Starting phenix.real_space_refine on Thu Sep 18 11:38:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xq7_38568/09_2025/8xq7_38568.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xq7_38568/09_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_38568/09_2025/8xq7_38568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xq7_38568/09_2025/8xq7_38568.map" model { file = "/net/cci-nas-00/data/ceres_data/8xq7_38568/09_2025/8xq7_38568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xq7_38568/09_2025/8xq7_38568.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.77, per 1000 atoms: 0.23 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: 0.98 Conformation dependent library (CDL) restraints added in 515.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.47 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: 2.73 Time building geometry restraints manager: 1.31 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: 0.03 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.150 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.900 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 431 TYR 0.012 0.001 TYR A1153 PHE 0.031 0.002 PHE B 766 TRP 0.014 0.001 TRP A 962 HIS 0.002 0.001 HIS B1133 Details of bonding type rmsd covalent geometry : bond 0.00453 (16740) covalent geometry : angle 0.79273 (22706) hydrogen bonds : bond 0.10702 ( 1163) hydrogen bonds : angle 5.79532 ( 3459) *********************** 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 : 0.626 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: 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: 0.8019 (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: 0.7899 (tpp) REVERT: A 581 GLU cc_start: 0.8381 (tp30) cc_final: 0.7911 (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: 0.8669 (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: 0.7518 (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: 0.8074 (p90) REVERT: A 1136 PHE cc_start: 0.7307 (t80) cc_final: 0.7060 (t80) 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: 0.8224 (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: 0.8055 (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: 0.8315 (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: 0.6957 (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: 0.8345 (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: 0.7409 (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: 0.8757 (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: 0.8050 (p90) REVERT: B 1162 ARG cc_start: 0.5414 (OUTLIER) cc_final: 0.5069 (tpm-80) REVERT: B 1173 LYS cc_start: 0.7526 (mtpp) cc_final: 0.7210 (mtpp) REVERT: B 1179 THR cc_start: 0.5317 (OUTLIER) cc_final: 0.5030 (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: 0.1379 time to fit residues: 141.8813 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 : 0.461 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.0070 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.0270 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- 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 B1054 ASN B1191 ASN B1220 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.145202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.121236 restraints weight = 25476.828| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.11 r_work: 0.3395 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16740 Z= 0.138 Angle : 0.630 16.635 22706 Z= 0.317 Chirality : 0.041 0.208 2734 Planarity : 0.005 0.074 2796 Dihedral : 8.939 133.179 2343 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.85 % Allowed : 17.19 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.18), residues: 2050 helix: 0.97 (0.13), residues: 1462 sheet: -3.32 (0.50), residues: 82 loop : -1.80 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 609 TYR 0.015 0.001 TYR B 415 PHE 0.019 0.001 PHE A 972 TRP 0.015 0.001 TRP B1112 HIS 0.006 0.001 HIS A 981 Details of bonding type rmsd covalent geometry : bond 0.00282 (16740) covalent geometry : angle 0.63016 (22706) hydrogen bonds : bond 0.04791 ( 1163) hydrogen bonds : angle 4.53432 ( 3459) *********************** 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 651 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 564 time to evaluate : 0.602 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: A 112 ILE cc_start: 0.8647 (mm) cc_final: 0.8223 (mt) REVERT: A 116 VAL cc_start: 0.8781 (t) cc_final: 0.8517 (t) REVERT: A 124 GLU cc_start: 0.7466 (tp30) cc_final: 0.7248 (tp30) REVERT: A 149 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7623 (tm-30) REVERT: A 174 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8123 (tt) REVERT: A 195 PHE cc_start: 0.8102 (t80) cc_final: 0.7844 (t80) REVERT: A 233 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7711 (tm-30) REVERT: A 266 LEU cc_start: 0.8440 (tp) cc_final: 0.8205 (tt) REVERT: A 269 LEU cc_start: 0.8485 (tp) cc_final: 0.8090 (tt) REVERT: A 300 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7935 (mt-10) REVERT: A 337 GLU cc_start: 0.7737 (tp30) cc_final: 0.7414 (tp30) REVERT: A 346 GLU cc_start: 0.7776 (tt0) cc_final: 0.7502 (tt0) REVERT: A 354 GLU cc_start: 0.8282 (tt0) cc_final: 0.7982 (tt0) REVERT: A 366 MET cc_start: 0.8594 (mmm) cc_final: 0.8178 (mmt) REVERT: A 375 LYS cc_start: 0.8745 (tppp) cc_final: 0.8442 (ttpp) REVERT: A 383 MET cc_start: 0.7216 (mmm) cc_final: 0.6630 (mmm) REVERT: A 385 TRP cc_start: 0.8514 (m100) cc_final: 0.8120 (m100) REVERT: A 387 TYR cc_start: 0.8612 (m-10) cc_final: 0.8149 (m-10) REVERT: A 443 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8099 (tm-30) REVERT: A 486 ILE cc_start: 0.8694 (mp) cc_final: 0.8481 (mm) REVERT: A 487 SER cc_start: 0.8284 (t) cc_final: 0.7987 (p) REVERT: A 511 MET cc_start: 0.8883 (tmm) cc_final: 0.8625 (tmm) REVERT: A 516 ARG cc_start: 0.8565 (ttp-110) cc_final: 0.8334 (ttp-110) REVERT: A 531 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6872 (tm-30) REVERT: A 554 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7772 (tp30) REVERT: A 578 MET cc_start: 0.8648 (mtp) cc_final: 0.8412 (mtp) REVERT: A 579 MET cc_start: 0.7980 (tmm) cc_final: 0.7741 (tpp) REVERT: A 580 GLU cc_start: 0.8120 (tp30) cc_final: 0.7693 (tp30) REVERT: A 602 MET cc_start: 0.7513 (mpp) cc_final: 0.7256 (mpp) REVERT: A 632 LYS cc_start: 0.8284 (ttpt) cc_final: 0.8049 (ttmm) REVERT: A 647 LYS cc_start: 0.8665 (mmtp) cc_final: 0.8380 (mmtm) REVERT: A 697 MET cc_start: 0.6491 (mmm) cc_final: 0.5884 (mmm) REVERT: A 815 LYS cc_start: 0.9023 (tttt) cc_final: 0.8683 (tppp) REVERT: A 820 LYS cc_start: 0.8301 (mmmt) cc_final: 0.8003 (mmmt) REVERT: A 853 ILE cc_start: 0.8712 (tp) cc_final: 0.8492 (tt) REVERT: A 864 LEU cc_start: 0.8534 (tp) cc_final: 0.8289 (tp) REVERT: A 877 GLN cc_start: 0.8607 (tt0) cc_final: 0.8404 (tt0) REVERT: A 911 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8199 (mm-30) REVERT: A 926 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7905 (mm-30) REVERT: A 942 MET cc_start: 0.8466 (tpp) cc_final: 0.8238 (tpt) REVERT: A 972 PHE cc_start: 0.8514 (t80) cc_final: 0.8231 (t80) REVERT: A 983 ASP cc_start: 0.7950 (t0) cc_final: 0.7750 (p0) REVERT: A 994 GLU cc_start: 0.7930 (pm20) cc_final: 0.7608 (pm20) REVERT: A 1003 SER cc_start: 0.8447 (t) cc_final: 0.8224 (m) REVERT: A 1008 LEU cc_start: 0.8221 (mp) cc_final: 0.7799 (tp) REVERT: A 1033 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7615 (mp0) REVERT: A 1044 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7750 (mt-10) REVERT: A 1057 VAL cc_start: 0.8805 (t) cc_final: 0.8363 (m) REVERT: A 1060 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7660 (mm-30) REVERT: A 1066 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7247 (m-80) REVERT: A 1080 PHE cc_start: 0.8036 (m-80) cc_final: 0.7394 (m-80) REVERT: A 1104 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7379 (tpt) REVERT: A 1121 LEU cc_start: 0.8863 (mm) cc_final: 0.8620 (mt) REVERT: A 1122 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7738 (tp30) REVERT: A 1136 PHE cc_start: 0.7016 (t80) cc_final: 0.6594 (t80) REVERT: A 1173 LYS cc_start: 0.7399 (mtpp) cc_final: 0.6970 (mtpp) REVERT: A 1190 ARG cc_start: 0.8226 (mmm-85) cc_final: 0.7800 (mmm-85) REVERT: A 1212 ILE cc_start: 0.5523 (OUTLIER) cc_final: 0.5006 (mp) REVERT: A 1220 ASN cc_start: 0.7950 (m-40) cc_final: 0.7748 (m-40) REVERT: B 149 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7512 (tm-30) REVERT: B 300 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7837 (mt-10) REVERT: B 337 GLU cc_start: 0.7875 (tp30) cc_final: 0.7535 (tp30) REVERT: B 375 LYS cc_start: 0.8785 (tppp) cc_final: 0.8234 (mtpp) REVERT: B 383 MET cc_start: 0.7288 (tpp) cc_final: 0.6741 (mmm) REVERT: B 385 TRP cc_start: 0.8431 (m100) cc_final: 0.8104 (m100) REVERT: B 410 LEU cc_start: 0.8552 (mt) cc_final: 0.8224 (mt) REVERT: B 419 TRP cc_start: 0.8097 (p-90) cc_final: 0.7730 (p-90) REVERT: B 443 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7880 (tm-30) REVERT: B 487 SER cc_start: 0.8424 (t) cc_final: 0.8151 (p) REVERT: B 511 MET cc_start: 0.8911 (tmm) cc_final: 0.8405 (tmm) REVERT: B 531 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6887 (tm-30) REVERT: B 578 MET cc_start: 0.8626 (mtp) cc_final: 0.8289 (mtp) REVERT: B 579 MET cc_start: 0.7867 (tmm) cc_final: 0.7531 (tpp) REVERT: B 588 LYS cc_start: 0.8677 (tppt) cc_final: 0.8376 (tttm) REVERT: B 647 LYS cc_start: 0.8506 (mmtm) cc_final: 0.8246 (mmtp) REVERT: B 697 MET cc_start: 0.5846 (mmm) cc_final: 0.5250 (mmm) REVERT: B 736 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8063 (t0) REVERT: B 808 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7973 (pt) REVERT: B 810 MET cc_start: 0.6971 (ptt) cc_final: 0.6767 (ptt) REVERT: B 815 LYS cc_start: 0.9138 (tttt) cc_final: 0.8823 (tppt) REVERT: B 820 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7977 (mmmt) REVERT: B 825 VAL cc_start: 0.8748 (t) cc_final: 0.8441 (p) REVERT: B 852 LYS cc_start: 0.8400 (mttp) cc_final: 0.8045 (ttmm) REVERT: B 884 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8100 (mm) REVERT: B 926 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7807 (mm-30) REVERT: B 932 LEU cc_start: 0.8292 (tp) cc_final: 0.8084 (tt) REVERT: B 942 MET cc_start: 0.8496 (tpp) cc_final: 0.8292 (tpt) REVERT: B 954 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7600 (mm-30) REVERT: B 958 LYS cc_start: 0.8864 (ttpt) cc_final: 0.8491 (ttmm) REVERT: B 968 LYS cc_start: 0.8701 (mtpp) cc_final: 0.8376 (mmmm) REVERT: B 972 PHE cc_start: 0.8814 (t80) cc_final: 0.8455 (t80) REVERT: B 993 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.6601 (m-30) REVERT: B 994 GLU cc_start: 0.7816 (pm20) cc_final: 0.7562 (pm20) REVERT: B 996 ASP cc_start: 0.7361 (p0) cc_final: 0.7107 (p0) REVERT: B 1003 SER cc_start: 0.8533 (t) cc_final: 0.8232 (m) REVERT: B 1060 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7709 (mm-30) REVERT: B 1073 MET cc_start: 0.8581 (tpp) cc_final: 0.8082 (tpp) REVERT: B 1098 ILE cc_start: 0.8900 (tt) cc_final: 0.8563 (tp) REVERT: B 1104 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7286 (tpp) REVERT: B 1118 LYS cc_start: 0.8590 (mtpp) cc_final: 0.8221 (mtmm) REVERT: B 1121 LEU cc_start: 0.8989 (mm) cc_final: 0.8721 (mt) REVERT: B 1126 LEU cc_start: 0.8477 (mt) cc_final: 0.7954 (pt) REVERT: B 1162 ARG cc_start: 0.5709 (OUTLIER) cc_final: 0.5138 (tpm-80) REVERT: B 1179 THR cc_start: 0.5555 (OUTLIER) cc_final: 0.5262 (p) REVERT: B 1212 ILE cc_start: 0.5533 (OUTLIER) cc_final: 0.5255 (mp) outliers start: 87 outliers final: 38 residues processed: 615 average time/residue: 0.1406 time to fit residues: 124.7779 Evaluate side-chains 590 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 538 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 217 LEU Chi-restraints excluded: chain A residue 257 LEU 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 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 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 316 ASP Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 395 ILE 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 804 LEU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 865 ARG Chi-restraints excluded: chain B residue 884 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 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 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 Chi-restraints excluded: chain B residue 1220 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 95 optimal weight: 0.7980 chunk 161 optimal weight: 7.9990 chunk 93 optimal weight: 0.0030 chunk 98 optimal weight: 8.9990 chunk 112 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 193 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN A 600 HIS A 981 HIS A1120 HIS ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.145031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.121397 restraints weight = 25619.604| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.11 r_work: 0.3396 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16740 Z= 0.132 Angle : 0.615 16.097 22706 Z= 0.305 Chirality : 0.041 0.176 2734 Planarity : 0.004 0.065 2796 Dihedral : 7.879 133.284 2300 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.02 % Allowed : 18.69 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.19), residues: 2050 helix: 1.54 (0.14), residues: 1456 sheet: -3.28 (0.47), residues: 82 loop : -1.74 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1185 TYR 0.012 0.001 TYR B1153 PHE 0.016 0.001 PHE A 972 TRP 0.024 0.001 TRP A1112 HIS 0.008 0.001 HIS A1120 Details of bonding type rmsd covalent geometry : bond 0.00268 (16740) covalent geometry : angle 0.61462 (22706) hydrogen bonds : bond 0.04551 ( 1163) hydrogen bonds : angle 4.34441 ( 3459) *********************** 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 646 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 556 time to evaluate : 0.618 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: A 112 ILE cc_start: 0.8663 (mm) cc_final: 0.8239 (mt) REVERT: A 116 VAL cc_start: 0.8771 (t) cc_final: 0.8512 (t) REVERT: A 149 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7515 (tm-30) REVERT: A 174 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8236 (tt) REVERT: A 176 VAL cc_start: 0.8853 (p) cc_final: 0.8593 (t) REVERT: A 195 PHE cc_start: 0.7961 (t80) cc_final: 0.7674 (t80) REVERT: A 225 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7634 (tp40) REVERT: A 233 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7658 (tm-30) REVERT: A 266 LEU cc_start: 0.8443 (tp) cc_final: 0.8201 (tt) REVERT: A 269 LEU cc_start: 0.8467 (tp) cc_final: 0.8197 (tt) REVERT: A 300 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7957 (mt-10) REVERT: A 337 GLU cc_start: 0.7778 (tp30) cc_final: 0.7450 (tp30) REVERT: A 346 GLU cc_start: 0.7686 (tt0) cc_final: 0.7413 (tt0) REVERT: A 354 GLU cc_start: 0.8218 (tt0) cc_final: 0.7891 (tt0) REVERT: A 366 MET cc_start: 0.8645 (mmm) cc_final: 0.8212 (mmt) REVERT: A 375 LYS cc_start: 0.8737 (tppp) cc_final: 0.8484 (ttpp) REVERT: A 383 MET cc_start: 0.7145 (mmm) cc_final: 0.6563 (mmm) REVERT: A 385 TRP cc_start: 0.8496 (m100) cc_final: 0.8144 (m100) REVERT: A 486 ILE cc_start: 0.8729 (mp) cc_final: 0.8497 (mm) REVERT: A 487 SER cc_start: 0.8309 (t) cc_final: 0.7984 (p) REVERT: A 511 MET cc_start: 0.8893 (tmm) cc_final: 0.8683 (tmm) REVERT: A 531 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6836 (tm-30) REVERT: A 554 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7769 (tp30) REVERT: A 565 MET cc_start: 0.6015 (pmm) cc_final: 0.5626 (pmm) REVERT: A 578 MET cc_start: 0.8623 (mtp) cc_final: 0.8395 (mtp) REVERT: A 579 MET cc_start: 0.7940 (tmm) cc_final: 0.7728 (tpp) REVERT: A 580 GLU cc_start: 0.8146 (tp30) cc_final: 0.7745 (tp30) REVERT: A 602 MET cc_start: 0.7589 (mpp) cc_final: 0.7325 (mpp) REVERT: A 632 LYS cc_start: 0.8221 (ttpt) cc_final: 0.7962 (ttmm) REVERT: A 634 SER cc_start: 0.8922 (m) cc_final: 0.8641 (t) REVERT: A 647 LYS cc_start: 0.8662 (mmtp) cc_final: 0.8411 (mmtm) REVERT: A 697 MET cc_start: 0.6486 (mmm) cc_final: 0.5890 (mmm) REVERT: A 815 LYS cc_start: 0.9044 (tttt) cc_final: 0.8681 (tppp) REVERT: A 820 LYS cc_start: 0.8296 (mmmt) cc_final: 0.7993 (mmmt) REVERT: A 841 LYS cc_start: 0.8968 (mtpt) cc_final: 0.8536 (mtpt) REVERT: A 853 ILE cc_start: 0.8782 (tp) cc_final: 0.8527 (tp) REVERT: A 877 GLN cc_start: 0.8601 (tt0) cc_final: 0.8310 (tt0) REVERT: A 942 MET cc_start: 0.8475 (tpp) cc_final: 0.8257 (tpt) REVERT: A 972 PHE cc_start: 0.8598 (t80) cc_final: 0.8327 (t80) REVERT: A 982 PHE cc_start: 0.8155 (m-80) cc_final: 0.7837 (m-80) REVERT: A 983 ASP cc_start: 0.8015 (t0) cc_final: 0.7668 (p0) REVERT: A 994 GLU cc_start: 0.7825 (pm20) cc_final: 0.7482 (pm20) REVERT: A 1003 SER cc_start: 0.8449 (t) cc_final: 0.8233 (m) REVERT: A 1008 LEU cc_start: 0.8174 (mp) cc_final: 0.7818 (tp) REVERT: A 1044 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7684 (mt-10) REVERT: A 1060 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7653 (mm-30) REVERT: A 1061 THR cc_start: 0.7735 (OUTLIER) cc_final: 0.7504 (p) REVERT: A 1066 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: A 1073 MET cc_start: 0.8639 (tpp) cc_final: 0.8299 (tpp) REVERT: A 1080 PHE cc_start: 0.8033 (m-80) cc_final: 0.7435 (m-80) REVERT: A 1116 LYS cc_start: 0.8526 (mttt) cc_final: 0.7756 (mttt) REVERT: A 1121 LEU cc_start: 0.8915 (mm) cc_final: 0.8659 (mt) REVERT: A 1122 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7842 (tp30) REVERT: A 1136 PHE cc_start: 0.6920 (t80) cc_final: 0.6556 (t80) REVERT: A 1173 LYS cc_start: 0.7565 (mtpp) cc_final: 0.7129 (mtpp) REVERT: A 1190 ARG cc_start: 0.8102 (mmm-85) cc_final: 0.7773 (mmm-85) REVERT: A 1212 ILE cc_start: 0.5475 (OUTLIER) cc_final: 0.4960 (mp) REVERT: B 134 ASP cc_start: 0.8199 (t0) cc_final: 0.7800 (t70) REVERT: B 300 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7896 (mt-10) REVERT: B 337 GLU cc_start: 0.7813 (tp30) cc_final: 0.7492 (tp30) REVERT: B 375 LYS cc_start: 0.8766 (tppp) cc_final: 0.8391 (mtmm) REVERT: B 383 MET cc_start: 0.7238 (tpp) cc_final: 0.6695 (mmm) REVERT: B 385 TRP cc_start: 0.8418 (m100) cc_final: 0.8095 (m100) REVERT: B 443 GLU cc_start: 0.8312 (tm-30) cc_final: 0.8003 (tm-30) REVERT: B 487 SER cc_start: 0.8411 (t) cc_final: 0.8133 (p) REVERT: B 511 MET cc_start: 0.8961 (tmm) cc_final: 0.8738 (tmm) REVERT: B 531 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6908 (tm-30) REVERT: B 578 MET cc_start: 0.8601 (mtp) cc_final: 0.8284 (mtp) REVERT: B 581 GLU cc_start: 0.8444 (tp30) cc_final: 0.8153 (tp30) REVERT: B 586 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8447 (ttp) REVERT: B 588 LYS cc_start: 0.8616 (tppt) cc_final: 0.8342 (tttm) REVERT: B 697 MET cc_start: 0.5795 (mmm) cc_final: 0.5192 (mmm) REVERT: B 736 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.7965 (t0) REVERT: B 810 MET cc_start: 0.7039 (ptt) cc_final: 0.6822 (ptt) REVERT: B 820 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7915 (mmmt) REVERT: B 825 VAL cc_start: 0.8761 (t) cc_final: 0.8464 (p) REVERT: B 832 GLN cc_start: 0.8601 (tt0) cc_final: 0.8315 (tp-100) REVERT: B 852 LYS cc_start: 0.8413 (mttp) cc_final: 0.8073 (ttmm) REVERT: B 859 ASP cc_start: 0.7988 (p0) cc_final: 0.7640 (p0) REVERT: B 926 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7726 (mm-30) REVERT: B 947 SER cc_start: 0.7990 (t) cc_final: 0.7788 (t) REVERT: B 954 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7629 (mm-30) REVERT: B 958 LYS cc_start: 0.8899 (ttpt) cc_final: 0.8549 (ttmm) REVERT: B 968 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8393 (mmmm) REVERT: B 972 PHE cc_start: 0.8788 (t80) cc_final: 0.8436 (t80) REVERT: B 980 LEU cc_start: 0.8835 (mt) cc_final: 0.8629 (mt) REVERT: B 993 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.6622 (m-30) REVERT: B 994 GLU cc_start: 0.7819 (pm20) cc_final: 0.7551 (pm20) REVERT: B 996 ASP cc_start: 0.7374 (p0) cc_final: 0.7127 (p0) REVERT: B 1003 SER cc_start: 0.8512 (t) cc_final: 0.8189 (m) REVERT: B 1006 VAL cc_start: 0.8409 (m) cc_final: 0.8164 (p) REVERT: B 1073 MET cc_start: 0.8601 (tpp) cc_final: 0.8131 (tpp) REVERT: B 1098 ILE cc_start: 0.8917 (tt) cc_final: 0.8560 (tp) REVERT: B 1104 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7406 (tpp) REVERT: B 1118 LYS cc_start: 0.8628 (mtpp) cc_final: 0.8302 (mtmm) REVERT: B 1121 LEU cc_start: 0.8978 (mm) cc_final: 0.8703 (mt) REVERT: B 1122 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7742 (tp30) REVERT: B 1126 LEU cc_start: 0.8362 (mt) cc_final: 0.7983 (pt) REVERT: B 1144 ASP cc_start: 0.7190 (m-30) cc_final: 0.6966 (m-30) REVERT: B 1160 GLU cc_start: 0.5990 (mp0) cc_final: 0.5776 (mt-10) REVERT: B 1162 ARG cc_start: 0.5707 (OUTLIER) cc_final: 0.5134 (tpm-80) REVERT: B 1179 THR cc_start: 0.5318 (OUTLIER) cc_final: 0.5074 (p) REVERT: B 1190 ARG cc_start: 0.7949 (mmm-85) cc_final: 0.7730 (mmm-85) REVERT: B 1212 ILE cc_start: 0.5518 (OUTLIER) cc_final: 0.5214 (mp) outliers start: 90 outliers final: 50 residues processed: 603 average time/residue: 0.1358 time to fit residues: 117.9591 Evaluate side-chains 594 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 531 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 174 LEU Chi-restraints excluded: chain A residue 191 TYR 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 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 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 624 GLN Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 876 LEU 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 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 137 VAL 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 372 VAL 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 418 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 963 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 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 1212 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 196 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 140 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 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 165 GLN A 981 HIS A1220 ASN B 165 GLN B 597 GLN B1220 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.144489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120980 restraints weight = 25351.915| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.10 r_work: 0.3386 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16740 Z= 0.145 Angle : 0.623 16.198 22706 Z= 0.306 Chirality : 0.041 0.171 2734 Planarity : 0.004 0.062 2796 Dihedral : 7.563 133.464 2292 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.30 % Allowed : 19.59 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.19), residues: 2050 helix: 1.77 (0.14), residues: 1456 sheet: -3.06 (0.48), residues: 82 loop : -1.69 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1185 TYR 0.010 0.001 TYR B1153 PHE 0.020 0.001 PHE B 680 TRP 0.032 0.001 TRP A1112 HIS 0.012 0.001 HIS A 981 Details of bonding type rmsd covalent geometry : bond 0.00305 (16740) covalent geometry : angle 0.62275 (22706) hydrogen bonds : bond 0.04626 ( 1163) hydrogen bonds : angle 4.26637 ( 3459) *********************** 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: 95 poor density : 549 time to evaluate : 0.648 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: A 112 ILE cc_start: 0.8706 (mm) cc_final: 0.8289 (mt) REVERT: A 116 VAL cc_start: 0.8787 (t) cc_final: 0.8520 (t) REVERT: A 149 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7476 (tm-30) REVERT: A 160 MET cc_start: 0.8385 (mmm) cc_final: 0.8181 (mpp) REVERT: A 174 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8267 (tt) REVERT: A 176 VAL cc_start: 0.8901 (p) cc_final: 0.8640 (t) REVERT: A 225 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7644 (tp40) REVERT: A 233 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7628 (tm-30) REVERT: A 266 LEU cc_start: 0.8405 (tp) cc_final: 0.8163 (tt) REVERT: A 269 LEU cc_start: 0.8505 (tp) cc_final: 0.8219 (tt) REVERT: A 337 GLU cc_start: 0.7760 (tp30) cc_final: 0.7456 (tp30) REVERT: A 346 GLU cc_start: 0.7737 (tt0) cc_final: 0.7472 (tt0) REVERT: A 354 GLU cc_start: 0.8224 (tt0) cc_final: 0.7895 (tt0) REVERT: A 375 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8552 (ttpp) REVERT: A 383 MET cc_start: 0.7070 (mmm) cc_final: 0.6577 (mmm) REVERT: A 387 TYR cc_start: 0.8540 (m-10) cc_final: 0.8101 (m-10) REVERT: A 443 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8156 (tm-30) REVERT: A 486 ILE cc_start: 0.8762 (mp) cc_final: 0.8523 (mm) REVERT: A 487 SER cc_start: 0.8268 (t) cc_final: 0.7932 (p) REVERT: A 531 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6831 (tm-30) REVERT: A 578 MET cc_start: 0.8613 (mtp) cc_final: 0.8412 (mtp) REVERT: A 579 MET cc_start: 0.7926 (tmm) cc_final: 0.7709 (tpp) REVERT: A 580 GLU cc_start: 0.8144 (tp30) cc_final: 0.7700 (tp30) REVERT: A 599 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: A 602 MET cc_start: 0.7559 (mpp) cc_final: 0.7288 (mpp) REVERT: A 632 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7978 (ttmm) REVERT: A 647 LYS cc_start: 0.8689 (mmtp) cc_final: 0.8443 (mmtm) REVERT: A 697 MET cc_start: 0.6534 (mmm) cc_final: 0.5921 (mmm) REVERT: A 815 LYS cc_start: 0.9020 (tttt) cc_final: 0.8648 (tppp) REVERT: A 820 LYS cc_start: 0.8311 (mmmt) cc_final: 0.7997 (mmmt) REVERT: A 841 LYS cc_start: 0.8970 (mtpt) cc_final: 0.8556 (mtpt) REVERT: A 877 GLN cc_start: 0.8605 (tt0) cc_final: 0.8299 (tt0) REVERT: A 897 LYS cc_start: 0.8958 (mttm) cc_final: 0.8719 (mmtp) REVERT: A 942 MET cc_start: 0.8512 (tpp) cc_final: 0.8307 (tpt) REVERT: A 978 SER cc_start: 0.8440 (t) cc_final: 0.8000 (p) REVERT: A 994 GLU cc_start: 0.7771 (pm20) cc_final: 0.7444 (pm20) REVERT: A 1003 SER cc_start: 0.8453 (t) cc_final: 0.8219 (m) REVERT: A 1008 LEU cc_start: 0.8189 (mp) cc_final: 0.7859 (tp) REVERT: A 1044 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7605 (mt-10) REVERT: A 1060 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7685 (mm-30) REVERT: A 1061 THR cc_start: 0.7699 (OUTLIER) cc_final: 0.7460 (p) REVERT: A 1066 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7610 (m-80) REVERT: A 1072 ASP cc_start: 0.7541 (m-30) cc_final: 0.7309 (m-30) REVERT: A 1080 PHE cc_start: 0.8042 (m-80) cc_final: 0.7537 (m-80) REVERT: A 1121 LEU cc_start: 0.8975 (mm) cc_final: 0.8712 (mt) REVERT: A 1122 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7928 (tp30) REVERT: A 1136 PHE cc_start: 0.6871 (t80) cc_final: 0.6631 (t80) REVERT: A 1139 ASP cc_start: 0.7719 (m-30) cc_final: 0.7392 (m-30) REVERT: A 1190 ARG cc_start: 0.8120 (mmm-85) cc_final: 0.7733 (mmm-85) REVERT: A 1212 ILE cc_start: 0.5517 (OUTLIER) cc_final: 0.4947 (mp) REVERT: B 103 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8343 (p) REVERT: B 116 VAL cc_start: 0.8624 (t) cc_final: 0.8285 (m) REVERT: B 134 ASP cc_start: 0.8208 (t0) cc_final: 0.7862 (t70) REVERT: B 149 GLU cc_start: 0.7906 (tp30) cc_final: 0.7583 (tm-30) REVERT: B 337 GLU cc_start: 0.7813 (tp30) cc_final: 0.7501 (tp30) REVERT: B 375 LYS cc_start: 0.8783 (tppp) cc_final: 0.8306 (mtpp) REVERT: B 383 MET cc_start: 0.7254 (tpp) cc_final: 0.6685 (mmm) REVERT: B 385 TRP cc_start: 0.8437 (m100) cc_final: 0.8170 (m100) REVERT: B 410 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8313 (mt) REVERT: B 487 SER cc_start: 0.8402 (t) cc_final: 0.8113 (p) REVERT: B 511 MET cc_start: 0.8955 (tmm) cc_final: 0.8547 (tmm) REVERT: B 531 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6954 (tm-30) REVERT: B 554 GLU cc_start: 0.8192 (tp30) cc_final: 0.7730 (tp30) REVERT: B 579 MET cc_start: 0.8137 (tpp) cc_final: 0.7784 (tpp) REVERT: B 580 GLU cc_start: 0.8008 (tp30) cc_final: 0.7732 (tp30) REVERT: B 581 GLU cc_start: 0.8445 (tp30) cc_final: 0.8241 (tp30) REVERT: B 588 LYS cc_start: 0.8608 (tppt) cc_final: 0.8340 (tttm) REVERT: B 647 LYS cc_start: 0.8543 (mmtm) cc_final: 0.8303 (mmtp) REVERT: B 697 MET cc_start: 0.5823 (mmm) cc_final: 0.5173 (mmm) REVERT: B 736 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.7997 (t0) REVERT: B 810 MET cc_start: 0.6895 (ptt) cc_final: 0.6656 (ptt) REVERT: B 815 LYS cc_start: 0.9114 (tttt) cc_final: 0.8642 (tppp) REVERT: B 820 LYS cc_start: 0.8194 (mmmt) cc_final: 0.7928 (mmmt) REVERT: B 832 GLN cc_start: 0.8576 (tt0) cc_final: 0.8291 (tp-100) REVERT: B 852 LYS cc_start: 0.8451 (mttp) cc_final: 0.8026 (mtpt) REVERT: B 856 ARG cc_start: 0.8035 (ttp80) cc_final: 0.7749 (ttp80) REVERT: B 859 ASP cc_start: 0.8008 (p0) cc_final: 0.7726 (p0) REVERT: B 884 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8150 (mm) REVERT: B 926 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7799 (mm-30) REVERT: B 947 SER cc_start: 0.8063 (t) cc_final: 0.7860 (t) REVERT: B 954 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7570 (mm-30) REVERT: B 958 LYS cc_start: 0.8917 (ttpt) cc_final: 0.8560 (ttmm) REVERT: B 968 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8379 (mmmm) REVERT: B 993 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.6768 (m-30) REVERT: B 994 GLU cc_start: 0.7843 (pm20) cc_final: 0.7474 (pm20) REVERT: B 996 ASP cc_start: 0.7398 (p0) cc_final: 0.7184 (p0) REVERT: B 1003 SER cc_start: 0.8542 (t) cc_final: 0.8273 (m) REVERT: B 1006 VAL cc_start: 0.8433 (m) cc_final: 0.8182 (t) REVERT: B 1066 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: B 1098 ILE cc_start: 0.8917 (tt) cc_final: 0.8564 (tp) REVERT: B 1118 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8317 (mtmm) REVERT: B 1121 LEU cc_start: 0.9019 (mm) cc_final: 0.8720 (mt) REVERT: B 1122 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7759 (tp30) REVERT: B 1144 ASP cc_start: 0.7194 (m-30) cc_final: 0.6944 (m-30) REVERT: B 1162 ARG cc_start: 0.5720 (OUTLIER) cc_final: 0.5092 (tpm-80) REVERT: B 1179 THR cc_start: 0.5331 (OUTLIER) cc_final: 0.5100 (p) REVERT: B 1212 ILE cc_start: 0.5352 (OUTLIER) cc_final: 0.5008 (mp) REVERT: B 1220 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7899 (m-40) outliers start: 95 outliers final: 58 residues processed: 599 average time/residue: 0.1514 time to fit residues: 130.6957 Evaluate side-chains 602 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 527 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 174 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 214 VAL 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 375 LYS 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 490 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 852 LYS 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 1100 THR Chi-restraints excluded: chain A residue 1102 LEU 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 1154 ASN 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 103 THR Chi-restraints excluded: chain B residue 137 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 410 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 451 ILE 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 736 ASN Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 865 ARG Chi-restraints excluded: chain B residue 884 LEU 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 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 1212 ILE Chi-restraints excluded: chain B residue 1220 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 65 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 52 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 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 600 HIS A 943 ASN B1220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.144380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121272 restraints weight = 25459.681| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.07 r_work: 0.3393 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16740 Z= 0.143 Angle : 0.628 16.515 22706 Z= 0.308 Chirality : 0.041 0.168 2734 Planarity : 0.004 0.062 2796 Dihedral : 7.368 133.299 2289 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.80 % Allowed : 19.92 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.19), residues: 2050 helix: 1.88 (0.14), residues: 1454 sheet: -2.37 (0.53), residues: 76 loop : -1.67 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1185 TYR 0.009 0.001 TYR B 415 PHE 0.023 0.001 PHE A 598 TRP 0.041 0.001 TRP A1112 HIS 0.008 0.001 HIS A 981 Details of bonding type rmsd covalent geometry : bond 0.00302 (16740) covalent geometry : angle 0.62839 (22706) hydrogen bonds : bond 0.04610 ( 1163) hydrogen bonds : angle 4.22685 ( 3459) *********************** 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 643 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 539 time to evaluate : 0.595 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: 0.8707 (mm) cc_final: 0.8302 (mt) REVERT: A 116 VAL cc_start: 0.8769 (t) cc_final: 0.8488 (t) REVERT: A 149 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7499 (tm-30) REVERT: A 174 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8254 (tt) REVERT: A 176 VAL cc_start: 0.8897 (p) cc_final: 0.8640 (t) REVERT: A 225 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7561 (tp40) REVERT: A 233 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7672 (tm-30) REVERT: A 266 LEU cc_start: 0.8395 (tp) cc_final: 0.8145 (tt) REVERT: A 269 LEU cc_start: 0.8563 (tp) cc_final: 0.8282 (tt) REVERT: A 337 GLU cc_start: 0.7794 (tp30) cc_final: 0.7502 (tp30) REVERT: A 338 LYS cc_start: 0.8731 (mtmm) cc_final: 0.8092 (mtmm) REVERT: A 346 GLU cc_start: 0.7815 (tt0) cc_final: 0.7490 (tt0) REVERT: A 354 GLU cc_start: 0.8253 (tt0) cc_final: 0.7900 (tt0) REVERT: A 375 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8539 (ttpp) REVERT: A 383 MET cc_start: 0.7071 (mmm) cc_final: 0.6610 (mmm) REVERT: A 486 ILE cc_start: 0.8752 (mp) cc_final: 0.8506 (mm) REVERT: A 487 SER cc_start: 0.8245 (t) cc_final: 0.7912 (p) REVERT: A 511 MET cc_start: 0.8836 (tmm) cc_final: 0.8525 (ttp) REVERT: A 531 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6820 (tm-30) REVERT: A 578 MET cc_start: 0.8631 (mtp) cc_final: 0.8416 (mtp) REVERT: A 579 MET cc_start: 0.7979 (tmm) cc_final: 0.7735 (tpp) REVERT: A 580 GLU cc_start: 0.8131 (tp30) cc_final: 0.7661 (tp30) REVERT: A 602 MET cc_start: 0.7640 (mpp) cc_final: 0.7354 (mpp) REVERT: A 632 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7988 (ttmm) REVERT: A 647 LYS cc_start: 0.8733 (mmtp) cc_final: 0.8479 (mmtm) REVERT: A 697 MET cc_start: 0.6579 (mmm) cc_final: 0.5973 (mmm) REVERT: A 815 LYS cc_start: 0.9015 (tttt) cc_final: 0.8637 (tppp) REVERT: A 820 LYS cc_start: 0.8265 (mmmt) cc_final: 0.7965 (mmmt) REVERT: A 841 LYS cc_start: 0.8985 (mtpt) cc_final: 0.8586 (mtpt) REVERT: A 877 GLN cc_start: 0.8612 (tt0) cc_final: 0.8297 (tt0) REVERT: A 897 LYS cc_start: 0.8947 (mttm) cc_final: 0.8723 (mmtp) REVERT: A 923 ASP cc_start: 0.7503 (p0) cc_final: 0.7156 (p0) REVERT: A 978 SER cc_start: 0.8527 (t) cc_final: 0.8086 (p) REVERT: A 994 GLU cc_start: 0.7743 (pm20) cc_final: 0.7424 (pm20) REVERT: A 1003 SER cc_start: 0.8462 (t) cc_final: 0.8253 (m) REVERT: A 1006 VAL cc_start: 0.8477 (m) cc_final: 0.8193 (t) REVERT: A 1008 LEU cc_start: 0.8208 (mp) cc_final: 0.7920 (tp) REVERT: A 1044 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7579 (mt-10) REVERT: A 1060 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7657 (mm-30) REVERT: A 1061 THR cc_start: 0.7739 (OUTLIER) cc_final: 0.7500 (p) REVERT: A 1066 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: A 1072 ASP cc_start: 0.7612 (m-30) cc_final: 0.7383 (m-30) REVERT: A 1073 MET cc_start: 0.8765 (tpp) cc_final: 0.8525 (tpp) REVERT: A 1080 PHE cc_start: 0.8029 (m-80) cc_final: 0.7553 (m-80) REVERT: A 1121 LEU cc_start: 0.8982 (mm) cc_final: 0.8723 (mt) REVERT: A 1122 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7936 (tp30) REVERT: A 1139 ASP cc_start: 0.7701 (m-30) cc_final: 0.7331 (m-30) REVERT: A 1190 ARG cc_start: 0.8105 (mmm-85) cc_final: 0.7720 (mmm-85) REVERT: A 1212 ILE cc_start: 0.5409 (OUTLIER) cc_final: 0.4870 (mp) REVERT: B 103 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8310 (p) REVERT: B 149 GLU cc_start: 0.7954 (tp30) cc_final: 0.7600 (tm-30) REVERT: B 155 ASP cc_start: 0.8262 (t0) cc_final: 0.7988 (t0) REVERT: B 337 GLU cc_start: 0.7831 (tp30) cc_final: 0.7529 (tp30) REVERT: B 375 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8407 (mtpp) REVERT: B 383 MET cc_start: 0.7264 (tpp) cc_final: 0.6713 (mmm) REVERT: B 385 TRP cc_start: 0.8441 (m100) cc_final: 0.8176 (m100) REVERT: B 419 TRP cc_start: 0.8175 (p-90) cc_final: 0.7876 (p-90) REVERT: B 443 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8107 (tm-30) REVERT: B 487 SER cc_start: 0.8409 (t) cc_final: 0.8110 (p) REVERT: B 511 MET cc_start: 0.8948 (tmm) cc_final: 0.8479 (ttp) REVERT: B 581 GLU cc_start: 0.8392 (tp30) cc_final: 0.8105 (tp30) REVERT: B 588 LYS cc_start: 0.8570 (tppt) cc_final: 0.8320 (tttm) REVERT: B 621 GLU cc_start: 0.7638 (pp20) cc_final: 0.7233 (pp20) REVERT: B 697 MET cc_start: 0.5897 (mmm) cc_final: 0.5272 (mmm) REVERT: B 736 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.7990 (t0) REVERT: B 810 MET cc_start: 0.6977 (ptt) cc_final: 0.6774 (ptt) REVERT: B 815 LYS cc_start: 0.9114 (tttt) cc_final: 0.8636 (tppp) REVERT: B 820 LYS cc_start: 0.8214 (mmmt) cc_final: 0.7925 (mmmt) REVERT: B 832 GLN cc_start: 0.8599 (tt0) cc_final: 0.8327 (tp-100) REVERT: B 852 LYS cc_start: 0.8511 (mttp) cc_final: 0.8160 (mtpt) REVERT: B 859 ASP cc_start: 0.8071 (p0) cc_final: 0.7812 (p0) REVERT: B 877 GLN cc_start: 0.8744 (tt0) cc_final: 0.8465 (tt0) REVERT: B 954 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7603 (mm-30) REVERT: B 958 LYS cc_start: 0.8950 (ttpt) cc_final: 0.8586 (ttmm) REVERT: B 968 LYS cc_start: 0.8692 (mtpp) cc_final: 0.8379 (mmmm) REVERT: B 993 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.6767 (m-30) REVERT: B 994 GLU cc_start: 0.7841 (pm20) cc_final: 0.7465 (pm20) REVERT: B 996 ASP cc_start: 0.7430 (p0) cc_final: 0.7218 (p0) REVERT: B 998 LEU cc_start: 0.8607 (mm) cc_final: 0.8392 (mt) REVERT: B 1003 SER cc_start: 0.8525 (t) cc_final: 0.8284 (m) REVERT: B 1007 LYS cc_start: 0.7987 (ttpp) cc_final: 0.7757 (ttpp) REVERT: B 1066 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: B 1098 ILE cc_start: 0.8907 (tt) cc_final: 0.8550 (tp) REVERT: B 1118 LYS cc_start: 0.8643 (mtpp) cc_final: 0.8367 (mtmm) REVERT: B 1121 LEU cc_start: 0.9024 (mm) cc_final: 0.8747 (mt) REVERT: B 1144 ASP cc_start: 0.7237 (m-30) cc_final: 0.7013 (m-30) REVERT: B 1162 ARG cc_start: 0.5848 (OUTLIER) cc_final: 0.5159 (tpm-80) REVERT: B 1179 THR cc_start: 0.5203 (OUTLIER) cc_final: 0.4985 (p) REVERT: B 1212 ILE cc_start: 0.5370 (OUTLIER) cc_final: 0.5014 (mp) outliers start: 104 outliers final: 63 residues processed: 589 average time/residue: 0.1416 time to fit residues: 120.2736 Evaluate side-chains 605 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 528 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 174 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 214 VAL 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 375 LYS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 MET 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 532 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 616 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 915 GLU Chi-restraints excluded: chain A residue 941 LEU 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 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 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 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 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 VAL 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 415 TYR 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 606 GLU Chi-restraints excluded: chain B residue 616 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 865 ARG 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 1061 THR Chi-restraints excluded: chain B residue 1066 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 176 optimal weight: 0.0010 chunk 181 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 195 optimal weight: 0.2980 chunk 7 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS A1220 ASN B 225 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.144476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.121531 restraints weight = 25417.212| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.07 r_work: 0.3392 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16740 Z= 0.135 Angle : 0.626 16.175 22706 Z= 0.307 Chirality : 0.041 0.167 2734 Planarity : 0.004 0.061 2796 Dihedral : 7.308 133.438 2289 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.97 % Allowed : 20.98 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.19), residues: 2050 helix: 1.99 (0.14), residues: 1456 sheet: -2.16 (0.55), residues: 76 loop : -1.68 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 609 TYR 0.014 0.001 TYR B 415 PHE 0.019 0.001 PHE A 598 TRP 0.034 0.001 TRP A1112 HIS 0.004 0.001 HIS A1156 Details of bonding type rmsd covalent geometry : bond 0.00284 (16740) covalent geometry : angle 0.62620 (22706) hydrogen bonds : bond 0.04488 ( 1163) hydrogen bonds : angle 4.17777 ( 3459) *********************** 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 624 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 535 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8681 (mm) cc_final: 0.8285 (mt) REVERT: A 116 VAL cc_start: 0.8745 (t) cc_final: 0.8464 (t) REVERT: A 149 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 174 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8271 (tt) REVERT: A 225 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7541 (tp40) REVERT: A 233 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7636 (tm-30) REVERT: A 266 LEU cc_start: 0.8382 (tp) cc_final: 0.8134 (tt) REVERT: A 269 LEU cc_start: 0.8547 (tp) cc_final: 0.8277 (tt) REVERT: A 337 GLU cc_start: 0.7726 (tp30) cc_final: 0.7442 (tp30) REVERT: A 338 LYS cc_start: 0.8733 (mtmm) cc_final: 0.8090 (mtmm) REVERT: A 346 GLU cc_start: 0.7775 (tt0) cc_final: 0.7472 (tt0) REVERT: A 354 GLU cc_start: 0.8229 (tt0) cc_final: 0.7885 (tt0) REVERT: A 383 MET cc_start: 0.6968 (mmm) cc_final: 0.6530 (mmm) REVERT: A 486 ILE cc_start: 0.8720 (mp) cc_final: 0.8478 (mm) REVERT: A 487 SER cc_start: 0.8199 (t) cc_final: 0.7864 (p) REVERT: A 511 MET cc_start: 0.8857 (tmm) cc_final: 0.8550 (ttp) REVERT: A 531 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6798 (tm-30) REVERT: A 578 MET cc_start: 0.8589 (mtp) cc_final: 0.8380 (mtp) REVERT: A 579 MET cc_start: 0.7970 (tmm) cc_final: 0.7759 (tpp) REVERT: A 580 GLU cc_start: 0.8101 (tp30) cc_final: 0.7642 (tp30) REVERT: A 602 MET cc_start: 0.7561 (mpp) cc_final: 0.7294 (mpp) REVERT: A 632 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7934 (ttmm) REVERT: A 634 SER cc_start: 0.8921 (m) cc_final: 0.8660 (t) REVERT: A 647 LYS cc_start: 0.8728 (mmtp) cc_final: 0.8492 (mmtm) REVERT: A 697 MET cc_start: 0.6563 (mmm) cc_final: 0.5942 (mmm) REVERT: A 815 LYS cc_start: 0.8987 (tttt) cc_final: 0.8655 (tppp) REVERT: A 820 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7831 (mmmt) REVERT: A 841 LYS cc_start: 0.8977 (mtpt) cc_final: 0.8591 (mtpt) REVERT: A 884 LEU cc_start: 0.8458 (mm) cc_final: 0.8232 (mm) REVERT: A 897 LYS cc_start: 0.8934 (mttm) cc_final: 0.8714 (mmtp) REVERT: A 923 ASP cc_start: 0.7461 (p0) cc_final: 0.7123 (p0) REVERT: A 967 MET cc_start: 0.8060 (tpp) cc_final: 0.7703 (mmm) REVERT: A 978 SER cc_start: 0.8531 (t) cc_final: 0.8100 (p) REVERT: A 994 GLU cc_start: 0.7673 (pm20) cc_final: 0.7355 (pm20) REVERT: A 1003 SER cc_start: 0.8445 (t) cc_final: 0.8201 (m) REVERT: A 1006 VAL cc_start: 0.8418 (m) cc_final: 0.8179 (t) REVERT: A 1008 LEU cc_start: 0.8207 (mp) cc_final: 0.7907 (tp) REVERT: A 1044 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7530 (mt-10) REVERT: A 1061 THR cc_start: 0.7734 (OUTLIER) cc_final: 0.7335 (p) REVERT: A 1066 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.7830 (m-80) REVERT: A 1072 ASP cc_start: 0.7562 (m-30) cc_final: 0.7344 (m-30) REVERT: A 1073 MET cc_start: 0.8753 (tpp) cc_final: 0.8532 (tpp) REVERT: A 1080 PHE cc_start: 0.7970 (m-80) cc_final: 0.7520 (m-80) REVERT: A 1087 GLU cc_start: 0.7461 (tm-30) cc_final: 0.6944 (tm-30) REVERT: A 1121 LEU cc_start: 0.8980 (mm) cc_final: 0.8742 (mt) REVERT: A 1139 ASP cc_start: 0.7622 (m-30) cc_final: 0.7258 (m-30) REVERT: A 1185 ARG cc_start: 0.6883 (mmt-90) cc_final: 0.6627 (mmt180) REVERT: A 1190 ARG cc_start: 0.8016 (mmm-85) cc_final: 0.7667 (mmm-85) REVERT: A 1212 ILE cc_start: 0.5409 (OUTLIER) cc_final: 0.4856 (mp) REVERT: B 116 VAL cc_start: 0.8605 (t) cc_final: 0.8299 (m) REVERT: B 149 GLU cc_start: 0.7913 (tp30) cc_final: 0.7580 (tm-30) REVERT: B 155 ASP cc_start: 0.8186 (t0) cc_final: 0.7915 (t0) REVERT: B 231 GLU cc_start: 0.8101 (tt0) cc_final: 0.7893 (tt0) REVERT: B 233 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7714 (tm-30) REVERT: B 265 VAL cc_start: 0.8670 (t) cc_final: 0.8370 (p) REVERT: B 337 GLU cc_start: 0.7776 (tp30) cc_final: 0.7469 (tp30) REVERT: B 375 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8407 (mtpp) REVERT: B 383 MET cc_start: 0.7216 (tpp) cc_final: 0.6737 (mmm) REVERT: B 419 TRP cc_start: 0.8120 (p-90) cc_final: 0.7872 (p-90) REVERT: B 424 ILE cc_start: 0.8768 (mm) cc_final: 0.8397 (tp) REVERT: B 487 SER cc_start: 0.8382 (t) cc_final: 0.8088 (p) REVERT: B 511 MET cc_start: 0.8939 (tmm) cc_final: 0.8483 (ttp) REVERT: B 579 MET cc_start: 0.8165 (tpp) cc_final: 0.7734 (tpp) REVERT: B 581 GLU cc_start: 0.8342 (tp30) cc_final: 0.8060 (tp30) REVERT: B 588 LYS cc_start: 0.8566 (tppt) cc_final: 0.8310 (tttm) REVERT: B 621 GLU cc_start: 0.7594 (pp20) cc_final: 0.7353 (pm20) REVERT: B 628 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7561 (t) REVERT: B 634 SER cc_start: 0.8960 (m) cc_final: 0.8733 (t) REVERT: B 697 MET cc_start: 0.5795 (mmm) cc_final: 0.5171 (mmm) REVERT: B 736 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.7983 (t0) REVERT: B 810 MET cc_start: 0.7011 (ptt) cc_final: 0.6793 (ptt) REVERT: B 815 LYS cc_start: 0.9096 (tttt) cc_final: 0.8645 (tppp) REVERT: B 820 LYS cc_start: 0.8077 (mmmt) cc_final: 0.7827 (mmmt) REVERT: B 852 LYS cc_start: 0.8489 (mttp) cc_final: 0.8045 (mtpt) REVERT: B 853 ILE cc_start: 0.8936 (tp) cc_final: 0.8627 (tt) REVERT: B 859 ASP cc_start: 0.8037 (p0) cc_final: 0.7782 (p0) REVERT: B 877 GLN cc_start: 0.8714 (tt0) cc_final: 0.8251 (tt0) REVERT: B 887 ARG cc_start: 0.8229 (tpp80) cc_final: 0.7942 (ttm-80) REVERT: B 910 ARG cc_start: 0.8690 (ttp-170) cc_final: 0.8194 (ttp-170) REVERT: B 935 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8138 (mm-30) REVERT: B 954 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7566 (mm-30) REVERT: B 958 LYS cc_start: 0.8939 (ttpt) cc_final: 0.8535 (ttmm) REVERT: B 968 LYS cc_start: 0.8638 (mtpp) cc_final: 0.8330 (mmmm) REVERT: B 972 PHE cc_start: 0.8725 (t80) cc_final: 0.8472 (t80) REVERT: B 993 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.6732 (m-30) REVERT: B 994 GLU cc_start: 0.7737 (pm20) cc_final: 0.7374 (pm20) REVERT: B 996 ASP cc_start: 0.7421 (p0) cc_final: 0.7208 (p0) REVERT: B 998 LEU cc_start: 0.8570 (mm) cc_final: 0.8364 (mt) REVERT: B 1003 SER cc_start: 0.8514 (t) cc_final: 0.8250 (m) REVERT: B 1006 VAL cc_start: 0.8480 (m) cc_final: 0.8241 (p) REVERT: B 1008 LEU cc_start: 0.7894 (mp) cc_final: 0.7693 (mm) REVERT: B 1066 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.8241 (m-80) REVERT: B 1073 MET cc_start: 0.8592 (tpp) cc_final: 0.8388 (tpp) REVERT: B 1075 ILE cc_start: 0.8939 (mt) cc_final: 0.8543 (tt) REVERT: B 1118 LYS cc_start: 0.8633 (mtpp) cc_final: 0.8359 (mtmm) REVERT: B 1121 LEU cc_start: 0.9013 (mm) cc_final: 0.8734 (mt) REVERT: B 1162 ARG cc_start: 0.5845 (OUTLIER) cc_final: 0.5178 (tpm-80) REVERT: B 1212 ILE cc_start: 0.5363 (OUTLIER) cc_final: 0.5013 (mp) outliers start: 89 outliers final: 55 residues processed: 578 average time/residue: 0.1487 time to fit residues: 124.4778 Evaluate side-chains 590 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 523 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 174 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL 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 395 ILE 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 451 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 963 LEU 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 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 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL 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 321 VAL 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 418 THR Chi-restraints excluded: chain B residue 445 LEU 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 863 ILE Chi-restraints excluded: chain B residue 865 ARG 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 1061 THR Chi-restraints excluded: chain B residue 1066 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 1156 HIS Chi-restraints excluded: chain B residue 1162 ARG 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 162 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.141068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.118019 restraints weight = 25202.109| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.04 r_work: 0.3374 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16740 Z= 0.237 Angle : 0.689 16.401 22706 Z= 0.345 Chirality : 0.044 0.193 2734 Planarity : 0.005 0.062 2796 Dihedral : 7.352 133.839 2286 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.80 % Allowed : 20.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.19), residues: 2050 helix: 1.76 (0.14), residues: 1456 sheet: -2.03 (0.53), residues: 96 loop : -1.60 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 500 TYR 0.015 0.002 TYR B 387 PHE 0.023 0.002 PHE A 253 TRP 0.028 0.002 TRP A1112 HIS 0.005 0.001 HIS A 889 Details of bonding type rmsd covalent geometry : bond 0.00512 (16740) covalent geometry : angle 0.68934 (22706) hydrogen bonds : bond 0.05603 ( 1163) hydrogen bonds : angle 4.35427 ( 3459) *********************** 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 645 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 541 time to evaluate : 0.642 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: A 112 ILE cc_start: 0.8745 (mm) cc_final: 0.8391 (mt) REVERT: A 116 VAL cc_start: 0.8880 (t) cc_final: 0.8610 (t) REVERT: A 149 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7382 (tm-30) REVERT: A 163 PHE cc_start: 0.8453 (t80) cc_final: 0.8241 (t80) REVERT: A 233 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7619 (tm-30) REVERT: A 280 TYR cc_start: 0.8396 (t80) cc_final: 0.8108 (t80) REVERT: A 337 GLU cc_start: 0.7756 (tp30) cc_final: 0.7429 (tp30) REVERT: A 354 GLU cc_start: 0.8211 (tt0) cc_final: 0.7891 (tt0) REVERT: A 375 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8567 (ttpp) REVERT: A 377 LEU cc_start: 0.8654 (tp) cc_final: 0.8344 (mp) REVERT: A 383 MET cc_start: 0.7161 (mmm) cc_final: 0.6575 (mmm) REVERT: A 487 SER cc_start: 0.8197 (t) cc_final: 0.7856 (p) REVERT: A 511 MET cc_start: 0.8875 (tmm) cc_final: 0.8600 (ttp) REVERT: A 578 MET cc_start: 0.8594 (mtp) cc_final: 0.8346 (mtp) REVERT: A 579 MET cc_start: 0.8028 (tmm) cc_final: 0.7802 (tpp) REVERT: A 599 GLU cc_start: 0.7803 (mp0) cc_final: 0.7385 (mp0) REVERT: A 609 ARG cc_start: 0.8296 (ttp-110) cc_final: 0.8085 (ttm-80) REVERT: A 632 LYS cc_start: 0.8279 (ttpt) cc_final: 0.8002 (ttmm) REVERT: A 634 SER cc_start: 0.8937 (m) cc_final: 0.8653 (t) REVERT: A 697 MET cc_start: 0.6511 (mmm) cc_final: 0.5862 (mmm) REVERT: A 815 LYS cc_start: 0.9009 (tttt) cc_final: 0.8724 (ttmm) REVERT: A 820 LYS cc_start: 0.8294 (mmmt) cc_final: 0.8024 (mmmt) REVERT: A 841 LYS cc_start: 0.8989 (mtpt) cc_final: 0.8592 (mtpt) REVERT: A 877 GLN cc_start: 0.8721 (tt0) cc_final: 0.8392 (tt0) REVERT: A 911 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8304 (mm-30) REVERT: A 994 GLU cc_start: 0.7698 (pm20) cc_final: 0.7352 (pm20) REVERT: A 1003 SER cc_start: 0.8574 (t) cc_final: 0.8350 (m) REVERT: A 1033 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7498 (tp30) REVERT: A 1035 TYR cc_start: 0.8279 (m-80) cc_final: 0.7899 (m-80) REVERT: A 1044 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7561 (mt-10) REVERT: A 1060 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7661 (mm-30) REVERT: A 1061 THR cc_start: 0.7706 (OUTLIER) cc_final: 0.7404 (p) REVERT: A 1066 TYR cc_start: 0.8493 (m-80) cc_final: 0.7934 (m-80) REVERT: A 1072 ASP cc_start: 0.7625 (m-30) cc_final: 0.7418 (m-30) REVERT: A 1087 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7345 (tm-30) REVERT: A 1104 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7677 (tpp) REVERT: A 1139 ASP cc_start: 0.7594 (m-30) cc_final: 0.7267 (m-30) REVERT: A 1190 ARG cc_start: 0.8058 (mmm-85) cc_final: 0.7668 (mmm-85) REVERT: B 103 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8367 (p) REVERT: B 116 VAL cc_start: 0.8732 (t) cc_final: 0.8413 (m) REVERT: B 134 ASP cc_start: 0.8250 (t0) cc_final: 0.7872 (t70) REVERT: B 149 GLU cc_start: 0.7873 (tp30) cc_final: 0.7551 (tm-30) REVERT: B 155 ASP cc_start: 0.8180 (t0) cc_final: 0.7673 (t0) REVERT: B 205 MET cc_start: 0.8446 (mmp) cc_final: 0.8128 (mmm) REVERT: B 265 VAL cc_start: 0.8664 (t) cc_final: 0.8394 (p) REVERT: B 337 GLU cc_start: 0.7816 (tp30) cc_final: 0.7470 (tp30) REVERT: B 375 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8468 (mtpp) REVERT: B 383 MET cc_start: 0.7364 (tpp) cc_final: 0.6972 (mmm) REVERT: B 385 TRP cc_start: 0.8418 (m100) cc_final: 0.8155 (m100) REVERT: B 410 LEU cc_start: 0.8652 (mp) cc_final: 0.8392 (mt) REVERT: B 419 TRP cc_start: 0.8132 (p-90) cc_final: 0.7875 (p-90) REVERT: B 487 SER cc_start: 0.8370 (t) cc_final: 0.8095 (p) REVERT: B 511 MET cc_start: 0.8853 (tmm) cc_final: 0.8524 (ttp) REVERT: B 578 MET cc_start: 0.8572 (mtp) cc_final: 0.8039 (mmm) REVERT: B 579 MET cc_start: 0.8219 (tpp) cc_final: 0.7890 (tpp) REVERT: B 588 LYS cc_start: 0.8583 (tppt) cc_final: 0.8338 (tttm) REVERT: B 621 GLU cc_start: 0.7729 (pp20) cc_final: 0.7199 (pp20) REVERT: B 697 MET cc_start: 0.5875 (mmm) cc_final: 0.5207 (mmm) REVERT: B 736 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.8010 (t0) REVERT: B 815 LYS cc_start: 0.9044 (tttt) cc_final: 0.8676 (tptt) REVERT: B 820 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7939 (mmmt) REVERT: B 852 LYS cc_start: 0.8604 (mttp) cc_final: 0.8140 (mtpt) REVERT: B 853 ILE cc_start: 0.9082 (tp) cc_final: 0.8796 (tt) REVERT: B 856 ARG cc_start: 0.7942 (ttp80) cc_final: 0.7697 (ttp80) REVERT: B 859 ASP cc_start: 0.7997 (p0) cc_final: 0.7708 (p0) REVERT: B 887 ARG cc_start: 0.8431 (tpp80) cc_final: 0.7966 (ttm-80) REVERT: B 942 MET cc_start: 0.8313 (tpt) cc_final: 0.8058 (tpp) REVERT: B 954 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7567 (mm-30) REVERT: B 958 LYS cc_start: 0.8919 (ttpt) cc_final: 0.8561 (ttmm) REVERT: B 968 LYS cc_start: 0.8687 (mtpp) cc_final: 0.8408 (mmmm) REVERT: B 993 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7084 (m-30) REVERT: B 994 GLU cc_start: 0.7739 (pm20) cc_final: 0.7347 (pm20) REVERT: B 996 ASP cc_start: 0.7486 (p0) cc_final: 0.7181 (p0) REVERT: B 1003 SER cc_start: 0.8591 (t) cc_final: 0.8331 (m) REVERT: B 1007 LYS cc_start: 0.7897 (ttpp) cc_final: 0.7400 (ttpp) REVERT: B 1035 TYR cc_start: 0.8367 (m-80) cc_final: 0.8104 (m-80) REVERT: B 1060 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7788 (mm-30) REVERT: B 1061 THR cc_start: 0.7519 (OUTLIER) cc_final: 0.7190 (p) REVERT: B 1066 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8292 (m-80) REVERT: B 1067 PHE cc_start: 0.8646 (t80) cc_final: 0.8377 (t80) REVERT: B 1075 ILE cc_start: 0.8977 (mt) cc_final: 0.8586 (tt) REVERT: B 1118 LYS cc_start: 0.8636 (mtpp) cc_final: 0.8365 (mtmm) REVERT: B 1121 LEU cc_start: 0.9028 (mm) cc_final: 0.8759 (mt) REVERT: B 1136 PHE cc_start: 0.6842 (t80) cc_final: 0.6471 (t80) REVERT: B 1162 ARG cc_start: 0.5898 (OUTLIER) cc_final: 0.5199 (tpm-80) REVERT: B 1212 ILE cc_start: 0.5474 (OUTLIER) cc_final: 0.5044 (mp) REVERT: B 1217 ILE cc_start: 0.8650 (mm) cc_final: 0.8434 (mm) outliers start: 104 outliers final: 63 residues processed: 593 average time/residue: 0.1570 time to fit residues: 134.0847 Evaluate side-chains 586 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 512 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 214 VAL Chi-restraints excluded: chain A residue 251 MET 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 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 606 GLU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 941 LEU 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 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 1158 ARG 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 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 375 LYS 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 480 ILE 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 633 LYS Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 865 ARG Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 931 GLU 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 1061 THR Chi-restraints excluded: chain B residue 1066 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 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 1212 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 34 optimal weight: 0.5980 chunk 172 optimal weight: 0.5980 chunk 179 optimal weight: 0.9980 chunk 191 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 959 ASN B 225 GLN B 263 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.142951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.120105 restraints weight = 25112.994| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.06 r_work: 0.3412 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16740 Z= 0.156 Angle : 0.658 15.653 22706 Z= 0.326 Chirality : 0.042 0.172 2734 Planarity : 0.004 0.062 2796 Dihedral : 7.141 133.825 2280 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.41 % Allowed : 22.27 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.19), residues: 2050 helix: 1.91 (0.14), residues: 1458 sheet: -1.87 (0.54), residues: 96 loop : -1.57 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 609 TYR 0.013 0.001 TYR B1009 PHE 0.020 0.001 PHE A1136 TRP 0.028 0.001 TRP A1112 HIS 0.004 0.001 HIS B 981 Details of bonding type rmsd covalent geometry : bond 0.00334 (16740) covalent geometry : angle 0.65825 (22706) hydrogen bonds : bond 0.04886 ( 1163) hydrogen bonds : angle 4.28437 ( 3459) *********************** 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 607 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 528 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8717 (mm) cc_final: 0.8361 (mt) REVERT: A 116 VAL cc_start: 0.8803 (t) cc_final: 0.8527 (t) REVERT: A 161 ARG cc_start: 0.8313 (mtm180) cc_final: 0.7975 (mtm-85) REVERT: A 163 PHE cc_start: 0.8436 (t80) cc_final: 0.8189 (t80) REVERT: A 184 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8474 (tt) REVERT: A 280 TYR cc_start: 0.8400 (t80) cc_final: 0.8121 (t80) REVERT: A 337 GLU cc_start: 0.7755 (tp30) cc_final: 0.7459 (tp30) REVERT: A 338 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8384 (mtmm) REVERT: A 354 GLU cc_start: 0.8253 (tt0) cc_final: 0.7877 (tt0) REVERT: A 375 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8469 (ttpp) REVERT: A 377 LEU cc_start: 0.8661 (tp) cc_final: 0.8345 (mp) REVERT: A 383 MET cc_start: 0.6963 (mmm) cc_final: 0.6482 (mmm) REVERT: A 387 TYR cc_start: 0.8699 (m-10) cc_final: 0.8333 (m-10) REVERT: A 411 SER cc_start: 0.8505 (p) cc_final: 0.8217 (p) REVERT: A 487 SER cc_start: 0.8160 (t) cc_final: 0.7830 (p) REVERT: A 511 MET cc_start: 0.8843 (tmm) cc_final: 0.8549 (ttp) REVERT: A 578 MET cc_start: 0.8428 (mtp) cc_final: 0.8134 (mtp) REVERT: A 579 MET cc_start: 0.7969 (tmm) cc_final: 0.7734 (tpp) REVERT: A 581 GLU cc_start: 0.8282 (tp30) cc_final: 0.8012 (tp30) REVERT: A 599 GLU cc_start: 0.7681 (mp0) cc_final: 0.7328 (mp0) REVERT: A 632 LYS cc_start: 0.8162 (ttpt) cc_final: 0.7931 (ttmm) REVERT: A 634 SER cc_start: 0.8916 (m) cc_final: 0.8662 (t) REVERT: A 697 MET cc_start: 0.6445 (mmm) cc_final: 0.5743 (mmm) REVERT: A 815 LYS cc_start: 0.8991 (tttt) cc_final: 0.8640 (tppp) REVERT: A 820 LYS cc_start: 0.8219 (mmmt) cc_final: 0.7930 (mmmt) REVERT: A 841 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8588 (mtpt) REVERT: A 853 ILE cc_start: 0.9061 (tp) cc_final: 0.8669 (tp) REVERT: A 877 GLN cc_start: 0.8723 (tt0) cc_final: 0.8398 (tt0) REVERT: A 911 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8245 (mm-30) REVERT: A 990 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7701 (tpp80) REVERT: A 994 GLU cc_start: 0.7782 (pm20) cc_final: 0.7393 (pm20) REVERT: A 1003 SER cc_start: 0.8557 (t) cc_final: 0.8306 (m) REVERT: A 1008 LEU cc_start: 0.8188 (mt) cc_final: 0.7933 (mm) REVERT: A 1035 TYR cc_start: 0.8168 (m-80) cc_final: 0.7680 (m-80) REVERT: A 1044 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7415 (mt-10) REVERT: A 1060 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7546 (mm-30) REVERT: A 1066 TYR cc_start: 0.8454 (m-80) cc_final: 0.7980 (m-80) REVERT: A 1072 ASP cc_start: 0.7627 (m-30) cc_final: 0.7426 (m-30) REVERT: A 1080 PHE cc_start: 0.8001 (m-80) cc_final: 0.7653 (m-80) REVERT: A 1087 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7129 (tt0) REVERT: A 1104 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7485 (tpp) REVERT: A 1139 ASP cc_start: 0.7664 (m-30) cc_final: 0.7365 (m-30) REVERT: A 1143 GLU cc_start: 0.7913 (tt0) cc_final: 0.7567 (tp30) REVERT: A 1185 ARG cc_start: 0.6858 (mmt-90) cc_final: 0.6649 (mmt180) REVERT: A 1190 ARG cc_start: 0.8021 (mmm-85) cc_final: 0.7666 (mmm-85) REVERT: A 1221 MET cc_start: 0.8041 (mmt) cc_final: 0.7813 (mmt) REVERT: B 116 VAL cc_start: 0.8699 (t) cc_final: 0.8357 (m) REVERT: B 128 ARG cc_start: 0.8011 (tmm-80) cc_final: 0.7588 (ttp80) REVERT: B 134 ASP cc_start: 0.8148 (t0) cc_final: 0.7803 (t70) REVERT: B 149 GLU cc_start: 0.7875 (tp30) cc_final: 0.7535 (tm-30) REVERT: B 155 ASP cc_start: 0.8169 (t0) cc_final: 0.7685 (t0) REVERT: B 205 MET cc_start: 0.8410 (mmp) cc_final: 0.7989 (mmp) REVERT: B 265 VAL cc_start: 0.8634 (t) cc_final: 0.8363 (p) REVERT: B 337 GLU cc_start: 0.7783 (tp30) cc_final: 0.7472 (tp30) REVERT: B 375 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8452 (mtpp) REVERT: B 383 MET cc_start: 0.7262 (tpp) cc_final: 0.6890 (mmm) REVERT: B 419 TRP cc_start: 0.8099 (p-90) cc_final: 0.7839 (p-90) REVERT: B 487 SER cc_start: 0.8335 (t) cc_final: 0.8069 (p) REVERT: B 511 MET cc_start: 0.8857 (tmm) cc_final: 0.8519 (ttp) REVERT: B 575 PHE cc_start: 0.8573 (t80) cc_final: 0.8074 (t80) REVERT: B 579 MET cc_start: 0.8132 (tpp) cc_final: 0.7816 (tpp) REVERT: B 588 LYS cc_start: 0.8551 (tppt) cc_final: 0.8313 (tttm) REVERT: B 634 SER cc_start: 0.8905 (m) cc_final: 0.8673 (t) REVERT: B 697 MET cc_start: 0.5788 (mmm) cc_final: 0.5133 (mmm) REVERT: B 736 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8002 (t0) REVERT: B 815 LYS cc_start: 0.9049 (tttt) cc_final: 0.8704 (tptt) REVERT: B 820 LYS cc_start: 0.8118 (mmmt) cc_final: 0.7878 (mmmt) REVERT: B 852 LYS cc_start: 0.8572 (mttp) cc_final: 0.8092 (mtpt) REVERT: B 853 ILE cc_start: 0.9056 (tp) cc_final: 0.8750 (tt) REVERT: B 856 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7690 (ttp80) REVERT: B 859 ASP cc_start: 0.7992 (p0) cc_final: 0.7735 (p0) REVERT: B 877 GLN cc_start: 0.8666 (tt0) cc_final: 0.8326 (tt0) REVERT: B 887 ARG cc_start: 0.8279 (tpp80) cc_final: 0.7901 (ttm-80) REVERT: B 942 MET cc_start: 0.8307 (tpt) cc_final: 0.8100 (tpt) REVERT: B 954 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7447 (mm-30) REVERT: B 958 LYS cc_start: 0.8896 (ttpt) cc_final: 0.8523 (ttmm) REVERT: B 968 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8320 (mmmm) REVERT: B 993 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.6913 (m-30) REVERT: B 994 GLU cc_start: 0.7695 (pm20) cc_final: 0.7215 (pm20) REVERT: B 1003 SER cc_start: 0.8498 (t) cc_final: 0.8211 (m) REVERT: B 1035 TYR cc_start: 0.8221 (m-80) cc_final: 0.7805 (m-80) REVERT: B 1066 TYR cc_start: 0.8598 (m-80) cc_final: 0.8248 (m-80) REVERT: B 1075 ILE cc_start: 0.8954 (mt) cc_final: 0.8581 (tt) REVERT: B 1088 TYR cc_start: 0.7312 (t80) cc_final: 0.6910 (t80) REVERT: B 1118 LYS cc_start: 0.8605 (mtpp) cc_final: 0.8338 (mtmm) REVERT: B 1121 LEU cc_start: 0.9004 (mm) cc_final: 0.8765 (mt) REVERT: B 1162 ARG cc_start: 0.5883 (OUTLIER) cc_final: 0.5193 (tpm-80) REVERT: B 1212 ILE cc_start: 0.5448 (OUTLIER) cc_final: 0.5028 (mp) outliers start: 79 outliers final: 54 residues processed: 568 average time/residue: 0.1561 time to fit residues: 127.2979 Evaluate side-chains 579 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 516 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 214 VAL 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 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 451 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 616 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 963 LEU Chi-restraints excluded: chain A residue 990 ARG Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 MET Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1158 ARG 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 375 LYS 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 532 ILE Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 931 GLU 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 1100 THR Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1151 THR 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 1212 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 51 optimal weight: 0.2980 chunk 201 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 174 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 943 ASN B 165 GLN B1191 ASN B1220 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.143659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.120562 restraints weight = 25186.841| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.07 r_work: 0.3406 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 0.045 16740 Z= 0.155 Angle : 0.668 15.617 22706 Z= 0.331 Chirality : 0.042 0.170 2734 Planarity : 0.004 0.062 2796 Dihedral : 7.016 133.101 2276 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.74 % Allowed : 23.38 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.19), residues: 2050 helix: 1.93 (0.14), residues: 1458 sheet: -1.74 (0.55), residues: 96 loop : -1.52 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 609 TYR 0.014 0.001 TYR B1009 PHE 0.023 0.001 PHE A1136 TRP 0.026 0.001 TRP A1112 HIS 0.004 0.001 HIS B 981 Details of bonding type rmsd covalent geometry : bond 0.00333 (16740) covalent geometry : angle 0.66756 (22706) hydrogen bonds : bond 0.04876 ( 1163) hydrogen bonds : angle 4.26087 ( 3459) *********************** 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 584 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 517 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8715 (mm) cc_final: 0.8358 (mt) REVERT: A 116 VAL cc_start: 0.8785 (t) cc_final: 0.8506 (t) REVERT: A 163 PHE cc_start: 0.8436 (t80) cc_final: 0.8221 (t80) REVERT: A 280 TYR cc_start: 0.8442 (t80) cc_final: 0.8171 (t80) REVERT: A 337 GLU cc_start: 0.7832 (tp30) cc_final: 0.7487 (tp30) REVERT: A 338 LYS cc_start: 0.8620 (mtmm) cc_final: 0.8394 (mtmm) REVERT: A 354 GLU cc_start: 0.8212 (tt0) cc_final: 0.7864 (tt0) REVERT: A 377 LEU cc_start: 0.8692 (tp) cc_final: 0.8397 (mp) REVERT: A 383 MET cc_start: 0.6805 (mmm) cc_final: 0.6320 (mmm) REVERT: A 387 TYR cc_start: 0.8653 (m-10) cc_final: 0.8272 (m-10) REVERT: A 411 SER cc_start: 0.8517 (p) cc_final: 0.8226 (p) REVERT: A 454 LYS cc_start: 0.8783 (mmtp) cc_final: 0.8554 (mmtt) REVERT: A 487 SER cc_start: 0.8177 (t) cc_final: 0.7843 (p) REVERT: A 499 ARG cc_start: 0.8701 (ttp-170) cc_final: 0.8493 (ttp80) REVERT: A 511 MET cc_start: 0.8879 (tmm) cc_final: 0.8591 (ttp) REVERT: A 578 MET cc_start: 0.8400 (mtp) cc_final: 0.8105 (mtp) REVERT: A 581 GLU cc_start: 0.8276 (tp30) cc_final: 0.8002 (tp30) REVERT: A 632 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7949 (ttmm) REVERT: A 634 SER cc_start: 0.8879 (m) cc_final: 0.8612 (t) REVERT: A 697 MET cc_start: 0.6518 (mmm) cc_final: 0.5799 (mmm) REVERT: A 815 LYS cc_start: 0.8996 (tttt) cc_final: 0.8636 (tppp) REVERT: A 820 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7968 (mmmt) REVERT: A 841 LYS cc_start: 0.8985 (mtpt) cc_final: 0.8600 (mtpt) REVERT: A 853 ILE cc_start: 0.9030 (tp) cc_final: 0.8649 (tp) REVERT: A 877 GLN cc_start: 0.8648 (tt0) cc_final: 0.8261 (tt0) REVERT: A 911 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8305 (mm-30) REVERT: A 978 SER cc_start: 0.8579 (t) cc_final: 0.8021 (p) REVERT: A 994 GLU cc_start: 0.7773 (pm20) cc_final: 0.7356 (pm20) REVERT: A 1003 SER cc_start: 0.8503 (t) cc_final: 0.8279 (m) REVERT: A 1035 TYR cc_start: 0.8185 (m-80) cc_final: 0.7769 (m-80) REVERT: A 1044 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7423 (mt-10) REVERT: A 1060 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7498 (mm-30) REVERT: A 1072 ASP cc_start: 0.7685 (m-30) cc_final: 0.7447 (m-30) REVERT: A 1080 PHE cc_start: 0.7981 (m-80) cc_final: 0.7634 (m-80) REVERT: A 1087 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7229 (tt0) REVERT: A 1104 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7522 (tpp) REVERT: A 1139 ASP cc_start: 0.7635 (m-30) cc_final: 0.7330 (m-30) REVERT: A 1185 ARG cc_start: 0.6926 (mmt-90) cc_final: 0.6671 (mmt180) REVERT: A 1190 ARG cc_start: 0.7989 (mmm-85) cc_final: 0.7599 (mmm-85) REVERT: B 116 VAL cc_start: 0.8677 (t) cc_final: 0.8340 (m) REVERT: B 128 ARG cc_start: 0.7970 (tmm-80) cc_final: 0.7374 (ttp80) REVERT: B 134 ASP cc_start: 0.8177 (t0) cc_final: 0.7829 (t70) REVERT: B 149 GLU cc_start: 0.7908 (tp30) cc_final: 0.7557 (tm-30) REVERT: B 155 ASP cc_start: 0.8176 (t0) cc_final: 0.7689 (t0) REVERT: B 205 MET cc_start: 0.8411 (mmp) cc_final: 0.7966 (mmp) REVERT: B 265 VAL cc_start: 0.8685 (t) cc_final: 0.8381 (p) REVERT: B 337 GLU cc_start: 0.7758 (tp30) cc_final: 0.7409 (tp30) REVERT: B 375 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8514 (mtpp) REVERT: B 419 TRP cc_start: 0.8090 (p-90) cc_final: 0.7838 (p-90) REVERT: B 487 SER cc_start: 0.8335 (t) cc_final: 0.8053 (p) REVERT: B 511 MET cc_start: 0.8871 (tmm) cc_final: 0.8529 (ttp) REVERT: B 579 MET cc_start: 0.8198 (tpp) cc_final: 0.7718 (tpp) REVERT: B 588 LYS cc_start: 0.8599 (tppt) cc_final: 0.8356 (tttm) REVERT: B 634 SER cc_start: 0.8883 (m) cc_final: 0.8646 (t) REVERT: B 697 MET cc_start: 0.5877 (mmm) cc_final: 0.5226 (mmm) REVERT: B 736 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8013 (t0) REVERT: B 815 LYS cc_start: 0.9066 (tttt) cc_final: 0.8707 (ttmm) REVERT: B 820 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7918 (mmmt) REVERT: B 852 LYS cc_start: 0.8599 (mttp) cc_final: 0.8110 (mtpt) REVERT: B 853 ILE cc_start: 0.9068 (tp) cc_final: 0.8780 (tt) REVERT: B 856 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7796 (ttp80) REVERT: B 859 ASP cc_start: 0.7983 (p0) cc_final: 0.7726 (p0) REVERT: B 863 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.7610 (mm) REVERT: B 877 GLN cc_start: 0.8717 (tt0) cc_final: 0.8360 (tt0) REVERT: B 887 ARG cc_start: 0.8292 (tpp80) cc_final: 0.7915 (ttm-80) REVERT: B 942 MET cc_start: 0.8373 (tpt) cc_final: 0.8159 (tpt) REVERT: B 954 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7573 (mm-30) REVERT: B 958 LYS cc_start: 0.8886 (ttpt) cc_final: 0.8492 (ttmm) REVERT: B 968 LYS cc_start: 0.8625 (mtpp) cc_final: 0.8306 (mmmm) REVERT: B 993 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7019 (m-30) REVERT: B 994 GLU cc_start: 0.7734 (pm20) cc_final: 0.7260 (pm20) REVERT: B 1003 SER cc_start: 0.8431 (t) cc_final: 0.8118 (m) REVERT: B 1035 TYR cc_start: 0.8153 (m-80) cc_final: 0.7672 (m-80) REVERT: B 1066 TYR cc_start: 0.8637 (m-80) cc_final: 0.8288 (m-80) REVERT: B 1075 ILE cc_start: 0.8940 (mt) cc_final: 0.8564 (tt) REVERT: B 1087 GLU cc_start: 0.7740 (tt0) cc_final: 0.7128 (tp30) REVERT: B 1118 LYS cc_start: 0.8578 (mtpp) cc_final: 0.8313 (mtmm) REVERT: B 1121 LEU cc_start: 0.9029 (mm) cc_final: 0.8790 (mt) REVERT: B 1162 ARG cc_start: 0.5912 (OUTLIER) cc_final: 0.5169 (tpm-80) outliers start: 67 outliers final: 53 residues processed: 548 average time/residue: 0.1453 time to fit residues: 114.2311 Evaluate side-chains 571 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 512 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 214 VAL 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 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 451 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 518 LEU 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 943 ASN Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 MET Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1158 ARG 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 375 LYS 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 532 ILE Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 863 ILE 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 993 ASP 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 1151 THR Chi-restraints excluded: chain B residue 1154 ASN Chi-restraints excluded: chain B residue 1156 HIS Chi-restraints excluded: chain B residue 1162 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 205 optimal weight: 0.5980 chunk 60 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 167 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 943 ASN A1220 ASN B1220 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.143152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120293 restraints weight = 24961.130| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.06 r_work: 0.3406 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16740 Z= 0.163 Angle : 0.682 15.669 22706 Z= 0.338 Chirality : 0.043 0.174 2734 Planarity : 0.005 0.062 2796 Dihedral : 7.003 133.118 2274 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.24 % Allowed : 24.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.19), residues: 2050 helix: 1.94 (0.14), residues: 1448 sheet: -1.42 (0.62), residues: 76 loop : -1.59 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 500 TYR 0.014 0.001 TYR B1009 PHE 0.023 0.001 PHE A1136 TRP 0.023 0.001 TRP A1112 HIS 0.005 0.001 HIS B 981 Details of bonding type rmsd covalent geometry : bond 0.00353 (16740) covalent geometry : angle 0.68232 (22706) hydrogen bonds : bond 0.04905 ( 1163) hydrogen bonds : angle 4.27680 ( 3459) ********************** 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 574 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 516 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8709 (mm) cc_final: 0.8350 (mt) REVERT: A 116 VAL cc_start: 0.8776 (t) cc_final: 0.8494 (t) REVERT: A 163 PHE cc_start: 0.8420 (t80) cc_final: 0.8211 (t80) REVERT: A 208 THR cc_start: 0.8281 (p) cc_final: 0.8074 (p) REVERT: A 280 TYR cc_start: 0.8390 (t80) cc_final: 0.8131 (t80) REVERT: A 337 GLU cc_start: 0.7824 (tp30) cc_final: 0.7488 (tp30) REVERT: A 338 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8425 (mtmm) REVERT: A 354 GLU cc_start: 0.8159 (tt0) cc_final: 0.7811 (tt0) REVERT: A 377 LEU cc_start: 0.8667 (tp) cc_final: 0.8380 (mp) REVERT: A 383 MET cc_start: 0.6835 (mmm) cc_final: 0.6334 (mmm) REVERT: A 411 SER cc_start: 0.8520 (p) cc_final: 0.8236 (p) REVERT: A 487 SER cc_start: 0.8144 (t) cc_final: 0.7816 (p) REVERT: A 499 ARG cc_start: 0.8657 (ttp-170) cc_final: 0.8446 (ttp80) REVERT: A 511 MET cc_start: 0.8864 (tmm) cc_final: 0.8561 (ttp) REVERT: A 578 MET cc_start: 0.8522 (mtp) cc_final: 0.8221 (mtp) REVERT: A 581 GLU cc_start: 0.8219 (tp30) cc_final: 0.7972 (tp30) REVERT: A 632 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7920 (ttmm) REVERT: A 634 SER cc_start: 0.8872 (m) cc_final: 0.8616 (t) REVERT: A 697 MET cc_start: 0.6471 (mmm) cc_final: 0.5748 (mmm) REVERT: A 815 LYS cc_start: 0.8960 (tttt) cc_final: 0.8616 (tppp) REVERT: A 820 LYS cc_start: 0.8187 (mmmt) cc_final: 0.7906 (mmmt) REVERT: A 841 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8571 (mtpt) REVERT: A 853 ILE cc_start: 0.9051 (tp) cc_final: 0.8669 (tp) REVERT: A 877 GLN cc_start: 0.8736 (tt0) cc_final: 0.8450 (tt0) REVERT: A 911 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8267 (mm-30) REVERT: A 978 SER cc_start: 0.8539 (t) cc_final: 0.8004 (p) REVERT: A 989 VAL cc_start: 0.7692 (t) cc_final: 0.7453 (t) REVERT: A 994 GLU cc_start: 0.7651 (pm20) cc_final: 0.7277 (pm20) REVERT: A 1003 SER cc_start: 0.8523 (t) cc_final: 0.8287 (m) REVERT: A 1035 TYR cc_start: 0.8336 (m-80) cc_final: 0.8007 (m-80) REVERT: A 1044 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7400 (mt-10) REVERT: A 1072 ASP cc_start: 0.7629 (m-30) cc_final: 0.7408 (m-30) REVERT: A 1080 PHE cc_start: 0.7951 (m-80) cc_final: 0.7594 (m-80) REVERT: A 1087 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7400 (tt0) REVERT: A 1104 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7482 (tpp) REVERT: A 1139 ASP cc_start: 0.7581 (m-30) cc_final: 0.7250 (m-30) REVERT: A 1190 ARG cc_start: 0.7984 (mmm-85) cc_final: 0.7594 (mmm-85) REVERT: B 116 VAL cc_start: 0.8663 (t) cc_final: 0.8319 (m) REVERT: B 128 ARG cc_start: 0.7950 (tmm-80) cc_final: 0.7370 (ttp80) REVERT: B 134 ASP cc_start: 0.8154 (t0) cc_final: 0.7809 (t70) REVERT: B 149 GLU cc_start: 0.7904 (tp30) cc_final: 0.7556 (tm-30) REVERT: B 155 ASP cc_start: 0.8146 (t0) cc_final: 0.7688 (t0) REVERT: B 205 MET cc_start: 0.8386 (mmp) cc_final: 0.7924 (mmp) REVERT: B 265 VAL cc_start: 0.8688 (t) cc_final: 0.8387 (p) REVERT: B 337 GLU cc_start: 0.7762 (tp30) cc_final: 0.7427 (tp30) REVERT: B 383 MET cc_start: 0.7266 (tpp) cc_final: 0.6890 (mmm) REVERT: B 419 TRP cc_start: 0.8079 (p-90) cc_final: 0.7827 (p-90) REVERT: B 487 SER cc_start: 0.8352 (t) cc_final: 0.8064 (p) REVERT: B 511 MET cc_start: 0.8878 (tmm) cc_final: 0.8540 (ttp) REVERT: B 579 MET cc_start: 0.8188 (tpp) cc_final: 0.7857 (tpp) REVERT: B 588 LYS cc_start: 0.8555 (tppt) cc_final: 0.8308 (tttm) REVERT: B 634 SER cc_start: 0.8919 (m) cc_final: 0.8681 (t) REVERT: B 644 LEU cc_start: 0.8537 (mp) cc_final: 0.8326 (mp) REVERT: B 697 MET cc_start: 0.5824 (mmm) cc_final: 0.5174 (mmm) REVERT: B 736 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.8000 (t0) REVERT: B 815 LYS cc_start: 0.9042 (tttt) cc_final: 0.8681 (tptt) REVERT: B 820 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7874 (mmmt) REVERT: B 852 LYS cc_start: 0.8594 (mttp) cc_final: 0.8136 (mtpt) REVERT: B 853 ILE cc_start: 0.9069 (tp) cc_final: 0.8777 (tt) REVERT: B 856 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7742 (ttp80) REVERT: B 859 ASP cc_start: 0.8010 (p0) cc_final: 0.7735 (p0) REVERT: B 877 GLN cc_start: 0.8673 (tt0) cc_final: 0.8314 (tt0) REVERT: B 887 ARG cc_start: 0.8306 (tpp80) cc_final: 0.7940 (ttm-80) REVERT: B 942 MET cc_start: 0.8321 (tpt) cc_final: 0.8109 (tpt) REVERT: B 954 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7478 (mm-30) REVERT: B 958 LYS cc_start: 0.8876 (ttpt) cc_final: 0.8515 (ttmm) REVERT: B 968 LYS cc_start: 0.8598 (mtpp) cc_final: 0.8275 (mmmm) REVERT: B 993 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.6948 (m-30) REVERT: B 994 GLU cc_start: 0.7681 (pm20) cc_final: 0.7205 (pm20) REVERT: B 1003 SER cc_start: 0.8472 (t) cc_final: 0.8158 (m) REVERT: B 1035 TYR cc_start: 0.8158 (m-80) cc_final: 0.7762 (m-80) REVERT: B 1066 TYR cc_start: 0.8617 (m-80) cc_final: 0.8267 (m-80) REVERT: B 1075 ILE cc_start: 0.8909 (mt) cc_final: 0.8543 (tt) REVERT: B 1086 LEU cc_start: 0.8167 (tp) cc_final: 0.7954 (tp) REVERT: B 1087 GLU cc_start: 0.7681 (tt0) cc_final: 0.7221 (tp30) REVERT: B 1118 LYS cc_start: 0.8604 (mtpp) cc_final: 0.8332 (mtmm) REVERT: B 1121 LEU cc_start: 0.9027 (mm) cc_final: 0.8782 (mt) REVERT: B 1162 ARG cc_start: 0.5849 (OUTLIER) cc_final: 0.5136 (tpm-80) outliers start: 58 outliers final: 52 residues processed: 543 average time/residue: 0.1465 time to fit residues: 114.3637 Evaluate side-chains 565 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 509 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 214 VAL 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 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 451 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 518 LEU 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 943 ASN Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 MET Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1158 ARG 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 380 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 876 LEU 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 1102 LEU Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1154 ASN Chi-restraints excluded: chain B residue 1156 HIS Chi-restraints excluded: chain B residue 1162 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 178 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 204 optimal weight: 0.0980 chunk 92 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 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 225 GLN A 943 ASN A1220 ASN B 132 HIS B1220 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.143706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120675 restraints weight = 25045.319| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.07 r_work: 0.3408 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16740 Z= 0.160 Angle : 0.689 15.644 22706 Z= 0.340 Chirality : 0.042 0.170 2734 Planarity : 0.004 0.062 2796 Dihedral : 6.997 133.243 2274 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.74 % Allowed : 24.67 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.19), residues: 2050 helix: 1.94 (0.14), residues: 1448 sheet: -1.91 (0.58), residues: 86 loop : -1.56 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1053 TYR 0.014 0.001 TYR B1009 PHE 0.026 0.001 PHE A1136 TRP 0.018 0.001 TRP A1112 HIS 0.005 0.001 HIS B 981 Details of bonding type rmsd covalent geometry : bond 0.00346 (16740) covalent geometry : angle 0.68930 (22706) hydrogen bonds : bond 0.04860 ( 1163) hydrogen bonds : angle 4.28311 ( 3459) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4926.87 seconds wall clock time: 84 minutes 50.59 seconds (5090.59 seconds total)