_start: 0.7765 (tp30) cc_final: 0.7412 (tp30) REVERT: B 375 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8509 (mtpp) REVERT: B 383 MET cc_start: 0.7311 (tpp) cc_final: 0.6816 (mmm) REVERT: B 407 SER cc_start: 0.8816 (t) cc_final: 0.8580 (p) REVERT: B 419 TRP cc_start: 0.8096 (p-90) cc_final: 0.7769 (p-90) REVERT: B 487 SER cc_start: 0.8383 (t) cc_final: 0.8107 (p) REVERT: B 511 MET cc_start: 0.8858 (tmm) cc_final: 0.8534 (ttp) REVERT: B 579 MET cc_start: 0.7921 (tpp) cc_final: 0.7688 (tpp) REVERT: B 581 GLU cc_start: 0.8294 (tp30) cc_final: 0.8018 (tp30) REVERT: B 584 LEU cc_start: 0.8794 (mm) cc_final: 0.8593 (mm) REVERT: B 588 LYS cc_start: 0.8600 (tppt) cc_final: 0.8372 (tttp) REVERT: B 599 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7654 (mt-10) REVERT: B 621 GLU cc_start: 0.7706 (pp20) cc_final: 0.7423 (pp20) REVERT: B 634 SER cc_start: 0.8927 (m) cc_final: 0.8687 (t) REVERT: B 697 MET cc_start: 0.5868 (mmm) cc_final: 0.5216 (mmm) REVERT: B 736 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.7997 (t0) REVERT: B 810 MET cc_start: 0.7018 (ptt) cc_final: 0.6801 (ptt) REVERT: B 815 LYS cc_start: 0.9078 (tttt) cc_final: 0.8698 (tttp) REVERT: B 820 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7908 (mmmt) REVERT: B 852 LYS cc_start: 0.8553 (mttp) cc_final: 0.8126 (mtpt) REVERT: B 853 ILE cc_start: 0.9018 (tp) cc_final: 0.8667 (tt) REVERT: B 859 ASP cc_start: 0.7999 (p0) cc_final: 0.7764 (p0) REVERT: B 877 GLN cc_start: 0.8636 (tt0) cc_final: 0.8317 (tt0) REVERT: B 954 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7615 (mm-30) REVERT: B 958 LYS cc_start: 0.8882 (ttpt) cc_final: 0.8487 (ttmm) REVERT: B 968 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8391 (mmmm) REVERT: B 972 PHE cc_start: 0.8781 (t80) cc_final: 0.8403 (t80) REVERT: B 993 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7005 (m-30) REVERT: B 1003 SER cc_start: 0.8322 (t) cc_final: 0.7900 (m) REVERT: B 1005 LEU cc_start: 0.8546 (tp) cc_final: 0.8324 (tt) REVERT: B 1035 TYR cc_start: 0.8165 (m-80) cc_final: 0.7851 (m-80) REVERT: B 1066 TYR cc_start: 0.8623 (m-80) cc_final: 0.8326 (m-80) REVERT: B 1118 LYS cc_start: 0.8607 (mtpp) cc_final: 0.8324 (mtmm) REVERT: B 1121 LEU cc_start: 0.9003 (mm) cc_final: 0.8762 (mt) REVERT: B 1138 ILE cc_start: 0.8387 (mm) cc_final: 0.8163 (mp) REVERT: B 1143 GLU cc_start: 0.7801 (tt0) cc_final: 0.7344 (tm-30) REVERT: B 1162 ARG cc_start: 0.5769 (OUTLIER) cc_final: 0.5144 (tpm-80) REVERT: B 1179 THR cc_start: 0.5193 (OUTLIER) cc_final: 0.4927 (p) REVERT: B 1212 ILE cc_start: 0.5501 (OUTLIER) cc_final: 0.5109 (mp) REVERT: B 1221 MET cc_start: 0.8063 (mmt) cc_final: 0.7519 (mmt) outliers start: 92 outliers final: 63 residues processed: 594 average time/residue: 0.3351 time to fit residues: 284.9633 Evaluate side-chains 614 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 537 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 981 HIS Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 MET Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1158 ARG Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1154 ASN Chi-restraints excluded: chain B residue 1156 HIS Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 0.9980 chunk 160 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS B 165 GLN B1220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.141969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.118831 restraints weight = 25127.288| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.04 r_work: 0.3371 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16740 Z= 0.191 Angle : 0.656 16.366 22706 Z= 0.325 Chirality : 0.042 0.175 2734 Planarity : 0.005 0.062 2796 Dihedral : 7.218 133.862 2276 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.41 % Allowed : 21.43 % Favored : 73.16 % 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: 1.23 (0.19), residues: 2050 helix: 1.82 (0.14), residues: 1458 sheet: -2.18 (0.51), residues: 96 loop : -1.63 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1112 HIS 0.004 0.001 HIS A 981 PHE 0.021 0.002 PHE A 598 TYR 0.014 0.001 TYR B 415 ARG 0.009 0.000 ARG B1053 Details of bonding type rmsd hydrogen bonds : bond 0.05211 ( 1163) hydrogen bonds : angle 4.31633 ( 3459) covalent geometry : bond 0.00413 (16740) covalent geometry : angle 0.65554 (22706) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 549 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8176 (mt) REVERT: A 112 ILE cc_start: 0.8768 (mm) cc_final: 0.8400 (mt) REVERT: A 116 VAL cc_start: 0.8819 (t) cc_final: 0.8569 (t) REVERT: A 149 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7463 (tm-30) REVERT: A 163 PHE cc_start: 0.8399 (t80) cc_final: 0.8188 (t80) REVERT: A 199 MET cc_start: 0.8487 (mmm) cc_final: 0.8128 (mmm) REVERT: A 229 ILE cc_start: 0.8365 (mm) cc_final: 0.8165 (mt) REVERT: A 280 TYR cc_start: 0.8418 (t80) cc_final: 0.8116 (t80) REVERT: A 337 GLU cc_start: 0.7765 (tp30) cc_final: 0.7443 (tp30) REVERT: A 346 GLU cc_start: 0.7768 (tt0) cc_final: 0.7552 (tt0) REVERT: A 354 GLU cc_start: 0.8201 (tt0) cc_final: 0.7859 (tt0) REVERT: A 375 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8427 (ttpp) REVERT: A 383 MET cc_start: 0.7093 (mmm) cc_final: 0.6564 (mmm) REVERT: A 411 SER cc_start: 0.8531 (p) cc_final: 0.8225 (p) REVERT: A 486 ILE cc_start: 0.8813 (mm) cc_final: 0.8576 (mp) REVERT: A 487 SER cc_start: 0.8199 (t) cc_final: 0.7843 (p) REVERT: A 511 MET cc_start: 0.8859 (tmm) cc_final: 0.8526 (ttp) REVERT: A 531 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7071 (tm-30) REVERT: A 554 GLU cc_start: 0.8151 (tp30) cc_final: 0.7809 (tp30) REVERT: A 578 MET cc_start: 0.8580 (mtp) cc_final: 0.8340 (mmm) REVERT: A 579 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.8005 (mmm) REVERT: A 580 GLU cc_start: 0.8181 (tp30) cc_final: 0.7792 (tp30) REVERT: A 599 GLU cc_start: 0.7718 (mp0) cc_final: 0.7446 (mp0) REVERT: A 609 ARG cc_start: 0.8382 (ttm170) cc_final: 0.8125 (ttm-80) REVERT: A 632 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7945 (ttmm) REVERT: A 634 SER cc_start: 0.8851 (m) cc_final: 0.8631 (t) REVERT: A 697 MET cc_start: 0.6494 (mmm) cc_final: 0.5815 (mmm) REVERT: A 820 LYS cc_start: 0.8269 (mmmt) cc_final: 0.7976 (mmmt) REVERT: A 841 LYS cc_start: 0.8725 (mtpt) cc_final: 0.8493 (mtpt) REVERT: A 853 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8434 (tp) REVERT: A 884 LEU cc_start: 0.8522 (mm) cc_final: 0.8193 (mt) REVERT: A 917 GLN cc_start: 0.8703 (tt0) cc_final: 0.8296 (tt0) REVERT: A 942 MET cc_start: 0.8582 (tpp) cc_final: 0.8236 (tpt) REVERT: A 983 ASP cc_start: 0.7941 (t0) cc_final: 0.7737 (p0) REVERT: A 994 GLU cc_start: 0.7781 (pm20) cc_final: 0.7391 (pm20) REVERT: A 1006 VAL cc_start: 0.8471 (m) cc_final: 0.8229 (p) REVERT: A 1008 LEU cc_start: 0.8199 (mp) cc_final: 0.7996 (mm) REVERT: A 1035 TYR cc_start: 0.8247 (m-80) cc_final: 0.7740 (m-80) REVERT: A 1041 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8031 (p) REVERT: A 1060 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7729 (mm-30) REVERT: A 1061 THR cc_start: 0.7734 (OUTLIER) cc_final: 0.7323 (p) REVERT: A 1072 ASP cc_start: 0.7713 (m-30) cc_final: 0.7498 (m-30) REVERT: A 1080 PHE cc_start: 0.7984 (m-80) cc_final: 0.7561 (m-80) REVERT: A 1087 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7119 (tm-30) REVERT: A 1104 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7692 (tpp) REVERT: A 1113 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.8040 (t) REVERT: A 1139 ASP cc_start: 0.7628 (m-30) cc_final: 0.7283 (m-30) REVERT: A 1143 GLU cc_start: 0.7898 (tt0) cc_final: 0.7577 (tp30) REVERT: A 1185 ARG cc_start: 0.6930 (mmt180) cc_final: 0.6584 (mmm-85) REVERT: A 1190 ARG cc_start: 0.7998 (mmm-85) cc_final: 0.7645 (mmm-85) REVERT: A 1220 ASN cc_start: 0.7875 (m-40) cc_final: 0.7599 (m-40) REVERT: B 96 LYS cc_start: 0.8413 (mmmm) cc_final: 0.7963 (tppp) REVERT: B 103 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8225 (p) REVERT: B 116 VAL cc_start: 0.8698 (t) cc_final: 0.8348 (m) REVERT: B 128 ARG cc_start: 0.7774 (tmm-80) cc_final: 0.7413 (ttp80) REVERT: B 134 ASP cc_start: 0.8165 (t0) cc_final: 0.7873 (t70) REVERT: B 149 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7431 (tm-30) REVERT: B 155 ASP cc_start: 0.8148 (t0) cc_final: 0.7666 (t0) REVERT: B 205 MET cc_start: 0.8461 (mmp) cc_final: 0.8049 (mmp) REVERT: B 231 GLU cc_start: 0.8088 (tt0) cc_final: 0.7864 (tt0) REVERT: B 250 LYS cc_start: 0.8435 (mttt) cc_final: 0.8158 (mttm) REVERT: B 265 VAL cc_start: 0.8641 (t) cc_final: 0.8358 (p) REVERT: B 337 GLU cc_start: 0.7726 (tp30) cc_final: 0.7364 (tp30) REVERT: B 375 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8486 (mtpp) REVERT: B 383 MET cc_start: 0.7333 (tpp) cc_final: 0.6856 (mmm) REVERT: B 385 TRP cc_start: 0.8419 (m100) cc_final: 0.8181 (m100) REVERT: B 407 SER cc_start: 0.8808 (t) cc_final: 0.8567 (p) REVERT: B 419 TRP cc_start: 0.8081 (p-90) cc_final: 0.7775 (p-90) REVERT: B 483 MET cc_start: 0.8373 (mtm) cc_final: 0.8140 (mtp) REVERT: B 487 SER cc_start: 0.8380 (t) cc_final: 0.8109 (p) REVERT: B 511 MET cc_start: 0.8875 (tmm) cc_final: 0.8567 (ttp) REVERT: B 579 MET cc_start: 0.7868 (tpp) cc_final: 0.7665 (tpp) REVERT: B 588 LYS cc_start: 0.8619 (tppt) cc_final: 0.8385 (tttp) REVERT: B 621 GLU cc_start: 0.7732 (pp20) cc_final: 0.7464 (pm20) REVERT: B 628 VAL cc_start: 0.8140 (OUTLIER) cc_final: 0.7900 (t) REVERT: B 634 SER cc_start: 0.8909 (m) cc_final: 0.8669 (t) REVERT: B 697 MET cc_start: 0.5830 (mmm) cc_final: 0.5152 (mmm) REVERT: B 736 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.7991 (t0) REVERT: B 810 MET cc_start: 0.7024 (ptt) cc_final: 0.6807 (ptt) REVERT: B 815 LYS cc_start: 0.9057 (tttt) cc_final: 0.8677 (tptt) REVERT: B 820 LYS cc_start: 0.8159 (mmmt) cc_final: 0.7912 (mmmt) REVERT: B 852 LYS cc_start: 0.8612 (mttp) cc_final: 0.8155 (mtpt) REVERT: B 853 ILE cc_start: 0.9050 (tp) cc_final: 0.8743 (tt) REVERT: B 856 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7723 (ttp80) REVERT: B 877 GLN cc_start: 0.8586 (tt0) cc_final: 0.8327 (tt0) REVERT: B 954 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7628 (mm-30) REVERT: B 958 LYS cc_start: 0.8869 (ttpt) cc_final: 0.8478 (ttmm) REVERT: B 968 LYS cc_start: 0.8706 (mtpp) cc_final: 0.8387 (mmmm) REVERT: B 972 PHE cc_start: 0.8790 (t80) cc_final: 0.8433 (t80) REVERT: B 1003 SER cc_start: 0.8364 (t) cc_final: 0.8015 (m) REVERT: B 1005 LEU cc_start: 0.8525 (tp) cc_final: 0.8302 (tt) REVERT: B 1035 TYR cc_start: 0.8326 (m-80) cc_final: 0.7884 (m-80) REVERT: B 1066 TYR cc_start: 0.8633 (m-80) cc_final: 0.8323 (m-80) REVERT: B 1118 LYS cc_start: 0.8581 (mtpp) cc_final: 0.8304 (mtmm) REVERT: B 1121 LEU cc_start: 0.9017 (mm) cc_final: 0.8787 (mt) REVERT: B 1136 PHE cc_start: 0.6652 (t80) cc_final: 0.6449 (t80) REVERT: B 1143 GLU cc_start: 0.7885 (tt0) cc_final: 0.7394 (tm-30) REVERT: B 1156 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7752 (p-80) REVERT: B 1162 ARG cc_start: 0.5768 (OUTLIER) cc_final: 0.5107 (tpm-80) REVERT: B 1179 THR cc_start: 0.5190 (OUTLIER) cc_final: 0.4959 (p) REVERT: B 1212 ILE cc_start: 0.5544 (OUTLIER) cc_final: 0.5116 (mp) outliers start: 97 outliers final: 69 residues processed: 588 average time/residue: 0.3877 time to fit residues: 330.0682 Evaluate side-chains 623 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 537 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 981 HIS Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1104 MET Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1158 ARG Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1154 ASN Chi-restraints excluded: chain B residue 1156 HIS Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 204 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 chunk 172 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 125 optimal weight: 0.2980 chunk 53 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 943 ASN A 981 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.143272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120222 restraints weight = 24929.190| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.06 r_work: 0.3398 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16740 Z= 0.151 Angle : 0.653 16.049 22706 Z= 0.323 Chirality : 0.042 0.173 2734 Planarity : 0.005 0.064 2796 Dihedral : 7.187 134.010 2276 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.08 % Allowed : 22.21 % Favored : 72.71 % 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: 1.33 (0.19), residues: 2050 helix: 1.91 (0.14), residues: 1458 sheet: -2.25 (0.55), residues: 82 loop : -1.68 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1112 HIS 0.004 0.001 HIS B 981 PHE 0.024 0.001 PHE B 680 TYR 0.015 0.001 TYR B1009 ARG 0.012 0.000 ARG B1053 Details of bonding type rmsd hydrogen bonds : bond 0.04908 ( 1163) hydrogen bonds : angle 4.27905 ( 3459) covalent geometry : bond 0.00319 (16740) covalent geometry : angle 0.65308 (22706) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 534 time to evaluate : 1.907 Fit side-chains revert: symmetry clash REVERT: A 94 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8144 (mt) REVERT: A 112 ILE cc_start: 0.8753 (mm) cc_final: 0.8377 (mt) REVERT: A 116 VAL cc_start: 0.8741 (t) cc_final: 0.8490 (t) REVERT: A 149 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7437 (tm-30) REVERT: A 163 PHE cc_start: 0.8389 (t80) cc_final: 0.8053 (t80) REVERT: A 199 MET cc_start: 0.8496 (mmm) cc_final: 0.8182 (mmm) REVERT: A 280 TYR cc_start: 0.8417 (t80) cc_final: 0.8106 (t80) REVERT: A 284 LYS cc_start: 0.8402 (mmmm) cc_final: 0.8136 (mmmm) REVERT: A 337 GLU cc_start: 0.7751 (tp30) cc_final: 0.7452 (tp30) REVERT: A 346 GLU cc_start: 0.7713 (tt0) cc_final: 0.7356 (tt0) REVERT: A 354 GLU cc_start: 0.8163 (tt0) cc_final: 0.7818 (tt0) REVERT: A 375 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8479 (ttpp) REVERT: A 383 MET cc_start: 0.7020 (mmm) cc_final: 0.6505 (mmm) REVERT: A 387 TYR cc_start: 0.8690 (m-10) cc_final: 0.8319 (m-10) REVERT: A 411 SER cc_start: 0.8509 (p) cc_final: 0.8229 (p) REVERT: A 487 SER cc_start: 0.8204 (t) cc_final: 0.7847 (p) REVERT: A 511 MET cc_start: 0.8849 (tmm) cc_final: 0.8528 (tmm) REVERT: A 531 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6998 (tm-30) REVERT: A 554 GLU cc_start: 0.8145 (tp30) cc_final: 0.7801 (tp30) REVERT: A 569 GLU cc_start: 0.8464 (tp30) cc_final: 0.8216 (tp30) REVERT: A 578 MET cc_start: 0.8503 (mtp) cc_final: 0.8214 (mmm) REVERT: A 579 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7980 (mmm) REVERT: A 580 GLU cc_start: 0.8135 (tp30) cc_final: 0.7782 (tp30) REVERT: A 599 GLU cc_start: 0.7696 (mp0) cc_final: 0.7439 (mp0) REVERT: A 609 ARG cc_start: 0.8324 (ttm170) cc_final: 0.8012 (ttm-80) REVERT: A 632 LYS cc_start: 0.8168 (ttpt) cc_final: 0.7896 (ttmm) REVERT: A 634 SER cc_start: 0.8833 (m) cc_final: 0.8615 (t) REVERT: A 697 MET cc_start: 0.6471 (mmm) cc_final: 0.5808 (mmm) REVERT: A 815 LYS cc_start: 0.8971 (tttt) cc_final: 0.8604 (tppp) REVERT: A 820 LYS cc_start: 0.8243 (mmmt) cc_final: 0.7962 (mmmt) REVERT: A 841 LYS cc_start: 0.8721 (mtpt) cc_final: 0.8478 (mtpt) REVERT: A 853 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8452 (tp) REVERT: A 884 LEU cc_start: 0.8491 (mm) cc_final: 0.8192 (mt) REVERT: A 942 MET cc_start: 0.8620 (tpp) cc_final: 0.8273 (tpt) REVERT: A 994 GLU cc_start: 0.7742 (pm20) cc_final: 0.7290 (pm20) REVERT: A 1006 VAL cc_start: 0.8437 (m) cc_final: 0.8184 (p) REVERT: A 1035 TYR cc_start: 0.8151 (m-80) cc_final: 0.7608 (m-80) REVERT: A 1044 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7393 (mt-10) REVERT: A 1060 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7641 (mm-30) REVERT: A 1061 THR cc_start: 0.7700 (OUTLIER) cc_final: 0.7450 (p) REVERT: A 1080 PHE cc_start: 0.7962 (m-80) cc_final: 0.7544 (m-80) REVERT: A 1087 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: A 1104 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7687 (tpp) REVERT: A 1139 ASP cc_start: 0.7629 (m-30) cc_final: 0.7275 (m-30) REVERT: A 1143 GLU cc_start: 0.7913 (tt0) cc_final: 0.7564 (tp30) REVERT: A 1185 ARG cc_start: 0.6786 (mmt180) cc_final: 0.6544 (mmm-85) REVERT: A 1190 ARG cc_start: 0.8076 (mmm-85) cc_final: 0.7703 (mmm-85) REVERT: A 1220 ASN cc_start: 0.7903 (m-40) cc_final: 0.7623 (m-40) REVERT: B 116 VAL cc_start: 0.8676 (t) cc_final: 0.8308 (m) REVERT: B 134 ASP cc_start: 0.8140 (t0) cc_final: 0.7801 (t70) REVERT: B 149 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7440 (tm-30) REVERT: B 155 ASP cc_start: 0.8153 (t0) cc_final: 0.7694 (t0) REVERT: B 163 PHE cc_start: 0.8312 (t80) cc_final: 0.8060 (t80) REVERT: B 199 MET cc_start: 0.8718 (mmm) cc_final: 0.8486 (tpp) REVERT: B 205 MET cc_start: 0.8442 (mmp) cc_final: 0.8027 (mmp) REVERT: B 250 LYS cc_start: 0.8434 (mttt) cc_final: 0.8146 (mttm) REVERT: B 265 VAL cc_start: 0.8640 (t) cc_final: 0.8352 (p) REVERT: B 337 GLU cc_start: 0.7745 (tp30) cc_final: 0.7388 (tp30) REVERT: B 375 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8489 (mtpp) REVERT: B 383 MET cc_start: 0.7306 (tpp) cc_final: 0.6823 (mmm) REVERT: B 386 PHE cc_start: 0.8397 (t80) cc_final: 0.8189 (t80) REVERT: B 407 SER cc_start: 0.8825 (t) cc_final: 0.8581 (p) REVERT: B 419 TRP cc_start: 0.8075 (p-90) cc_final: 0.7818 (p-90) REVERT: B 487 SER cc_start: 0.8365 (t) cc_final: 0.8082 (p) REVERT: B 511 MET cc_start: 0.8866 (tmm) cc_final: 0.8541 (ttp) REVERT: B 579 MET cc_start: 0.7864 (tpp) cc_final: 0.7658 (tpp) REVERT: B 588 LYS cc_start: 0.8570 (tppt) cc_final: 0.8342 (tttp) REVERT: B 628 VAL cc_start: 0.8115 (OUTLIER) cc_final: 0.7745 (t) REVERT: B 634 SER cc_start: 0.8902 (m) cc_final: 0.8663 (t) REVERT: B 697 MET cc_start: 0.5871 (mmm) cc_final: 0.5199 (mmm) REVERT: B 736 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.7997 (t0) REVERT: B 810 MET cc_start: 0.7001 (ptt) cc_final: 0.6781 (ptt) REVERT: B 815 LYS cc_start: 0.9059 (tttt) cc_final: 0.8676 (tttm) REVERT: B 820 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7872 (mmmt) REVERT: B 852 LYS cc_start: 0.8595 (mttp) cc_final: 0.8149 (mtpt) REVERT: B 853 ILE cc_start: 0.9041 (tp) cc_final: 0.8733 (tt) REVERT: B 856 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7726 (ttp80) REVERT: B 877 GLN cc_start: 0.8524 (tt0) cc_final: 0.8183 (tt0) REVERT: B 954 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7558 (mm-30) REVERT: B 958 LYS cc_start: 0.8854 (ttpt) cc_final: 0.8454 (ttmm) REVERT: B 968 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8364 (mmmm) REVERT: B 972 PHE cc_start: 0.8738 (t80) cc_final: 0.8404 (t80) REVERT: B 1003 SER cc_start: 0.8344 (t) cc_final: 0.7947 (m) REVERT: B 1033 GLU cc_start: 0.7424 (tp30) cc_final: 0.7172 (tp30) REVERT: B 1035 TYR cc_start: 0.8265 (m-80) cc_final: 0.7839 (m-80) REVERT: B 1066 TYR cc_start: 0.8614 (m-80) cc_final: 0.8305 (m-80) REVERT: B 1118 LYS cc_start: 0.8572 (mtpp) cc_final: 0.8290 (mtmm) REVERT: B 1121 LEU cc_start: 0.8995 (mm) cc_final: 0.8775 (mt) REVERT: B 1143 GLU cc_start: 0.7858 (tt0) cc_final: 0.7405 (tm-30) REVERT: B 1162 ARG cc_start: 0.5733 (OUTLIER) cc_final: 0.5093 (tpm-80) REVERT: B 1179 THR cc_start: 0.4870 (OUTLIER) cc_final: 0.4657 (p) outliers start: 91 outliers final: 67 residues processed: 573 average time/residue: 0.3254 time to fit residues: 267.4877 Evaluate side-chains 607 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 528 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1104 MET Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1158 ARG Chi-restraints excluded: chain A residue 1222 CYS Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1154 ASN Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1179 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 173 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: A 292 HIS A 943 ASN B1156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.143505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.120440 restraints weight = 25039.302| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.06 r_work: 0.3394 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16740 Z= 0.155 Angle : 0.660 16.174 22706 Z= 0.326 Chirality : 0.042 0.171 2734 Planarity : 0.005 0.062 2796 Dihedral : 7.031 133.994 2272 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.58 % Allowed : 22.88 % Favored : 72.54 % 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: 1.34 (0.19), residues: 2050 helix: 1.92 (0.14), residues: 1458 sheet: -2.23 (0.55), residues: 82 loop : -1.68 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1112 HIS 0.004 0.001 HIS B 981 PHE 0.020 0.001 PHE B 680 TYR 0.014 0.001 TYR B1009 ARG 0.012 0.000 ARG B1053 Details of bonding type rmsd hydrogen bonds : bond 0.04907 ( 1163) hydrogen bonds : angle 4.26096 ( 3459) covalent geometry : bond 0.00330 (16740) covalent geometry : angle 0.65966 (22706) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 529 time to evaluate : 1.774 Fit side-chains revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8758 (mm) cc_final: 0.8384 (mt) REVERT: A 116 VAL cc_start: 0.8725 (t) cc_final: 0.8485 (t) REVERT: A 149 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7454 (tm-30) REVERT: A 163 PHE cc_start: 0.8396 (t80) cc_final: 0.8071 (t80) REVERT: A 165 GLN cc_start: 0.8656 (tt0) cc_final: 0.8433 (tt0) REVERT: A 199 MET cc_start: 0.8468 (mmm) cc_final: 0.8117 (mmm) REVERT: A 280 TYR cc_start: 0.8411 (t80) cc_final: 0.8102 (t80) REVERT: A 284 LYS cc_start: 0.8418 (mmmm) cc_final: 0.8140 (mmmm) REVERT: A 337 GLU cc_start: 0.7771 (tp30) cc_final: 0.7419 (tp30) REVERT: A 354 GLU cc_start: 0.8175 (tt0) cc_final: 0.7826 (tt0) REVERT: A 375 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8471 (ttpp) REVERT: A 383 MET cc_start: 0.7018 (mmm) cc_final: 0.6497 (mmm) REVERT: A 395 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8431 (mm) REVERT: A 411 SER cc_start: 0.8517 (p) cc_final: 0.8248 (p) REVERT: A 487 SER cc_start: 0.8185 (t) cc_final: 0.7830 (p) REVERT: A 511 MET cc_start: 0.8865 (tmm) cc_final: 0.8553 (tmm) REVERT: A 531 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6971 (tm-30) REVERT: A 554 GLU cc_start: 0.8199 (tp30) cc_final: 0.7842 (tp30) REVERT: A 578 MET cc_start: 0.8452 (mtp) cc_final: 0.8239 (mmm) REVERT: A 579 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.8031 (mmm) REVERT: A 580 GLU cc_start: 0.8142 (tp30) cc_final: 0.7788 (tp30) REVERT: A 599 GLU cc_start: 0.7653 (mp0) cc_final: 0.7397 (mp0) REVERT: A 609 ARG cc_start: 0.8341 (ttm170) cc_final: 0.7990 (ttm-80) REVERT: A 632 LYS cc_start: 0.8159 (ttpt) cc_final: 0.7732 (ttmm) REVERT: A 634 SER cc_start: 0.8836 (m) cc_final: 0.8632 (t) REVERT: A 697 MET cc_start: 0.6441 (mmm) cc_final: 0.5786 (mmm) REVERT: A 815 LYS cc_start: 0.8973 (tttt) cc_final: 0.8706 (ttmm) REVERT: A 820 LYS cc_start: 0.8250 (mmmt) cc_final: 0.7965 (mmmt) REVERT: A 841 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8490 (mtpt) REVERT: A 853 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8367 (tp) REVERT: A 884 LEU cc_start: 0.8486 (mm) cc_final: 0.8179 (mt) REVERT: A 917 GLN cc_start: 0.8753 (tt0) cc_final: 0.8354 (tt0) REVERT: A 942 MET cc_start: 0.8611 (tpp) cc_final: 0.8213 (tpt) REVERT: A 994 GLU cc_start: 0.7730 (pm20) cc_final: 0.7266 (pm20) REVERT: A 1006 VAL cc_start: 0.8398 (m) cc_final: 0.8170 (p) REVERT: A 1035 TYR cc_start: 0.8131 (m-80) cc_final: 0.7590 (m-80) REVERT: A 1044 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7423 (mt-10) REVERT: A 1060 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7669 (mm-30) REVERT: A 1061 THR cc_start: 0.7692 (OUTLIER) cc_final: 0.7454 (p) REVERT: A 1080 PHE cc_start: 0.7957 (m-80) cc_final: 0.7559 (m-80) REVERT: A 1087 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7139 (tm-30) REVERT: A 1104 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7658 (tpp) REVERT: A 1116 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8149 (ttmt) REVERT: A 1139 ASP cc_start: 0.7612 (m-30) cc_final: 0.7197 (m-30) REVERT: A 1143 GLU cc_start: 0.7953 (tt0) cc_final: 0.7656 (tp30) REVERT: A 1185 ARG cc_start: 0.6856 (mmt180) cc_final: 0.6648 (mmm-85) REVERT: A 1190 ARG cc_start: 0.8012 (mmm-85) cc_final: 0.7619 (mmm-85) REVERT: A 1220 ASN cc_start: 0.7881 (m-40) cc_final: 0.7572 (m-40) REVERT: B 96 LYS cc_start: 0.8381 (mmmm) cc_final: 0.7953 (tppp) REVERT: B 134 ASP cc_start: 0.8128 (t0) cc_final: 0.7794 (t70) REVERT: B 149 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7446 (tm-30) REVERT: B 155 ASP cc_start: 0.8133 (t0) cc_final: 0.7689 (t0) REVERT: B 163 PHE cc_start: 0.8337 (t80) cc_final: 0.8085 (t80) REVERT: B 199 MET cc_start: 0.8743 (mmm) cc_final: 0.8521 (tpp) REVERT: B 205 MET cc_start: 0.8408 (mmp) cc_final: 0.7977 (mmp) REVERT: B 250 LYS cc_start: 0.8422 (mttt) cc_final: 0.8134 (mttm) REVERT: B 265 VAL cc_start: 0.8633 (t) cc_final: 0.8372 (p) REVERT: B 337 GLU cc_start: 0.7779 (tp30) cc_final: 0.7403 (tp30) REVERT: B 375 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8503 (mtpp) REVERT: B 383 MET cc_start: 0.7300 (tpp) cc_final: 0.6831 (mmm) REVERT: B 407 SER cc_start: 0.8828 (t) cc_final: 0.8583 (p) REVERT: B 419 TRP cc_start: 0.8059 (p-90) cc_final: 0.7813 (p-90) REVERT: B 487 SER cc_start: 0.8389 (t) cc_final: 0.8102 (p) REVERT: B 511 MET cc_start: 0.8874 (tmm) cc_final: 0.8557 (ttp) REVERT: B 563 LYS cc_start: 0.7968 (mtmm) cc_final: 0.7707 (mtmm) REVERT: B 579 MET cc_start: 0.7891 (tpp) cc_final: 0.7670 (tpp) REVERT: B 588 LYS cc_start: 0.8600 (tppt) cc_final: 0.8368 (tttp) REVERT: B 598 PHE cc_start: 0.8868 (t80) cc_final: 0.8379 (t80) REVERT: B 599 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7686 (mt-10) REVERT: B 628 VAL cc_start: 0.8107 (OUTLIER) cc_final: 0.7848 (t) REVERT: B 634 SER cc_start: 0.8906 (m) cc_final: 0.8671 (t) REVERT: B 697 MET cc_start: 0.5844 (mmm) cc_final: 0.5179 (mmm) REVERT: B 736 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.7976 (t0) REVERT: B 810 MET cc_start: 0.7007 (ptt) cc_final: 0.6782 (ptt) REVERT: B 815 LYS cc_start: 0.9058 (tttt) cc_final: 0.8695 (ttmm) REVERT: B 820 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7858 (mmmt) REVERT: B 852 LYS cc_start: 0.8602 (mttp) cc_final: 0.8153 (mtpt) REVERT: B 853 ILE cc_start: 0.9065 (tp) cc_final: 0.8758 (tt) REVERT: B 856 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7729 (ttp80) REVERT: B 877 GLN cc_start: 0.8543 (tt0) cc_final: 0.8273 (tt0) REVERT: B 954 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7552 (mm-30) REVERT: B 958 LYS cc_start: 0.8857 (ttpt) cc_final: 0.8456 (ttmm) REVERT: B 968 LYS cc_start: 0.8652 (mtpp) cc_final: 0.8337 (mmmm) REVERT: B 972 PHE cc_start: 0.8733 (t80) cc_final: 0.8401 (t80) REVERT: B 1003 SER cc_start: 0.8288 (t) cc_final: 0.7896 (m) REVERT: B 1033 GLU cc_start: 0.7463 (tp30) cc_final: 0.7243 (tp30) REVERT: B 1035 TYR cc_start: 0.8248 (m-80) cc_final: 0.7875 (m-80) REVERT: B 1066 TYR cc_start: 0.8617 (m-80) cc_final: 0.8297 (m-80) REVERT: B 1118 LYS cc_start: 0.8595 (mtpp) cc_final: 0.8298 (mtmm) REVERT: B 1121 LEU cc_start: 0.8997 (mm) cc_final: 0.8787 (mt) REVERT: B 1143 GLU cc_start: 0.7889 (tt0) cc_final: 0.7333 (mt-10) REVERT: B 1156 HIS cc_start: 0.8005 (OUTLIER) cc_final: 0.7551 (p90) REVERT: B 1162 ARG cc_start: 0.5726 (OUTLIER) cc_final: 0.5100 (tpm-80) REVERT: B 1179 THR cc_start: 0.4830 (OUTLIER) cc_final: 0.4617 (p) REVERT: B 1212 ILE cc_start: 0.5530 (OUTLIER) cc_final: 0.5084 (mp) outliers start: 82 outliers final: 62 residues processed: 564 average time/residue: 0.3420 time to fit residues: 276.7760 Evaluate side-chains 602 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 525 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1104 MET Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1158 ARG Chi-restraints excluded: chain A residue 1222 CYS Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1154 ASN Chi-restraints excluded: chain B residue 1156 HIS Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 174 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 chunk 159 optimal weight: 0.0000 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 182 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN A 943 ASN ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.143524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120756 restraints weight = 25180.645| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.05 r_work: 0.3411 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16740 Z= 0.146 Angle : 0.663 16.139 22706 Z= 0.327 Chirality : 0.042 0.171 2734 Planarity : 0.005 0.062 2796 Dihedral : 7.010 134.469 2272 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.46 % Allowed : 23.44 % Favored : 72.10 % 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: 1.40 (0.19), residues: 2050 helix: 1.97 (0.14), residues: 1458 sheet: -2.20 (0.55), residues: 82 loop : -1.66 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 962 HIS 0.011 0.001 HIS B1156 PHE 0.037 0.001 PHE A 972 TYR 0.014 0.001 TYR B1009 ARG 0.008 0.000 ARG B1053 Details of bonding type rmsd hydrogen bonds : bond 0.04799 ( 1163) hydrogen bonds : angle 4.25603 ( 3459) covalent geometry : bond 0.00310 (16740) covalent geometry : angle 0.66292 (22706) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 525 time to evaluate : 2.149 Fit side-chains revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8742 (mm) cc_final: 0.8375 (mt) REVERT: A 116 VAL cc_start: 0.8722 (t) cc_final: 0.8481 (t) REVERT: A 149 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7409 (tm-30) REVERT: A 163 PHE cc_start: 0.8397 (t80) cc_final: 0.8184 (t80) REVERT: A 199 MET cc_start: 0.8485 (mmm) cc_final: 0.8167 (mmm) REVERT: A 280 TYR cc_start: 0.8411 (t80) cc_final: 0.8107 (t80) REVERT: A 284 LYS cc_start: 0.8394 (mmmm) cc_final: 0.8111 (mmmm) REVERT: A 337 GLU cc_start: 0.7782 (tp30) cc_final: 0.7453 (tp30) REVERT: A 354 GLU cc_start: 0.8242 (tt0) cc_final: 0.7864 (tt0) REVERT: A 375 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8506 (ttpp) REVERT: A 383 MET cc_start: 0.7009 (mmm) cc_final: 0.6493 (mmm) REVERT: A 387 TYR cc_start: 0.8711 (m-10) cc_final: 0.8343 (m-10) REVERT: A 411 SER cc_start: 0.8494 (p) cc_final: 0.8230 (p) REVERT: A 487 SER cc_start: 0.8164 (t) cc_final: 0.7841 (m) REVERT: A 511 MET cc_start: 0.8844 (tmm) cc_final: 0.8529 (tmm) REVERT: A 531 GLU cc_start: 0.7452 (mm-30) cc_final: 0.6942 (tm-30) REVERT: A 569 GLU cc_start: 0.8451 (tp30) cc_final: 0.8246 (tp30) REVERT: A 578 MET cc_start: 0.8391 (mtp) cc_final: 0.8175 (mmm) REVERT: A 579 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7936 (mmm) REVERT: A 580 GLU cc_start: 0.8151 (tp30) cc_final: 0.7813 (tp30) REVERT: A 609 ARG cc_start: 0.8273 (ttm170) cc_final: 0.7935 (ttm-80) REVERT: A 632 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7709 (ttmm) REVERT: A 647 LYS cc_start: 0.8603 (mmtm) cc_final: 0.8328 (mtmm) REVERT: A 697 MET cc_start: 0.6453 (mmm) cc_final: 0.5750 (mmm) REVERT: A 815 LYS cc_start: 0.8972 (tttt) cc_final: 0.8699 (ttmm) REVERT: A 820 LYS cc_start: 0.8128 (mmmt) cc_final: 0.7857 (mmmt) REVERT: A 841 LYS cc_start: 0.8730 (mtpt) cc_final: 0.8479 (mtpt) REVERT: A 853 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8382 (tp) REVERT: A 884 LEU cc_start: 0.8516 (mm) cc_final: 0.8217 (mt) REVERT: A 917 GLN cc_start: 0.8709 (tt0) cc_final: 0.8309 (tt0) REVERT: A 942 MET cc_start: 0.8643 (tpp) cc_final: 0.8273 (tpt) REVERT: A 994 GLU cc_start: 0.7702 (pm20) cc_final: 0.7235 (pm20) REVERT: A 1035 TYR cc_start: 0.8097 (m-80) cc_final: 0.7622 (m-80) REVERT: A 1044 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7366 (mt-10) REVERT: A 1060 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7706 (mm-30) REVERT: A 1080 PHE cc_start: 0.7950 (m-80) cc_final: 0.7702 (m-80) REVERT: A 1087 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6864 (tm-30) REVERT: A 1104 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7668 (tpp) REVERT: A 1116 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8103 (mttt) REVERT: A 1139 ASP cc_start: 0.7587 (m-30) cc_final: 0.7225 (m-30) REVERT: A 1185 ARG cc_start: 0.6739 (mmt180) cc_final: 0.6376 (mtt-85) REVERT: A 1190 ARG cc_start: 0.7983 (mmm-85) cc_final: 0.7599 (mmm-85) REVERT: A 1220 ASN cc_start: 0.7829 (m-40) cc_final: 0.7216 (m-40) REVERT: B 116 VAL cc_start: 0.8651 (t) cc_final: 0.8364 (m) REVERT: B 134 ASP cc_start: 0.8113 (t0) cc_final: 0.7780 (t70) REVERT: B 149 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7434 (tm-30) REVERT: B 155 ASP cc_start: 0.8094 (t0) cc_final: 0.7684 (t0) REVERT: B 199 MET cc_start: 0.8697 (mmm) cc_final: 0.8471 (tpp) REVERT: B 205 MET cc_start: 0.8399 (mmp) cc_final: 0.7981 (mmp) REVERT: B 250 LYS cc_start: 0.8378 (mttt) cc_final: 0.8068 (mttm) REVERT: B 265 VAL cc_start: 0.8628 (t) cc_final: 0.8360 (p) REVERT: B 337 GLU cc_start: 0.7811 (tp30) cc_final: 0.7443 (tp30) REVERT: B 375 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8455 (mtpp) REVERT: B 383 MET cc_start: 0.7236 (tpp) cc_final: 0.6794 (mmm) REVERT: B 407 SER cc_start: 0.8844 (t) cc_final: 0.8600 (p) REVERT: B 419 TRP cc_start: 0.8041 (p-90) cc_final: 0.7806 (p-90) REVERT: B 487 SER cc_start: 0.8349 (t) cc_final: 0.8058 (p) REVERT: B 511 MET cc_start: 0.8880 (tmm) cc_final: 0.8571 (ttp) REVERT: B 520 ASP cc_start: 0.8413 (p0) cc_final: 0.8173 (p0) REVERT: B 579 MET cc_start: 0.7954 (tpp) cc_final: 0.7699 (tpp) REVERT: B 588 LYS cc_start: 0.8559 (tppt) cc_final: 0.8335 (tttp) REVERT: B 598 PHE cc_start: 0.8857 (t80) cc_final: 0.8420 (t80) REVERT: B 599 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7618 (mt-10) REVERT: B 628 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7889 (t) REVERT: B 634 SER cc_start: 0.8928 (m) cc_final: 0.8694 (t) REVERT: B 644 LEU cc_start: 0.8539 (mt) cc_final: 0.8266 (mp) REVERT: B 647 LYS cc_start: 0.8469 (mmtp) cc_final: 0.8150 (mtmt) REVERT: B 697 MET cc_start: 0.5836 (mmm) cc_final: 0.5176 (mmm) REVERT: B 736 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.7989 (t0) REVERT: B 810 MET cc_start: 0.6906 (ptt) cc_final: 0.6703 (ptt) REVERT: B 815 LYS cc_start: 0.9043 (tttt) cc_final: 0.8666 (tttm) REVERT: B 820 LYS cc_start: 0.8063 (mmmt) cc_final: 0.7796 (mmmt) REVERT: B 852 LYS cc_start: 0.8580 (mttp) cc_final: 0.8120 (mtpt) REVERT: B 853 ILE cc_start: 0.9063 (tp) cc_final: 0.8765 (tt) REVERT: B 877 GLN cc_start: 0.8504 (tt0) cc_final: 0.8250 (tt0) REVERT: B 954 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7551 (mm-30) REVERT: B 958 LYS cc_start: 0.8863 (ttpt) cc_final: 0.8457 (ttmm) REVERT: B 968 LYS cc_start: 0.8618 (mtpp) cc_final: 0.8292 (mmmm) REVERT: B 972 PHE cc_start: 0.8666 (t80) cc_final: 0.8309 (t80) REVERT: B 1003 SER cc_start: 0.8294 (t) cc_final: 0.7902 (m) REVERT: B 1035 TYR cc_start: 0.8209 (m-80) cc_final: 0.7757 (m-80) REVERT: B 1086 LEU cc_start: 0.8308 (tp) cc_final: 0.8108 (tp) REVERT: B 1118 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8324 (mtmm) REVERT: B 1121 LEU cc_start: 0.8975 (mm) cc_final: 0.8749 (mt) REVERT: B 1143 GLU cc_start: 0.7872 (tt0) cc_final: 0.7343 (mt-10) REVERT: B 1162 ARG cc_start: 0.5740 (OUTLIER) cc_final: 0.5102 (tpm-80) REVERT: B 1212 ILE cc_start: 0.5503 (OUTLIER) cc_final: 0.5072 (mp) outliers start: 80 outliers final: 63 residues processed: 559 average time/residue: 0.3291 time to fit residues: 265.3598 Evaluate side-chains 595 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 521 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1104 MET Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1158 ARG Chi-restraints excluded: chain A residue 1222 CYS Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1154 ASN Chi-restraints excluded: chain B residue 1158 ARG Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 58 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 176 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 163 optimal weight: 8.9990 chunk 147 optimal weight: 0.5980 chunk 64 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.143441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.120675 restraints weight = 25151.235| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.06 r_work: 0.3409 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16740 Z= 0.156 Angle : 0.669 16.195 22706 Z= 0.330 Chirality : 0.042 0.172 2734 Planarity : 0.005 0.062 2796 Dihedral : 6.886 134.187 2270 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.46 % Allowed : 23.49 % Favored : 72.04 % 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: 1.44 (0.19), residues: 2050 helix: 1.99 (0.14), residues: 1458 sheet: -1.98 (0.57), residues: 82 loop : -1.66 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1112 HIS 0.005 0.001 HIS B 981 PHE 0.020 0.001 PHE A1136 TYR 0.014 0.001 TYR B1009 ARG 0.008 0.000 ARG B 500 Details of bonding type rmsd hydrogen bonds : bond 0.04836 ( 1163) hydrogen bonds : angle 4.24124 ( 3459) covalent geometry : bond 0.00336 (16740) covalent geometry : angle 0.66918 (22706) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11203.25 seconds wall clock time: 196 minutes 22.66 seconds (11782.66 seconds total)