Starting phenix.real_space_refine on Thu Aug 6 17:24:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xq7_38568/08_2026/8xq7_38568.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xq7_38568/08_2026/8xq7_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_38568/08_2026/8xq7_38568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xq7_38568/08_2026/8xq7_38568.map" model { file = "/net/cci-nas-00/data/ceres_data/8xq7_38568/08_2026/8xq7_38568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xq7_38568/08_2026/8xq7_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-2.2rc3-6140/lib/python3.11/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: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 4.05, per 1000 atoms: 0.25 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: 1.44 Conformation dependent library (CDL) restraints added in 747.1 milliseconds 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: 0.52 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: 3.30 Time building geometry restraints manager: 1.95 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: 22470 3.07 - 6.15: 195 6.15 - 9.22: 29 9.22 - 12.29: 8 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 - 15.82: 9012 15.82 - 31.64: 772 31.64 - 47.47: 184 47.47 - 63.29: 51 63.29 - 79.11: 7 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: 2420 0.072 - 0.144: 272 0.144 - 0.216: 35 0.216 - 0.288: 3 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: 0.04 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.230 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 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= 0.240 Angle : 0.810 15.366 22706 Z= 0.440 Chirality : 0.049 0.360 2734 Planarity : 0.007 0.095 2796 Dihedral : 13.147 79.112 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 are 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/Z covalent geometry : bond 0.00455 / 0.24 (16740) covalent geometry : angle 0.81002 / 0.44 (22706) hydrogen bonds : bond 0.10702 / 7.35 ( 1163) hydrogen bonds : angle 5.79532 / 4.20 ( 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 : 0.589 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: 0.7811 (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: 0.7872 (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: 0.8846 (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: 0.1449 time to fit residues: 150.3260 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 : 0.601 ------------------------------------------------------------------------------- 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... 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 = 0.3870 r_free = 0.3870 target = 0.145328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.121317 restraints weight = 25420.669| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.11 r_work: 0.3395 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2005 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= 0.133 Angle : 0.646 17.014 22706 Z= 0.317 Chirality : 0.041 0.202 2734 Planarity : 0.005 0.073 2796 Dihedral : 7.999 59.845 2343 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.80 % Allowed : 17.35 % Favored : 77.85 % 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 are not related in a simple way. whole: 0.18 (0.18), residues: 2050 helix: 1.00 (0.13), residues: 1462 sheet: -3.30 (0.50), residues: 82 loop : -1.79 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 609 TYR 0.015 0.001 TYR A1009 PHE 0.020 0.001 PHE A 972 TRP 0.011 0.001 TRP B 962 HIS 0.006 0.001 HIS A 981 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (16740) covalent geometry : angle 0.64640 / 0.32 (22706) hydrogen bonds : bond 0.04733 / 3.24 ( 1163) hydrogen bonds : angle 4.49681 / 3.27 ( 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 647 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 561 time to evaluate : 0.630 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: 0.8670 (mm) cc_final: 0.8245 (mt) REVERT: A 116 VAL cc_start: 0.8809 (t) cc_final: 0.8549 (t) REVERT: A 124 GLU cc_start: 0.7480 (tp30) cc_final: 0.7276 (tp30) REVERT: A 149 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7644 (tm-30) REVERT: A 174 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8148 (tt) REVERT: A 176 VAL cc_start: 0.8842 (p) cc_final: 0.8558 (t) REVERT: A 195 PHE cc_start: 0.8109 (t80) cc_final: 0.7849 (t80) REVERT: A 233 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7723 (tm-30) REVERT: A 266 LEU cc_start: 0.8456 (tp) cc_final: 0.8217 (tt) REVERT: A 269 LEU cc_start: 0.8497 (tp) cc_final: 0.8106 (tt) REVERT: A 300 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7935 (mt-10) REVERT: A 337 GLU cc_start: 0.7730 (tp30) cc_final: 0.7419 (tp30) REVERT: A 346 GLU cc_start: 0.7770 (tt0) cc_final: 0.7504 (tt0) REVERT: A 354 GLU cc_start: 0.8270 (tt0) cc_final: 0.7977 (tt0) REVERT: A 366 MET cc_start: 0.8584 (mmm) cc_final: 0.8164 (mmt) REVERT: A 375 LYS cc_start: 0.8744 (tppp) cc_final: 0.8453 (ttpp) REVERT: A 383 MET cc_start: 0.7198 (mmm) cc_final: 0.6639 (mmm) REVERT: A 385 TRP cc_start: 0.8515 (m100) cc_final: 0.8115 (m100) REVERT: A 387 TYR cc_start: 0.8630 (m-10) cc_final: 0.8175 (m-10) REVERT: A 443 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8096 (tm-30) REVERT: A 486 ILE cc_start: 0.8700 (mp) cc_final: 0.8493 (mm) REVERT: A 487 SER cc_start: 0.8300 (t) cc_final: 0.8011 (p) REVERT: A 511 MET cc_start: 0.8870 (tmm) cc_final: 0.8596 (tmm) REVERT: A 516 ARG cc_start: 0.8561 (ttp-110) cc_final: 0.8310 (ttp-110) REVERT: A 531 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6873 (tm-30) REVERT: A 554 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7780 (tp30) REVERT: A 578 MET cc_start: 0.8649 (mtp) cc_final: 0.8393 (mtp) REVERT: A 579 MET cc_start: 0.7994 (tmm) cc_final: 0.7728 (tpp) REVERT: A 580 GLU cc_start: 0.8119 (tp30) cc_final: 0.7734 (tp30) REVERT: A 602 MET cc_start: 0.7476 (mpp) cc_final: 0.7196 (mpp) REVERT: A 632 LYS cc_start: 0.8342 (ttpt) cc_final: 0.8094 (ttmm) REVERT: A 647 LYS cc_start: 0.8672 (mmtp) cc_final: 0.8395 (mmtm) REVERT: A 697 MET cc_start: 0.6457 (mmm) cc_final: 0.5853 (mmm) REVERT: A 815 LYS cc_start: 0.9029 (tttt) cc_final: 0.8713 (tppp) REVERT: A 820 LYS cc_start: 0.8286 (mmmt) cc_final: 0.7998 (mmmt) REVERT: A 864 LEU cc_start: 0.8526 (tp) cc_final: 0.8286 (tp) REVERT: A 911 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8214 (mm-30) REVERT: A 926 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7785 (mm-30) REVERT: A 942 MET cc_start: 0.8472 (tpp) cc_final: 0.8242 (tpt) REVERT: A 972 PHE cc_start: 0.8528 (t80) cc_final: 0.8292 (t80) REVERT: A 994 GLU cc_start: 0.7940 (pm20) cc_final: 0.7626 (pm20) REVERT: A 1003 SER cc_start: 0.8448 (t) cc_final: 0.8236 (m) REVERT: A 1008 LEU cc_start: 0.8193 (mp) cc_final: 0.7794 (tp) REVERT: A 1033 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7635 (mp0) REVERT: A 1044 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7727 (mt-10) REVERT: A 1060 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7661 (mm-30) REVERT: A 1066 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: A 1080 PHE cc_start: 0.7988 (m-80) cc_final: 0.7357 (m-80) REVERT: A 1104 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7500 (tpt) REVERT: A 1121 LEU cc_start: 0.8860 (mm) cc_final: 0.8608 (mt) REVERT: A 1136 PHE cc_start: 0.6950 (t80) cc_final: 0.6534 (t80) REVERT: A 1173 LYS cc_start: 0.7390 (mtpp) cc_final: 0.6980 (mtpp) REVERT: A 1190 ARG cc_start: 0.8221 (mmm-85) cc_final: 0.7783 (mmm-85) REVERT: A 1212 ILE cc_start: 0.5499 (OUTLIER) cc_final: 0.4976 (mp) REVERT: A 1220 ASN cc_start: 0.7937 (m-40) cc_final: 0.7727 (m-40) REVERT: B 250 LYS cc_start: 0.8429 (mttt) cc_final: 0.8229 (mmtp) REVERT: B 300 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7851 (mt-10) REVERT: B 337 GLU cc_start: 0.7854 (tp30) cc_final: 0.7540 (tp30) REVERT: B 375 LYS cc_start: 0.8774 (tppp) cc_final: 0.8238 (mtpp) REVERT: B 383 MET cc_start: 0.7271 (tpp) cc_final: 0.6738 (mmm) REVERT: B 385 TRP cc_start: 0.8441 (m100) cc_final: 0.8114 (m100) REVERT: B 410 LEU cc_start: 0.8559 (mt) cc_final: 0.8258 (mt) REVERT: B 419 TRP cc_start: 0.8097 (p-90) cc_final: 0.7740 (p-90) REVERT: B 443 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7897 (tm-30) REVERT: B 487 SER cc_start: 0.8418 (t) cc_final: 0.8159 (p) REVERT: B 511 MET cc_start: 0.8891 (tmm) cc_final: 0.8386 (tmm) REVERT: B 531 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6900 (tm-30) REVERT: B 578 MET cc_start: 0.8596 (mtp) cc_final: 0.8259 (mtp) REVERT: B 579 MET cc_start: 0.7848 (tmm) cc_final: 0.7538 (tpp) REVERT: B 588 LYS cc_start: 0.8665 (tppt) cc_final: 0.8380 (tttm) REVERT: B 647 LYS cc_start: 0.8517 (mmtm) cc_final: 0.8268 (mmtp) REVERT: B 697 MET cc_start: 0.5786 (mmm) cc_final: 0.5200 (mmm) REVERT: B 736 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.8054 (t0) REVERT: B 808 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7969 (pt) REVERT: B 810 MET cc_start: 0.7003 (ptt) cc_final: 0.6792 (ptt) REVERT: B 815 LYS cc_start: 0.9161 (tttt) cc_final: 0.8861 (tppt) REVERT: B 820 LYS cc_start: 0.8238 (mmmt) cc_final: 0.7983 (mmmt) REVERT: B 825 VAL cc_start: 0.8763 (t) cc_final: 0.8470 (p) REVERT: B 832 GLN cc_start: 0.8579 (tt0) cc_final: 0.8297 (tp-100) REVERT: B 852 LYS cc_start: 0.8391 (mttp) cc_final: 0.8075 (ttmm) REVERT: B 872 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7462 (pt0) REVERT: B 926 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7731 (mm-30) REVERT: B 931 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7722 (mt-10) REVERT: B 954 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7574 (mm-30) REVERT: B 958 LYS cc_start: 0.8870 (ttpt) cc_final: 0.8501 (ttmm) REVERT: B 968 LYS cc_start: 0.8695 (mtpp) cc_final: 0.8380 (mmmm) REVERT: B 972 PHE cc_start: 0.8814 (t80) cc_final: 0.8466 (t80) REVERT: B 993 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6514 (m-30) REVERT: B 994 GLU cc_start: 0.7809 (pm20) cc_final: 0.7553 (pm20) REVERT: B 996 ASP cc_start: 0.7345 (p0) cc_final: 0.7108 (p0) REVERT: B 1003 SER cc_start: 0.8543 (t) cc_final: 0.8252 (m) REVERT: B 1054 ASN cc_start: 0.7633 (OUTLIER) cc_final: 0.7430 (p0) REVERT: B 1060 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7710 (mm-30) REVERT: B 1073 MET cc_start: 0.8572 (tpp) cc_final: 0.8096 (tpp) REVERT: B 1098 ILE cc_start: 0.8875 (tt) cc_final: 0.8540 (tp) REVERT: B 1104 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7315 (tpp) REVERT: B 1118 LYS cc_start: 0.8582 (mtpp) cc_final: 0.8231 (mtmm) REVERT: B 1121 LEU cc_start: 0.8972 (mm) cc_final: 0.8682 (mt) REVERT: B 1122 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7768 (tp30) REVERT: B 1126 LEU cc_start: 0.8409 (mt) cc_final: 0.8006 (pt) REVERT: B 1162 ARG cc_start: 0.5735 (OUTLIER) cc_final: 0.5142 (tpm-80) REVERT: B 1179 THR cc_start: 0.5519 (OUTLIER) cc_final: 0.5244 (p) REVERT: B 1212 ILE cc_start: 0.5472 (OUTLIER) cc_final: 0.5179 (mp) outliers start: 86 outliers final: 36 residues processed: 612 average time/residue: 0.1497 time to fit residues: 133.2343 Evaluate side-chains 584 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 533 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 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 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 872 GLU 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 1054 ASN 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: 7.9990 chunk 161 optimal weight: 10.0000 chunk 93 optimal weight: 0.0000 chunk 98 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN A 600 HIS A 981 HIS A1120 HIS ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1220 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.144137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.120361 restraints weight = 25567.618| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.10 r_work: 0.3383 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16740 Z= 0.146 Angle : 0.637 16.928 22706 Z= 0.310 Chirality : 0.041 0.183 2734 Planarity : 0.004 0.065 2796 Dihedral : 6.797 59.092 2300 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.97 % Allowed : 19.20 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.19), residues: 2050 helix: 1.52 (0.14), residues: 1456 sheet: -3.27 (0.48), residues: 82 loop : -1.72 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1185 TYR 0.011 0.001 TYR B1153 PHE 0.016 0.001 PHE B 766 TRP 0.027 0.001 TRP A1112 HIS 0.008 0.001 HIS A1120 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (16740) covalent geometry : angle 0.63705 / 0.31 (22706) hydrogen bonds : bond 0.04720 / 3.24 ( 1163) hydrogen bonds : angle 4.35088 / 3.16 ( 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: 89 poor density : 557 time to evaluate : 0.651 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: 0.8719 (mm) cc_final: 0.8303 (mt) REVERT: A 116 VAL cc_start: 0.8818 (t) cc_final: 0.8530 (t) REVERT: A 149 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7518 (tm-30) REVERT: A 174 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8257 (tt) REVERT: A 176 VAL cc_start: 0.8867 (p) cc_final: 0.8612 (t) REVERT: A 225 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7628 (tp40) REVERT: A 233 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7669 (tm-30) REVERT: A 266 LEU cc_start: 0.8431 (tp) cc_final: 0.8188 (tt) REVERT: A 269 LEU cc_start: 0.8488 (tp) cc_final: 0.8203 (tt) REVERT: A 300 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7993 (mt-10) REVERT: A 337 GLU cc_start: 0.7762 (tp30) cc_final: 0.7433 (tp30) REVERT: A 346 GLU cc_start: 0.7757 (tt0) cc_final: 0.7488 (tt0) REVERT: A 354 GLU cc_start: 0.8202 (tt0) cc_final: 0.7877 (tt0) REVERT: A 375 LYS cc_start: 0.8721 (tppp) cc_final: 0.8492 (ttpp) REVERT: A 383 MET cc_start: 0.7176 (mmm) cc_final: 0.6589 (mmm) REVERT: A 385 TRP cc_start: 0.8492 (m100) cc_final: 0.8080 (m100) REVERT: A 486 ILE cc_start: 0.8750 (mp) cc_final: 0.8513 (mm) REVERT: A 487 SER cc_start: 0.8300 (t) cc_final: 0.7975 (p) REVERT: A 511 MET cc_start: 0.8928 (tmm) cc_final: 0.8716 (tmm) REVERT: A 531 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6906 (tm-30) REVERT: A 554 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7770 (tp30) REVERT: A 578 MET cc_start: 0.8654 (mtp) cc_final: 0.8446 (mtp) REVERT: A 579 MET cc_start: 0.7929 (tmm) cc_final: 0.7724 (tpp) REVERT: A 580 GLU cc_start: 0.8170 (tp30) cc_final: 0.7773 (tp30) REVERT: A 599 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: A 602 MET cc_start: 0.7551 (mpp) cc_final: 0.7293 (mpp) REVERT: A 632 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7987 (ttmm) REVERT: A 634 SER cc_start: 0.8921 (m) cc_final: 0.8648 (t) REVERT: A 647 LYS cc_start: 0.8670 (mmtp) cc_final: 0.8416 (mmtm) REVERT: A 697 MET cc_start: 0.6510 (mmm) cc_final: 0.5924 (mmm) REVERT: A 815 LYS cc_start: 0.9053 (tttt) cc_final: 0.8679 (tppp) REVERT: A 820 LYS cc_start: 0.8298 (mmmt) cc_final: 0.7996 (mmmt) REVERT: A 828 LYS cc_start: 0.8517 (mmmm) cc_final: 0.8259 (mmmm) REVERT: A 841 LYS cc_start: 0.8990 (mtpt) cc_final: 0.8571 (mtpt) REVERT: A 897 LYS cc_start: 0.8949 (mttm) cc_final: 0.8722 (mmtp) REVERT: A 942 MET cc_start: 0.8519 (tpp) cc_final: 0.8294 (tpt) REVERT: A 972 PHE cc_start: 0.8600 (t80) cc_final: 0.8319 (t80) REVERT: A 994 GLU cc_start: 0.7886 (pm20) cc_final: 0.7521 (pm20) REVERT: A 1003 SER cc_start: 0.8484 (t) cc_final: 0.8261 (m) REVERT: A 1008 LEU cc_start: 0.8196 (mp) cc_final: 0.7833 (tp) REVERT: A 1044 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 1060 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7646 (mm-30) REVERT: A 1061 THR cc_start: 0.7762 (OUTLIER) cc_final: 0.7531 (p) REVERT: A 1066 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7478 (m-80) REVERT: A 1073 MET cc_start: 0.8629 (tpp) cc_final: 0.8284 (tpp) REVERT: A 1080 PHE cc_start: 0.8046 (m-80) cc_final: 0.7447 (m-80) REVERT: A 1116 LYS cc_start: 0.8508 (mttt) cc_final: 0.8294 (mttt) REVERT: A 1121 LEU cc_start: 0.8916 (mm) cc_final: 0.8636 (mt) REVERT: A 1136 PHE cc_start: 0.6922 (t80) cc_final: 0.6532 (t80) REVERT: A 1173 LYS cc_start: 0.7588 (mtpp) cc_final: 0.7153 (mtpp) REVERT: A 1190 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7772 (mmm-85) REVERT: A 1212 ILE cc_start: 0.5492 (OUTLIER) cc_final: 0.4981 (mp) REVERT: B 134 ASP cc_start: 0.8215 (t0) cc_final: 0.7826 (t70) REVERT: B 149 GLU cc_start: 0.7951 (tp30) cc_final: 0.7624 (tm-30) REVERT: B 300 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7882 (mt-10) REVERT: B 337 GLU cc_start: 0.7798 (tp30) cc_final: 0.7483 (tp30) REVERT: B 375 LYS cc_start: 0.8762 (tppp) cc_final: 0.8239 (mtpp) REVERT: B 383 MET cc_start: 0.7274 (tpp) cc_final: 0.6722 (mmm) REVERT: B 385 TRP cc_start: 0.8412 (m100) cc_final: 0.8098 (m100) REVERT: B 487 SER cc_start: 0.8406 (t) cc_final: 0.8127 (p) REVERT: B 531 GLU cc_start: 0.7471 (mm-30) cc_final: 0.6978 (tm-30) REVERT: B 578 MET cc_start: 0.8604 (mtp) cc_final: 0.8268 (mtp) REVERT: B 579 MET cc_start: 0.7819 (tmm) cc_final: 0.7599 (tpp) REVERT: B 581 GLU cc_start: 0.8470 (tp30) cc_final: 0.8218 (tp30) REVERT: B 586 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8421 (ttp) REVERT: B 588 LYS cc_start: 0.8592 (tppt) cc_final: 0.8325 (tttm) REVERT: B 697 MET cc_start: 0.5841 (mmm) cc_final: 0.5208 (mmm) REVERT: B 736 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.7954 (t0) REVERT: B 808 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7987 (pp) REVERT: B 810 MET cc_start: 0.7046 (ptt) cc_final: 0.6837 (ptt) REVERT: B 815 LYS cc_start: 0.9141 (tttt) cc_final: 0.8674 (tppp) REVERT: B 820 LYS cc_start: 0.8176 (mmmt) cc_final: 0.7912 (mmmt) REVERT: B 825 VAL cc_start: 0.8763 (t) cc_final: 0.8466 (p) REVERT: B 832 GLN cc_start: 0.8626 (tt0) cc_final: 0.8326 (tp-100) REVERT: B 852 LYS cc_start: 0.8430 (mttp) cc_final: 0.8074 (ttmm) REVERT: B 859 ASP cc_start: 0.7983 (p0) cc_final: 0.7635 (p0) REVERT: B 877 GLN cc_start: 0.8703 (tt0) cc_final: 0.8432 (tt0) REVERT: B 926 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7802 (mm-30) REVERT: B 931 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7733 (mt-10) REVERT: B 954 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7601 (mm-30) REVERT: B 958 LYS cc_start: 0.8905 (ttpt) cc_final: 0.8531 (ttmm) REVERT: B 968 LYS cc_start: 0.8717 (mtpp) cc_final: 0.8414 (mmmm) REVERT: B 972 PHE cc_start: 0.8803 (t80) cc_final: 0.8440 (t80) REVERT: B 993 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.6784 (m-30) REVERT: B 994 GLU cc_start: 0.7821 (pm20) cc_final: 0.7469 (pm20) REVERT: B 1003 SER cc_start: 0.8540 (t) cc_final: 0.8263 (m) REVERT: B 1066 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.7719 (m-80) REVERT: B 1073 MET cc_start: 0.8590 (tpp) cc_final: 0.8082 (tpp) REVERT: B 1098 ILE cc_start: 0.8916 (tt) cc_final: 0.8563 (tp) REVERT: B 1104 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7433 (tpp) REVERT: B 1118 LYS cc_start: 0.8628 (mtpp) cc_final: 0.8309 (mtmm) REVERT: B 1121 LEU cc_start: 0.8963 (mm) cc_final: 0.8681 (mt) REVERT: B 1122 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7776 (tp30) REVERT: B 1144 ASP cc_start: 0.7209 (m-30) cc_final: 0.6985 (m-30) REVERT: B 1162 ARG cc_start: 0.5703 (OUTLIER) cc_final: 0.5107 (tpm-80) REVERT: B 1179 THR cc_start: 0.5283 (OUTLIER) cc_final: 0.5045 (p) REVERT: B 1190 ARG cc_start: 0.7911 (mmm-85) cc_final: 0.7700 (mmm-85) REVERT: B 1212 ILE cc_start: 0.5519 (OUTLIER) cc_final: 0.5207 (mp) outliers start: 89 outliers final: 49 residues processed: 602 average time/residue: 0.1512 time to fit residues: 132.2921 Evaluate side-chains 602 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 537 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 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 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 1104 MET Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1128 ASP 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 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 372 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 808 LEU 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 1054 ASN 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: 2.9990 chunk 132 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 177 optimal weight: 0.3980 chunk 196 optimal weight: 0.0270 chunk 121 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.8844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 600 HIS A 981 HIS A1220 ASN B 165 GLN B 256 GLN B 597 GLN B1220 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.143589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120060 restraints weight = 25251.526| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.07 r_work: 0.3379 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16740 Z= 0.162 Angle : 0.638 16.532 22706 Z= 0.311 Chirality : 0.042 0.176 2734 Planarity : 0.004 0.063 2796 Dihedral : 6.513 59.772 2294 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.41 % Allowed : 19.75 % Favored : 74.83 % 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 are not related in a simple way. whole: 1.07 (0.19), residues: 2050 helix: 1.72 (0.14), residues: 1454 sheet: -2.59 (0.54), residues: 72 loop : -1.71 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1185 TYR 0.018 0.001 TYR B1153 PHE 0.020 0.001 PHE B 680 TRP 0.017 0.001 TRP A1112 HIS 0.003 0.001 HIS B 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (16740) covalent geometry : angle 0.63805 / 0.31 (22706) hydrogen bonds : bond 0.04827 / 3.33 ( 1163) hydrogen bonds : angle 4.29873 / 3.12 ( 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 642 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 545 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: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8717 (mm) cc_final: 0.8318 (mt) REVERT: A 116 VAL cc_start: 0.8764 (t) cc_final: 0.8490 (t) REVERT: A 149 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7469 (tm-30) REVERT: A 163 PHE cc_start: 0.8345 (t80) cc_final: 0.8018 (t80) REVERT: A 174 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8266 (tt) REVERT: A 176 VAL cc_start: 0.8908 (p) cc_final: 0.8661 (t) REVERT: A 225 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7593 (tp40) REVERT: A 233 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7637 (tm-30) REVERT: A 266 LEU cc_start: 0.8419 (tp) cc_final: 0.8175 (tt) REVERT: A 269 LEU cc_start: 0.8595 (tp) cc_final: 0.8325 (tt) REVERT: A 337 GLU cc_start: 0.7764 (tp30) cc_final: 0.7448 (tp30) REVERT: A 346 GLU cc_start: 0.7768 (tt0) cc_final: 0.7508 (tt0) REVERT: A 354 GLU cc_start: 0.8237 (tt0) cc_final: 0.7898 (tt0) REVERT: A 383 MET cc_start: 0.7069 (mmm) cc_final: 0.6521 (mmm) REVERT: A 443 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8110 (tm-30) REVERT: A 486 ILE cc_start: 0.8754 (mp) cc_final: 0.8497 (mm) REVERT: A 487 SER cc_start: 0.8217 (t) cc_final: 0.7894 (p) REVERT: A 531 GLU cc_start: 0.7473 (mm-30) cc_final: 0.6942 (tm-30) REVERT: A 554 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7756 (tp30) REVERT: A 578 MET cc_start: 0.8558 (mtp) cc_final: 0.8338 (mtp) REVERT: A 580 GLU cc_start: 0.8117 (tp30) cc_final: 0.7691 (tp30) REVERT: A 599 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: A 602 MET cc_start: 0.7523 (mpp) cc_final: 0.7299 (mpp) REVERT: A 632 LYS cc_start: 0.8248 (ttpt) cc_final: 0.7985 (ttmm) REVERT: A 647 LYS cc_start: 0.8716 (mmtp) cc_final: 0.8447 (mmtm) REVERT: A 697 MET cc_start: 0.6539 (mmm) cc_final: 0.5923 (mmm) REVERT: A 815 LYS cc_start: 0.9019 (tttt) cc_final: 0.8644 (tppp) REVERT: A 820 LYS cc_start: 0.8303 (mmmt) cc_final: 0.8008 (mmmt) REVERT: A 841 LYS cc_start: 0.8990 (mtpt) cc_final: 0.8587 (mtpt) REVERT: A 923 ASP cc_start: 0.7496 (p0) cc_final: 0.7162 (p0) REVERT: A 942 MET cc_start: 0.8529 (tpp) cc_final: 0.8320 (tpt) REVERT: A 990 ARG cc_start: 0.7972 (tpp80) cc_final: 0.7665 (tpp80) REVERT: A 994 GLU cc_start: 0.7872 (pm20) cc_final: 0.7552 (pm20) REVERT: A 1003 SER cc_start: 0.8439 (t) cc_final: 0.8211 (m) REVERT: A 1006 VAL cc_start: 0.8488 (m) cc_final: 0.8212 (p) REVERT: A 1008 LEU cc_start: 0.8202 (mp) cc_final: 0.7859 (tp) REVERT: A 1044 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7608 (mt-10) REVERT: A 1060 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7737 (mm-30) REVERT: A 1061 THR cc_start: 0.7770 (OUTLIER) cc_final: 0.7533 (p) REVERT: A 1066 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: A 1072 ASP cc_start: 0.7540 (m-30) cc_final: 0.7297 (m-30) REVERT: A 1080 PHE cc_start: 0.8017 (m-80) cc_final: 0.7540 (m-80) REVERT: A 1112 TRP cc_start: 0.7888 (m100) cc_final: 0.7554 (m100) REVERT: A 1116 LYS cc_start: 0.8516 (mttt) cc_final: 0.7590 (mttt) REVERT: A 1121 LEU cc_start: 0.8911 (mm) cc_final: 0.8666 (mt) REVERT: A 1136 PHE cc_start: 0.6873 (t80) cc_final: 0.6611 (t80) REVERT: A 1139 ASP cc_start: 0.7708 (m-30) cc_final: 0.7376 (m-30) REVERT: A 1190 ARG cc_start: 0.8098 (mmm-85) cc_final: 0.7713 (mmm-85) REVERT: A 1212 ILE cc_start: 0.5558 (OUTLIER) cc_final: 0.4992 (mp) REVERT: B 116 VAL cc_start: 0.8645 (t) cc_final: 0.8315 (m) REVERT: B 134 ASP cc_start: 0.8190 (t0) cc_final: 0.7842 (t70) REVERT: B 149 GLU cc_start: 0.7943 (tp30) cc_final: 0.7594 (tm-30) REVERT: B 337 GLU cc_start: 0.7771 (tp30) cc_final: 0.7429 (tp30) REVERT: B 375 LYS cc_start: 0.8804 (tppp) cc_final: 0.8334 (mtpp) REVERT: B 383 MET cc_start: 0.7268 (tpp) cc_final: 0.6688 (mmm) REVERT: B 385 TRP cc_start: 0.8432 (m100) cc_final: 0.8171 (m100) REVERT: B 410 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8304 (mt) REVERT: B 419 TRP cc_start: 0.8113 (p-90) cc_final: 0.7807 (p-90) REVERT: B 487 SER cc_start: 0.8396 (t) cc_final: 0.8095 (p) REVERT: B 511 MET cc_start: 0.8915 (tmm) cc_final: 0.8617 (ttp) REVERT: B 531 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7062 (tm-30) REVERT: B 580 GLU cc_start: 0.8086 (tp30) cc_final: 0.7820 (tp30) REVERT: B 588 LYS cc_start: 0.8630 (tppt) cc_final: 0.8365 (tttm) REVERT: B 697 MET cc_start: 0.5821 (mmm) cc_final: 0.5172 (mmm) REVERT: B 736 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.7992 (t0) REVERT: B 808 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8014 (pp) REVERT: B 810 MET cc_start: 0.7079 (ptt) cc_final: 0.6873 (ptt) REVERT: B 815 LYS cc_start: 0.9103 (tttt) cc_final: 0.8634 (tppp) REVERT: B 820 LYS cc_start: 0.8216 (mmmt) cc_final: 0.7946 (mmmt) REVERT: B 825 VAL cc_start: 0.8748 (t) cc_final: 0.8470 (p) REVERT: B 832 GLN cc_start: 0.8595 (tt0) cc_final: 0.8318 (tp-100) REVERT: B 852 LYS cc_start: 0.8491 (mttp) cc_final: 0.8015 (mttt) REVERT: B 856 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7743 (ttp80) REVERT: B 859 ASP cc_start: 0.7993 (p0) cc_final: 0.7703 (p0) REVERT: B 877 GLN cc_start: 0.8710 (tt0) cc_final: 0.8430 (tt0) REVERT: B 926 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7805 (mm-30) REVERT: B 931 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7688 (mt-10) REVERT: B 954 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7598 (mm-30) REVERT: B 958 LYS cc_start: 0.8932 (ttpt) cc_final: 0.8570 (ttmm) REVERT: B 968 LYS cc_start: 0.8688 (mtpp) cc_final: 0.8370 (mmmm) REVERT: B 978 SER cc_start: 0.8547 (t) cc_final: 0.8123 (p) REVERT: B 993 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.6871 (m-30) REVERT: B 994 GLU cc_start: 0.7814 (pm20) cc_final: 0.7440 (pm20) REVERT: B 1003 SER cc_start: 0.8513 (t) cc_final: 0.8262 (m) REVERT: B 1005 LEU cc_start: 0.8442 (tp) cc_final: 0.8028 (tp) REVERT: B 1061 THR cc_start: 0.7521 (OUTLIER) cc_final: 0.7253 (p) REVERT: B 1066 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8097 (m-80) REVERT: B 1098 ILE cc_start: 0.8927 (tt) cc_final: 0.8564 (tp) REVERT: B 1118 LYS cc_start: 0.8628 (mtpp) cc_final: 0.8333 (mtmm) REVERT: B 1121 LEU cc_start: 0.9018 (mm) cc_final: 0.8716 (mt) REVERT: B 1122 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7658 (mm-30) REVERT: B 1144 ASP cc_start: 0.7216 (m-30) cc_final: 0.6977 (m-30) REVERT: B 1162 ARG cc_start: 0.5789 (OUTLIER) cc_final: 0.5176 (tpm-80) REVERT: B 1179 THR cc_start: 0.5323 (OUTLIER) cc_final: 0.5085 (p) REVERT: B 1212 ILE cc_start: 0.5394 (OUTLIER) cc_final: 0.5033 (mp) outliers start: 97 outliers final: 56 residues processed: 599 average time/residue: 0.1513 time to fit residues: 131.7514 Evaluate side-chains 609 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 538 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 395 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 492 LEU 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 624 GLN Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 981 HIS Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1063 VAL 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 1147 LEU Chi-restraints excluded: chain A residue 1151 THR 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 123 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 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 616 GLU Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1154 ASN Chi-restraints excluded: chain B residue 1156 HIS Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1199 LEU Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 65 optimal weight: 0.5980 chunk 161 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 159 optimal weight: 0.0770 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 943 ASN A 981 HIS B1220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.144158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.120745 restraints weight = 25191.931| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.07 r_work: 0.3387 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16740 Z= 0.146 Angle : 0.640 16.589 22706 Z= 0.309 Chirality : 0.041 0.170 2734 Planarity : 0.004 0.062 2796 Dihedral : 6.280 58.624 2291 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.41 % Allowed : 19.81 % Favored : 74.78 % 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 are not related in a simple way. whole: 1.24 (0.19), residues: 2050 helix: 1.85 (0.14), residues: 1452 sheet: -2.40 (0.53), residues: 76 loop : -1.66 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 499 TYR 0.010 0.001 TYR B 415 PHE 0.022 0.001 PHE A 598 TRP 0.012 0.001 TRP B 962 HIS 0.003 0.001 HIS A 981 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (16740) covalent geometry : angle 0.64008 / 0.31 (22706) hydrogen bonds : bond 0.04705 / 3.23 ( 1163) hydrogen bonds : angle 4.27901 / 3.11 ( 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 653 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 556 time to evaluate : 0.614 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: 0.8692 (mm) cc_final: 0.8303 (mt) REVERT: A 116 VAL cc_start: 0.8714 (t) cc_final: 0.8465 (t) REVERT: A 149 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7425 (tm-30) REVERT: A 163 PHE cc_start: 0.8323 (t80) cc_final: 0.7960 (t80) REVERT: A 174 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8234 (tt) REVERT: A 176 VAL cc_start: 0.8899 (p) cc_final: 0.8652 (t) REVERT: A 225 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7564 (tp40) REVERT: A 233 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7590 (tm-30) REVERT: A 266 LEU cc_start: 0.8405 (tp) cc_final: 0.8160 (tt) REVERT: A 269 LEU cc_start: 0.8572 (tp) cc_final: 0.8304 (tt) REVERT: A 337 GLU cc_start: 0.7785 (tp30) cc_final: 0.7468 (tp30) REVERT: A 338 LYS cc_start: 0.8710 (mtmm) cc_final: 0.8058 (mtmm) REVERT: A 346 GLU cc_start: 0.7773 (tt0) cc_final: 0.7447 (tt0) REVERT: A 354 GLU cc_start: 0.8197 (tt0) cc_final: 0.7851 (tt0) REVERT: A 375 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8418 (ttpp) REVERT: A 383 MET cc_start: 0.6989 (mmm) cc_final: 0.6477 (mmm) REVERT: A 387 TYR cc_start: 0.8559 (m-10) cc_final: 0.8164 (m-10) REVERT: A 486 ILE cc_start: 0.8745 (mp) cc_final: 0.8509 (mm) REVERT: A 487 SER cc_start: 0.8204 (t) cc_final: 0.7871 (p) REVERT: A 511 MET cc_start: 0.8840 (tmm) cc_final: 0.8553 (ttp) REVERT: A 531 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6947 (tm-30) REVERT: A 554 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7773 (tp30) REVERT: A 580 GLU cc_start: 0.8106 (tp30) cc_final: 0.7866 (tp30) REVERT: A 602 MET cc_start: 0.7539 (mpp) cc_final: 0.7314 (mpp) REVERT: A 632 LYS cc_start: 0.8215 (ttpt) cc_final: 0.7959 (ttmm) REVERT: A 634 SER cc_start: 0.8915 (m) cc_final: 0.8648 (t) REVERT: A 647 LYS cc_start: 0.8712 (mmtp) cc_final: 0.8450 (mmtm) REVERT: A 697 MET cc_start: 0.6506 (mmm) cc_final: 0.5899 (mmm) REVERT: A 815 LYS cc_start: 0.9000 (tttt) cc_final: 0.8649 (tppp) REVERT: A 820 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7959 (mmmt) REVERT: A 841 LYS cc_start: 0.8981 (mtpt) cc_final: 0.8586 (mtpt) REVERT: A 854 ILE cc_start: 0.8912 (tp) cc_final: 0.8703 (tp) REVERT: A 884 LEU cc_start: 0.8446 (mm) cc_final: 0.8162 (mm) REVERT: A 923 ASP cc_start: 0.7448 (p0) cc_final: 0.7099 (p0) REVERT: A 937 LYS cc_start: 0.8689 (mttm) cc_final: 0.8458 (mttm) REVERT: A 942 MET cc_start: 0.8565 (tpp) cc_final: 0.8357 (tpt) REVERT: A 994 GLU cc_start: 0.7884 (pm20) cc_final: 0.7547 (pm20) REVERT: A 1003 SER cc_start: 0.8395 (t) cc_final: 0.8136 (m) REVERT: A 1006 VAL cc_start: 0.8512 (m) cc_final: 0.8224 (t) REVERT: A 1008 LEU cc_start: 0.8199 (mp) cc_final: 0.7888 (tp) REVERT: A 1044 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7542 (mt-10) REVERT: A 1060 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7666 (mm-30) REVERT: A 1061 THR cc_start: 0.7727 (OUTLIER) cc_final: 0.7492 (p) REVERT: A 1066 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: A 1072 ASP cc_start: 0.7641 (m-30) cc_final: 0.7393 (m-30) REVERT: A 1073 MET cc_start: 0.8753 (tpp) cc_final: 0.8545 (tpp) REVERT: A 1080 PHE cc_start: 0.8005 (m-80) cc_final: 0.7540 (m-80) REVERT: A 1104 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7515 (tpp) REVERT: A 1112 TRP cc_start: 0.7996 (m100) cc_final: 0.7542 (m100) REVERT: A 1116 LYS cc_start: 0.8508 (mttt) cc_final: 0.7840 (mttt) REVERT: A 1121 LEU cc_start: 0.8906 (mm) cc_final: 0.8684 (mt) REVERT: A 1136 PHE cc_start: 0.6820 (t80) cc_final: 0.6227 (t80) REVERT: A 1139 ASP cc_start: 0.7705 (m-30) cc_final: 0.7326 (m-30) REVERT: A 1173 LYS cc_start: 0.7630 (mtpp) cc_final: 0.7292 (mtpp) REVERT: A 1190 ARG cc_start: 0.8103 (mmm-85) cc_final: 0.7738 (mmm-85) REVERT: A 1212 ILE cc_start: 0.5487 (OUTLIER) cc_final: 0.4929 (mp) REVERT: B 116 VAL cc_start: 0.8631 (t) cc_final: 0.8295 (m) REVERT: B 149 GLU cc_start: 0.7907 (tp30) cc_final: 0.7467 (tm-30) REVERT: B 155 ASP cc_start: 0.8209 (t0) cc_final: 0.7958 (t0) REVERT: B 265 VAL cc_start: 0.8666 (t) cc_final: 0.8353 (p) REVERT: B 337 GLU cc_start: 0.7758 (tp30) cc_final: 0.7411 (tp30) REVERT: B 375 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8318 (mtpp) REVERT: B 383 MET cc_start: 0.7261 (tpp) cc_final: 0.6704 (mmm) REVERT: B 385 TRP cc_start: 0.8417 (m100) cc_final: 0.8142 (m100) REVERT: B 419 TRP cc_start: 0.8091 (p-90) cc_final: 0.7747 (p-90) REVERT: B 487 SER cc_start: 0.8376 (t) cc_final: 0.8078 (p) REVERT: B 511 MET cc_start: 0.8883 (tmm) cc_final: 0.8633 (ttp) REVERT: B 531 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7038 (tm-30) REVERT: B 580 GLU cc_start: 0.8042 (tp30) cc_final: 0.7639 (tp30) REVERT: B 584 LEU cc_start: 0.8805 (mm) cc_final: 0.8516 (mm) REVERT: B 588 LYS cc_start: 0.8582 (tppt) cc_final: 0.8339 (tttm) REVERT: B 621 GLU cc_start: 0.7655 (pp20) cc_final: 0.7240 (pp20) REVERT: B 697 MET cc_start: 0.5792 (mmm) cc_final: 0.5150 (mmm) REVERT: B 736 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.7976 (t0) REVERT: B 810 MET cc_start: 0.7074 (ptt) cc_final: 0.6862 (ptt) REVERT: B 815 LYS cc_start: 0.9119 (tttt) cc_final: 0.8656 (tppp) REVERT: B 820 LYS cc_start: 0.8193 (mmmt) cc_final: 0.7944 (mmmt) REVERT: B 832 GLN cc_start: 0.8559 (tt0) cc_final: 0.8351 (tp-100) REVERT: B 852 LYS cc_start: 0.8503 (mttp) cc_final: 0.8048 (mtpt) REVERT: B 853 ILE cc_start: 0.8893 (tp) cc_final: 0.8586 (tt) REVERT: B 859 ASP cc_start: 0.8023 (p0) cc_final: 0.7740 (p0) REVERT: B 877 GLN cc_start: 0.8686 (tt0) cc_final: 0.8481 (tt0) REVERT: B 887 ARG cc_start: 0.8224 (tpp80) cc_final: 0.7937 (ttm-80) REVERT: B 926 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7783 (mm-30) REVERT: B 931 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7670 (mt-10) REVERT: B 947 SER cc_start: 0.7945 (p) cc_final: 0.7744 (t) REVERT: B 954 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7570 (mm-30) REVERT: B 958 LYS cc_start: 0.8918 (ttpt) cc_final: 0.8544 (ttmm) REVERT: B 968 LYS cc_start: 0.8675 (mtpp) cc_final: 0.8353 (mmmm) REVERT: B 978 SER cc_start: 0.8548 (t) cc_final: 0.8095 (p) REVERT: B 993 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.6814 (m-30) REVERT: B 994 GLU cc_start: 0.7843 (pm20) cc_final: 0.7452 (pm20) REVERT: B 998 LEU cc_start: 0.8603 (mm) cc_final: 0.8378 (mt) REVERT: B 1003 SER cc_start: 0.8480 (t) cc_final: 0.8222 (m) REVERT: B 1005 LEU cc_start: 0.8424 (tp) cc_final: 0.8211 (tp) REVERT: B 1007 LYS cc_start: 0.7896 (ttpp) cc_final: 0.7546 (ttpp) REVERT: B 1060 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7521 (mm-30) REVERT: B 1066 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.8065 (m-80) REVERT: B 1075 ILE cc_start: 0.8961 (mt) cc_final: 0.8657 (tt) REVERT: B 1098 ILE cc_start: 0.8920 (tt) cc_final: 0.8558 (tp) REVERT: B 1118 LYS cc_start: 0.8617 (mtpp) cc_final: 0.8338 (mtmm) REVERT: B 1121 LEU cc_start: 0.9020 (mm) cc_final: 0.8746 (mt) REVERT: B 1122 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7634 (mm-30) REVERT: B 1144 ASP cc_start: 0.7216 (m-30) cc_final: 0.7009 (m-30) REVERT: B 1162 ARG cc_start: 0.5843 (OUTLIER) cc_final: 0.5174 (tpm-80) REVERT: B 1179 THR cc_start: 0.5114 (OUTLIER) cc_final: 0.4902 (p) REVERT: B 1212 ILE cc_start: 0.5398 (OUTLIER) cc_final: 0.5029 (mp) outliers start: 97 outliers final: 56 residues processed: 606 average time/residue: 0.1464 time to fit residues: 129.5426 Evaluate side-chains 616 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 546 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 321 VAL 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 425 MET Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 MET Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1158 ARG Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 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 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 872 GLU Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 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: 2.9990 chunk 181 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 6 optimal weight: 0.0980 chunk 195 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN A 943 ASN A1220 ASN B 225 GLN 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 = 0.143497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120460 restraints weight = 25332.532| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.06 r_work: 0.3386 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16740 Z= 0.152 Angle : 0.649 16.571 22706 Z= 0.314 Chirality : 0.042 0.170 2734 Planarity : 0.004 0.061 2796 Dihedral : 6.154 58.687 2285 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 5.19 % Allowed : 20.65 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.19), residues: 2050 helix: 1.91 (0.14), residues: 1452 sheet: -2.13 (0.57), residues: 72 loop : -1.64 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 500 TYR 0.013 0.001 TYR B 415 PHE 0.031 0.001 PHE A 575 TRP 0.019 0.001 TRP B1112 HIS 0.002 0.001 HIS B 981 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (16740) covalent geometry : angle 0.64950 / 0.31 (22706) hydrogen bonds : bond 0.04756 / 3.26 ( 1163) hydrogen bonds : angle 4.24442 / 3.09 ( 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 633 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 540 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8697 (mm) cc_final: 0.8317 (mt) REVERT: A 116 VAL cc_start: 0.8737 (t) cc_final: 0.8484 (t) REVERT: A 163 PHE cc_start: 0.8383 (t80) cc_final: 0.8131 (t80) REVERT: A 174 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8177 (tt) REVERT: A 176 VAL cc_start: 0.8919 (p) cc_final: 0.8678 (t) REVERT: A 233 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7586 (tm-30) REVERT: A 266 LEU cc_start: 0.8357 (tp) cc_final: 0.8117 (tt) REVERT: A 269 LEU cc_start: 0.8553 (tp) cc_final: 0.8311 (tt) REVERT: A 337 GLU cc_start: 0.7760 (tp30) cc_final: 0.7424 (tp30) REVERT: A 338 LYS cc_start: 0.8746 (mtmm) cc_final: 0.8331 (mtmm) REVERT: A 346 GLU cc_start: 0.7886 (tt0) cc_final: 0.7676 (tp30) REVERT: A 354 GLU cc_start: 0.8197 (tt0) cc_final: 0.7867 (tt0) REVERT: A 375 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8533 (ttpp) REVERT: A 383 MET cc_start: 0.7008 (mmm) cc_final: 0.6445 (mmm) REVERT: A 387 TYR cc_start: 0.8627 (m-10) cc_final: 0.8198 (m-10) REVERT: A 454 LYS cc_start: 0.8787 (mmtp) cc_final: 0.8409 (mmtt) REVERT: A 486 ILE cc_start: 0.8746 (mp) cc_final: 0.8460 (mm) REVERT: A 487 SER cc_start: 0.8217 (t) cc_final: 0.7884 (p) REVERT: A 511 MET cc_start: 0.8831 (tmm) cc_final: 0.8498 (ttp) REVERT: A 578 MET cc_start: 0.8665 (mtp) cc_final: 0.8358 (mmm) REVERT: A 581 GLU cc_start: 0.8227 (tp30) cc_final: 0.8014 (tp30) REVERT: A 632 LYS cc_start: 0.8203 (ttpt) cc_final: 0.7942 (ttmm) REVERT: A 634 SER cc_start: 0.8921 (m) cc_final: 0.8644 (t) REVERT: A 697 MET cc_start: 0.6623 (mmm) cc_final: 0.5997 (mmm) REVERT: A 815 LYS cc_start: 0.9010 (tttt) cc_final: 0.8642 (tppp) REVERT: A 820 LYS cc_start: 0.8220 (mmmt) cc_final: 0.7921 (mmmt) REVERT: A 828 LYS cc_start: 0.8425 (mmmm) cc_final: 0.8166 (mmmm) REVERT: A 841 LYS cc_start: 0.8992 (mtpt) cc_final: 0.8600 (mtpt) REVERT: A 854 ILE cc_start: 0.8934 (tp) cc_final: 0.8710 (tp) REVERT: A 859 ASP cc_start: 0.8105 (m-30) cc_final: 0.7739 (m-30) REVERT: A 884 LEU cc_start: 0.8514 (mm) cc_final: 0.8239 (mt) REVERT: A 911 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8378 (mm-30) REVERT: A 937 LYS cc_start: 0.8704 (mttm) cc_final: 0.8480 (mttm) REVERT: A 942 MET cc_start: 0.8590 (tpp) cc_final: 0.8179 (tpt) REVERT: A 972 PHE cc_start: 0.8629 (t80) cc_final: 0.8178 (t80) REVERT: A 989 VAL cc_start: 0.7853 (t) cc_final: 0.7583 (t) REVERT: A 994 GLU cc_start: 0.7858 (pm20) cc_final: 0.7537 (pm20) REVERT: A 1003 SER cc_start: 0.8521 (t) cc_final: 0.8235 (m) REVERT: A 1006 VAL cc_start: 0.8485 (m) cc_final: 0.8203 (p) REVERT: A 1008 LEU cc_start: 0.8225 (mp) cc_final: 0.7826 (tp) REVERT: A 1033 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7604 (tp30) REVERT: A 1044 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7508 (mt-10) REVERT: A 1061 THR cc_start: 0.7730 (OUTLIER) cc_final: 0.7326 (p) REVERT: A 1072 ASP cc_start: 0.7639 (m-30) cc_final: 0.7409 (m-30) REVERT: A 1073 MET cc_start: 0.8800 (tpp) cc_final: 0.8580 (tpp) REVERT: A 1080 PHE cc_start: 0.7990 (m-80) cc_final: 0.7536 (m-80) REVERT: A 1112 TRP cc_start: 0.7905 (m100) cc_final: 0.7575 (m100) REVERT: A 1116 LYS cc_start: 0.8517 (mttt) cc_final: 0.7798 (mttt) REVERT: A 1121 LEU cc_start: 0.8938 (mm) cc_final: 0.8723 (mt) REVERT: A 1136 PHE cc_start: 0.6809 (t80) cc_final: 0.6526 (t80) REVERT: A 1139 ASP cc_start: 0.7713 (m-30) cc_final: 0.7377 (m-30) REVERT: A 1173 LYS cc_start: 0.7621 (mtpp) cc_final: 0.7178 (mtpp) REVERT: A 1190 ARG cc_start: 0.8098 (mmm-85) cc_final: 0.7716 (mmm-85) REVERT: A 1212 ILE cc_start: 0.5433 (OUTLIER) cc_final: 0.4834 (mp) REVERT: B 116 VAL cc_start: 0.8632 (t) cc_final: 0.8295 (m) REVERT: B 134 ASP cc_start: 0.8217 (t0) cc_final: 0.7869 (t70) REVERT: B 149 GLU cc_start: 0.7930 (tp30) cc_final: 0.7580 (tm-30) REVERT: B 155 ASP cc_start: 0.8206 (t0) cc_final: 0.7748 (t0) REVERT: B 265 VAL cc_start: 0.8638 (t) cc_final: 0.8373 (p) REVERT: B 300 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7974 (mt-10) REVERT: B 337 GLU cc_start: 0.7812 (tp30) cc_final: 0.7489 (tp30) REVERT: B 375 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8331 (mtpp) REVERT: B 419 TRP cc_start: 0.8140 (p-90) cc_final: 0.7841 (p-90) REVERT: B 487 SER cc_start: 0.8363 (t) cc_final: 0.8072 (p) REVERT: B 511 MET cc_start: 0.8887 (tmm) cc_final: 0.8573 (ttp) REVERT: B 531 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7071 (tm-30) REVERT: B 580 GLU cc_start: 0.8085 (tp30) cc_final: 0.7758 (tp30) REVERT: B 581 GLU cc_start: 0.8298 (tp30) cc_final: 0.7697 (tp30) REVERT: B 584 LEU cc_start: 0.8794 (mm) cc_final: 0.8478 (mm) REVERT: B 588 LYS cc_start: 0.8582 (tppt) cc_final: 0.8343 (tttm) REVERT: B 621 GLU cc_start: 0.7666 (pp20) cc_final: 0.7289 (pp20) REVERT: B 634 SER cc_start: 0.8995 (m) cc_final: 0.8779 (t) REVERT: B 697 MET cc_start: 0.5912 (mmm) cc_final: 0.5295 (mmm) REVERT: B 736 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.7972 (t0) REVERT: B 820 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7895 (mmmt) REVERT: B 852 LYS cc_start: 0.8577 (mttp) cc_final: 0.8120 (mtpt) REVERT: B 853 ILE cc_start: 0.8981 (tp) cc_final: 0.8672 (tt) REVERT: B 859 ASP cc_start: 0.8031 (p0) cc_final: 0.7738 (p0) REVERT: B 877 GLN cc_start: 0.8657 (tt0) cc_final: 0.8445 (tt0) REVERT: B 887 ARG cc_start: 0.8306 (tpp80) cc_final: 0.7970 (ttm-80) REVERT: B 926 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7808 (mm-30) REVERT: B 931 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7652 (mt-10) REVERT: B 954 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7561 (mm-30) REVERT: B 958 LYS cc_start: 0.8919 (ttpt) cc_final: 0.8533 (ttmm) REVERT: B 968 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8365 (mmmm) REVERT: B 972 PHE cc_start: 0.8719 (t80) cc_final: 0.8447 (t80) REVERT: B 978 SER cc_start: 0.8565 (t) cc_final: 0.8112 (p) REVERT: B 993 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.6881 (m-30) REVERT: B 994 GLU cc_start: 0.7815 (pm20) cc_final: 0.7419 (pm20) REVERT: B 998 LEU cc_start: 0.8650 (mm) cc_final: 0.8416 (mt) REVERT: B 1003 SER cc_start: 0.8493 (t) cc_final: 0.8214 (m) REVERT: B 1005 LEU cc_start: 0.8420 (tp) cc_final: 0.8218 (tp) REVERT: B 1061 THR cc_start: 0.7470 (OUTLIER) cc_final: 0.7211 (p) REVERT: B 1066 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.8132 (m-80) REVERT: B 1075 ILE cc_start: 0.8953 (mt) cc_final: 0.8561 (tt) REVERT: B 1118 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8377 (mtmm) REVERT: B 1121 LEU cc_start: 0.9015 (mm) cc_final: 0.8731 (mt) REVERT: B 1122 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7704 (mm-30) REVERT: B 1136 PHE cc_start: 0.6829 (t80) cc_final: 0.6444 (t80) REVERT: B 1162 ARG cc_start: 0.5896 (OUTLIER) cc_final: 0.5229 (tpm-80) REVERT: B 1212 ILE cc_start: 0.5434 (OUTLIER) cc_final: 0.5037 (mp) outliers start: 93 outliers final: 62 residues processed: 586 average time/residue: 0.1426 time to fit residues: 121.7956 Evaluate side-chains 600 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 527 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 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 425 MET Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 492 LEU 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 963 LEU Chi-restraints excluded: chain A residue 968 LYS 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 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 123 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 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 412 ARG 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 532 ILE Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 684 ILE Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 872 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 162 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 195 optimal weight: 0.1980 chunk 139 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN A 943 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.143470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.120621 restraints weight = 25271.898| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.06 r_work: 0.3418 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16740 Z= 0.149 Angle : 0.655 16.241 22706 Z= 0.316 Chirality : 0.042 0.169 2734 Planarity : 0.004 0.061 2796 Dihedral : 5.973 58.465 2282 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.74 % Allowed : 21.54 % Favored : 73.72 % 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 are not related in a simple way. whole: 1.44 (0.19), residues: 2050 helix: 1.95 (0.14), residues: 1454 sheet: -1.85 (0.58), residues: 76 loop : -1.53 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1053 TYR 0.011 0.001 TYR B 415 PHE 0.035 0.001 PHE A 972 TRP 0.019 0.001 TRP B1112 HIS 0.003 0.001 HIS B 981 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (16740) covalent geometry : angle 0.65455 / 0.32 (22706) hydrogen bonds : bond 0.04727 / 3.23 ( 1163) hydrogen bonds : angle 4.20853 / 3.07 ( 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 618 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 533 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8709 (mm) cc_final: 0.8334 (mt) REVERT: A 116 VAL cc_start: 0.8735 (t) cc_final: 0.8488 (t) REVERT: A 163 PHE cc_start: 0.8405 (t80) cc_final: 0.8173 (t80) REVERT: A 174 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8212 (tt) REVERT: A 176 VAL cc_start: 0.8926 (p) cc_final: 0.8670 (t) REVERT: A 233 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7590 (tm-30) REVERT: A 266 LEU cc_start: 0.8384 (tp) cc_final: 0.8151 (tt) REVERT: A 269 LEU cc_start: 0.8592 (tp) cc_final: 0.8354 (tt) REVERT: A 280 TYR cc_start: 0.8407 (t80) cc_final: 0.8101 (t80) REVERT: A 337 GLU cc_start: 0.7730 (tp30) cc_final: 0.7436 (tp30) REVERT: A 346 GLU cc_start: 0.7801 (tt0) cc_final: 0.7414 (tt0) REVERT: A 354 GLU cc_start: 0.8181 (tt0) cc_final: 0.7860 (tt0) REVERT: A 375 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8515 (ttpp) REVERT: A 377 LEU cc_start: 0.8596 (tp) cc_final: 0.8274 (mp) REVERT: A 383 MET cc_start: 0.6968 (mmm) cc_final: 0.6477 (mmm) REVERT: A 387 TYR cc_start: 0.8625 (m-10) cc_final: 0.8237 (m-10) REVERT: A 411 SER cc_start: 0.8458 (p) cc_final: 0.8177 (p) REVERT: A 486 ILE cc_start: 0.8748 (mp) cc_final: 0.8462 (mm) REVERT: A 487 SER cc_start: 0.8222 (t) cc_final: 0.7903 (p) REVERT: A 511 MET cc_start: 0.8850 (tmm) cc_final: 0.8522 (ttp) REVERT: A 632 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7922 (ttmm) REVERT: A 634 SER cc_start: 0.8904 (m) cc_final: 0.8625 (t) REVERT: A 697 MET cc_start: 0.6538 (mmm) cc_final: 0.5872 (mmm) REVERT: A 815 LYS cc_start: 0.9016 (tttt) cc_final: 0.8664 (tppp) REVERT: A 820 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7927 (mmmt) REVERT: A 828 LYS cc_start: 0.8384 (mmmm) cc_final: 0.8142 (mmmm) REVERT: A 841 LYS cc_start: 0.8984 (mtpt) cc_final: 0.8584 (mtpt) REVERT: A 853 ILE cc_start: 0.9053 (tp) cc_final: 0.8752 (tp) REVERT: A 859 ASP cc_start: 0.8074 (m-30) cc_final: 0.7705 (m-30) REVERT: A 884 LEU cc_start: 0.8509 (mm) cc_final: 0.8203 (mt) REVERT: A 910 ARG cc_start: 0.8572 (ttp-170) cc_final: 0.7999 (ttp-170) REVERT: A 911 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8261 (mm-30) REVERT: A 937 LYS cc_start: 0.8686 (mttm) cc_final: 0.8455 (mttm) REVERT: A 942 MET cc_start: 0.8607 (tpp) cc_final: 0.8184 (tpt) REVERT: A 989 VAL cc_start: 0.7652 (t) cc_final: 0.7359 (t) REVERT: A 994 GLU cc_start: 0.7764 (pm20) cc_final: 0.7479 (pm20) REVERT: A 1003 SER cc_start: 0.8534 (t) cc_final: 0.8274 (m) REVERT: A 1006 VAL cc_start: 0.8467 (m) cc_final: 0.8170 (t) REVERT: A 1007 LYS cc_start: 0.7873 (tttp) cc_final: 0.7504 (ttpp) REVERT: A 1008 LEU cc_start: 0.8271 (mp) cc_final: 0.8010 (mm) REVERT: A 1044 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7491 (mt-10) REVERT: A 1060 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7509 (mm-30) REVERT: A 1061 THR cc_start: 0.7523 (OUTLIER) cc_final: 0.7245 (p) REVERT: A 1072 ASP cc_start: 0.7555 (m-30) cc_final: 0.7342 (m-30) REVERT: A 1112 TRP cc_start: 0.7731 (m100) cc_final: 0.7209 (m100) REVERT: A 1116 LYS cc_start: 0.8514 (mttt) cc_final: 0.7867 (mttt) REVERT: A 1136 PHE cc_start: 0.6770 (t80) cc_final: 0.6476 (t80) REVERT: A 1139 ASP cc_start: 0.7752 (m-30) cc_final: 0.7436 (m-30) REVERT: A 1173 LYS cc_start: 0.7581 (mtpp) cc_final: 0.7166 (mtpp) REVERT: A 1185 ARG cc_start: 0.6825 (mmm-85) cc_final: 0.6590 (mmt180) REVERT: A 1190 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.7665 (mmm-85) REVERT: A 1199 LEU cc_start: 0.7882 (tp) cc_final: 0.7676 (tt) REVERT: A 1212 ILE cc_start: 0.5494 (OUTLIER) cc_final: 0.4907 (mp) REVERT: B 134 ASP cc_start: 0.8178 (t0) cc_final: 0.7828 (t70) REVERT: B 149 GLU cc_start: 0.7910 (tp30) cc_final: 0.7570 (tm-30) REVERT: B 155 ASP cc_start: 0.8159 (t0) cc_final: 0.7736 (t0) REVERT: B 233 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7632 (tm-30) REVERT: B 265 VAL cc_start: 0.8660 (t) cc_final: 0.8389 (p) REVERT: B 300 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7957 (mt-10) REVERT: B 337 GLU cc_start: 0.7768 (tp30) cc_final: 0.7436 (tp30) REVERT: B 375 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8376 (mtpp) REVERT: B 419 TRP cc_start: 0.8120 (p-90) cc_final: 0.7863 (p-90) REVERT: B 487 SER cc_start: 0.8361 (t) cc_final: 0.8081 (p) REVERT: B 494 MET cc_start: 0.8941 (tpp) cc_final: 0.8716 (tpp) REVERT: B 511 MET cc_start: 0.8829 (tmm) cc_final: 0.8503 (ttp) REVERT: B 531 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7065 (tm-30) REVERT: B 580 GLU cc_start: 0.8056 (tp30) cc_final: 0.7739 (tp30) REVERT: B 584 LEU cc_start: 0.8777 (mm) cc_final: 0.8479 (mm) REVERT: B 588 LYS cc_start: 0.8540 (tppt) cc_final: 0.8308 (tttm) REVERT: B 598 PHE cc_start: 0.8886 (t80) cc_final: 0.8426 (t80) REVERT: B 599 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: B 634 SER cc_start: 0.8955 (m) cc_final: 0.8732 (t) REVERT: B 697 MET cc_start: 0.5814 (mmm) cc_final: 0.5196 (mmm) REVERT: B 736 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.7979 (t0) REVERT: B 820 LYS cc_start: 0.8130 (mmmt) cc_final: 0.7867 (mmmt) REVERT: B 852 LYS cc_start: 0.8576 (mttp) cc_final: 0.8138 (mtpt) REVERT: B 853 ILE cc_start: 0.9021 (tp) cc_final: 0.8704 (tt) REVERT: B 859 ASP cc_start: 0.8019 (p0) cc_final: 0.7726 (p0) REVERT: B 877 GLN cc_start: 0.8639 (tt0) cc_final: 0.8415 (tt0) REVERT: B 887 ARG cc_start: 0.8318 (tpp80) cc_final: 0.7990 (ttm-80) REVERT: B 926 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7802 (mm-30) REVERT: B 931 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7602 (mt-10) REVERT: B 954 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7499 (mm-30) REVERT: B 958 LYS cc_start: 0.8904 (ttpt) cc_final: 0.8497 (ttmm) REVERT: B 968 LYS cc_start: 0.8624 (mtpp) cc_final: 0.8328 (mmmm) REVERT: B 972 PHE cc_start: 0.8686 (t80) cc_final: 0.8411 (t80) REVERT: B 978 SER cc_start: 0.8570 (t) cc_final: 0.8111 (p) REVERT: B 993 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6757 (m-30) REVERT: B 994 GLU cc_start: 0.7744 (pm20) cc_final: 0.7347 (pm20) REVERT: B 998 LEU cc_start: 0.8631 (mm) cc_final: 0.8386 (mt) REVERT: B 1003 SER cc_start: 0.8429 (t) cc_final: 0.8125 (m) REVERT: B 1005 LEU cc_start: 0.8415 (tp) cc_final: 0.8193 (tp) REVERT: B 1044 GLU cc_start: 0.7306 (mp0) cc_final: 0.6607 (mp0) REVERT: B 1061 THR cc_start: 0.7390 (OUTLIER) cc_final: 0.7153 (p) REVERT: B 1075 ILE cc_start: 0.8934 (mt) cc_final: 0.8550 (tt) REVERT: B 1118 LYS cc_start: 0.8628 (mtpp) cc_final: 0.8374 (mtmm) REVERT: B 1121 LEU cc_start: 0.9009 (mm) cc_final: 0.8734 (mt) REVERT: B 1122 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7699 (mm-30) REVERT: B 1136 PHE cc_start: 0.6785 (t80) cc_final: 0.6407 (t80) REVERT: B 1162 ARG cc_start: 0.5832 (OUTLIER) cc_final: 0.5179 (tpm-80) REVERT: B 1212 ILE cc_start: 0.5417 (OUTLIER) cc_final: 0.5013 (mp) outliers start: 85 outliers final: 61 residues processed: 576 average time/residue: 0.1441 time to fit residues: 120.8805 Evaluate side-chains 593 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 521 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 425 MET Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 492 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 876 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 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 123 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 412 ARG 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 599 GLU Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 684 ILE Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1061 THR 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 1199 LEU 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: 0.9990 chunk 172 optimal weight: 0.5980 chunk 179 optimal weight: 0.3980 chunk 191 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 85 optimal weight: 0.4980 chunk 95 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.144743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.121977 restraints weight = 25266.660| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.07 r_work: 0.3416 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16740 Z= 0.136 Angle : 0.655 15.965 22706 Z= 0.315 Chirality : 0.041 0.168 2734 Planarity : 0.004 0.061 2796 Dihedral : 5.860 58.713 2280 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.24 % Allowed : 22.27 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.19), residues: 2050 helix: 2.03 (0.14), residues: 1458 sheet: -1.72 (0.58), residues: 76 loop : -1.49 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 500 TYR 0.008 0.001 TYR B 387 PHE 0.051 0.001 PHE A 972 TRP 0.018 0.001 TRP B1112 HIS 0.003 0.001 HIS B 981 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (16740) covalent geometry : angle 0.65533 / 0.32 (22706) hydrogen bonds : bond 0.04547 / 3.10 ( 1163) hydrogen bonds : angle 4.17713 / 3.04 ( 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 615 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 539 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8694 (mm) cc_final: 0.8325 (mt) REVERT: A 116 VAL cc_start: 0.8596 (t) cc_final: 0.8357 (t) REVERT: A 163 PHE cc_start: 0.8361 (t80) cc_final: 0.8136 (t80) REVERT: A 174 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8170 (tt) REVERT: A 176 VAL cc_start: 0.8887 (p) cc_final: 0.8627 (t) REVERT: A 233 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7607 (tm-30) REVERT: A 266 LEU cc_start: 0.8373 (tp) cc_final: 0.8131 (tt) REVERT: A 269 LEU cc_start: 0.8569 (tp) cc_final: 0.8319 (tt) REVERT: A 337 GLU cc_start: 0.7775 (tp30) cc_final: 0.7450 (tp30) REVERT: A 354 GLU cc_start: 0.8192 (tt0) cc_final: 0.7857 (tt0) REVERT: A 375 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8517 (ttpp) REVERT: A 377 LEU cc_start: 0.8640 (tp) cc_final: 0.8326 (mp) REVERT: A 383 MET cc_start: 0.6848 (mmm) cc_final: 0.6377 (mmm) REVERT: A 411 SER cc_start: 0.8455 (p) cc_final: 0.8214 (p) REVERT: A 487 SER cc_start: 0.8209 (t) cc_final: 0.7917 (m) REVERT: A 511 MET cc_start: 0.8857 (tmm) cc_final: 0.8523 (ttp) REVERT: A 577 ASP cc_start: 0.8166 (m-30) cc_final: 0.7771 (m-30) REVERT: A 632 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7887 (ttmm) REVERT: A 634 SER cc_start: 0.8915 (m) cc_final: 0.8641 (t) REVERT: A 647 LYS cc_start: 0.8572 (mmtp) cc_final: 0.8279 (mtmm) REVERT: A 697 MET cc_start: 0.6485 (mmm) cc_final: 0.5785 (mmm) REVERT: A 815 LYS cc_start: 0.8994 (tttt) cc_final: 0.8653 (tppp) REVERT: A 820 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7824 (mmmt) REVERT: A 828 LYS cc_start: 0.8382 (mmmm) cc_final: 0.8126 (mmmm) REVERT: A 841 LYS cc_start: 0.8976 (mtpt) cc_final: 0.8607 (mtpt) REVERT: A 853 ILE cc_start: 0.9027 (tp) cc_final: 0.8717 (tp) REVERT: A 884 LEU cc_start: 0.8503 (mm) cc_final: 0.8166 (mm) REVERT: A 910 ARG cc_start: 0.8528 (ttp-170) cc_final: 0.7951 (ttp-170) REVERT: A 911 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8261 (mm-30) REVERT: A 931 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7899 (mm-30) REVERT: A 937 LYS cc_start: 0.8694 (mttm) cc_final: 0.8444 (mttm) REVERT: A 942 MET cc_start: 0.8643 (tpp) cc_final: 0.8234 (tpt) REVERT: A 994 GLU cc_start: 0.7747 (pm20) cc_final: 0.7351 (pm20) REVERT: A 1003 SER cc_start: 0.8505 (t) cc_final: 0.8228 (m) REVERT: A 1006 VAL cc_start: 0.8425 (m) cc_final: 0.8191 (t) REVERT: A 1035 TYR cc_start: 0.8109 (m-80) cc_final: 0.7657 (m-80) REVERT: A 1044 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7440 (mt-10) REVERT: A 1060 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7380 (mm-30) REVERT: A 1072 ASP cc_start: 0.7597 (m-30) cc_final: 0.7379 (m-30) REVERT: A 1104 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7466 (tpp) REVERT: A 1112 TRP cc_start: 0.7709 (m100) cc_final: 0.7436 (m100) REVERT: A 1116 LYS cc_start: 0.8542 (mttt) cc_final: 0.7972 (mttt) REVERT: A 1120 HIS cc_start: 0.8853 (t-90) cc_final: 0.8592 (t-90) REVERT: A 1136 PHE cc_start: 0.6734 (t80) cc_final: 0.6454 (t80) REVERT: A 1139 ASP cc_start: 0.7699 (m-30) cc_final: 0.7360 (m-30) REVERT: A 1173 LYS cc_start: 0.7594 (mtpp) cc_final: 0.7171 (mtpp) REVERT: A 1190 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7685 (mmm-85) REVERT: A 1212 ILE cc_start: 0.5470 (OUTLIER) cc_final: 0.4828 (mp) REVERT: A 1221 MET cc_start: 0.7913 (mmt) cc_final: 0.7633 (mmt) REVERT: B 116 VAL cc_start: 0.8624 (t) cc_final: 0.8331 (m) REVERT: B 134 ASP cc_start: 0.8182 (t0) cc_final: 0.7823 (t70) REVERT: B 149 GLU cc_start: 0.7891 (tp30) cc_final: 0.7555 (tm-30) REVERT: B 155 ASP cc_start: 0.8139 (t0) cc_final: 0.7691 (t0) REVERT: B 233 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7616 (tm-30) REVERT: B 265 VAL cc_start: 0.8689 (t) cc_final: 0.8392 (p) REVERT: B 300 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7967 (mt-10) REVERT: B 337 GLU cc_start: 0.7765 (tp30) cc_final: 0.7427 (tp30) REVERT: B 375 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8363 (mtpp) REVERT: B 419 TRP cc_start: 0.8103 (p-90) cc_final: 0.7858 (p-90) REVERT: B 487 SER cc_start: 0.8338 (t) cc_final: 0.8041 (p) REVERT: B 511 MET cc_start: 0.8829 (tmm) cc_final: 0.8483 (ttp) REVERT: B 531 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6941 (tm-30) REVERT: B 554 GLU cc_start: 0.8192 (tp30) cc_final: 0.7748 (tp30) REVERT: B 580 GLU cc_start: 0.8042 (tp30) cc_final: 0.7677 (tp30) REVERT: B 584 LEU cc_start: 0.8726 (mm) cc_final: 0.8415 (mm) REVERT: B 588 LYS cc_start: 0.8551 (tppt) cc_final: 0.8316 (tttm) REVERT: B 598 PHE cc_start: 0.8883 (t80) cc_final: 0.8421 (t80) REVERT: B 599 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: B 634 SER cc_start: 0.8954 (m) cc_final: 0.8724 (t) REVERT: B 697 MET cc_start: 0.5830 (mmm) cc_final: 0.5162 (mmm) REVERT: B 736 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.7980 (t0) REVERT: B 820 LYS cc_start: 0.8032 (mmmt) cc_final: 0.7772 (mmmt) REVERT: B 852 LYS cc_start: 0.8581 (mttp) cc_final: 0.8086 (mtpt) REVERT: B 853 ILE cc_start: 0.9008 (tp) cc_final: 0.8690 (tt) REVERT: B 859 ASP cc_start: 0.8021 (p0) cc_final: 0.7730 (p0) REVERT: B 862 LYS cc_start: 0.7383 (ptmm) cc_final: 0.7152 (ptmm) REVERT: B 877 GLN cc_start: 0.8608 (tt0) cc_final: 0.8393 (tt0) REVERT: B 887 ARG cc_start: 0.8304 (tpp80) cc_final: 0.7918 (ttm-80) REVERT: B 926 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7795 (mm-30) REVERT: B 931 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7606 (mt-10) REVERT: B 954 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7526 (mm-30) REVERT: B 958 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8491 (ttmm) REVERT: B 968 LYS cc_start: 0.8634 (mtpp) cc_final: 0.8328 (mmmm) REVERT: B 978 SER cc_start: 0.8596 (t) cc_final: 0.8088 (p) REVERT: B 993 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6708 (m-30) REVERT: B 994 GLU cc_start: 0.7756 (pm20) cc_final: 0.7395 (pm20) REVERT: B 998 LEU cc_start: 0.8615 (mm) cc_final: 0.8401 (mt) REVERT: B 1003 SER cc_start: 0.8384 (t) cc_final: 0.8066 (m) REVERT: B 1005 LEU cc_start: 0.8385 (tp) cc_final: 0.8180 (tp) REVERT: B 1035 TYR cc_start: 0.8119 (m-80) cc_final: 0.7649 (m-80) REVERT: B 1075 ILE cc_start: 0.8889 (mt) cc_final: 0.8503 (tt) REVERT: B 1118 LYS cc_start: 0.8649 (mtpp) cc_final: 0.8381 (mtmm) REVERT: B 1121 LEU cc_start: 0.9002 (mm) cc_final: 0.8747 (mt) REVERT: B 1122 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7737 (mm-30) REVERT: B 1136 PHE cc_start: 0.6763 (t80) cc_final: 0.6361 (t80) REVERT: B 1162 ARG cc_start: 0.5794 (OUTLIER) cc_final: 0.5127 (tpm-80) REVERT: B 1212 ILE cc_start: 0.5412 (OUTLIER) cc_final: 0.4989 (mp) outliers start: 76 outliers final: 51 residues processed: 575 average time/residue: 0.1369 time to fit residues: 113.9979 Evaluate side-chains 592 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 531 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 419 TRP Chi-restraints excluded: chain A residue 425 MET 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 628 VAL Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 979 LEU 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 123 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 375 LYS 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 599 GLU Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 684 ILE Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 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 1199 LEU 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: 0.2980 chunk 11 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 201 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 174 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN B 225 GLN B1220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.145027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122120 restraints weight = 25383.199| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.08 r_work: 0.3439 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16740 Z= 0.135 Angle : 0.660 15.757 22706 Z= 0.319 Chirality : 0.042 0.168 2734 Planarity : 0.004 0.061 2796 Dihedral : 5.792 59.538 2278 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.13 % Allowed : 22.66 % Favored : 73.21 % 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 are not related in a simple way. whole: 1.57 (0.19), residues: 2050 helix: 2.06 (0.14), residues: 1458 sheet: -2.03 (0.56), residues: 86 loop : -1.47 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1053 TYR 0.014 0.001 TYR A1009 PHE 0.017 0.001 PHE A 598 TRP 0.014 0.001 TRP A1112 HIS 0.004 0.001 HIS B 981 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (16740) covalent geometry : angle 0.66003 / 0.32 (22706) hydrogen bonds : bond 0.04525 / 3.06 ( 1163) hydrogen bonds : angle 4.16576 / 3.02 ( 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 604 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 530 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8678 (mm) cc_final: 0.8313 (mt) REVERT: A 116 VAL cc_start: 0.8639 (t) cc_final: 0.8378 (t) REVERT: A 174 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8263 (tt) REVERT: A 266 LEU cc_start: 0.8375 (tp) cc_final: 0.8136 (tt) REVERT: A 269 LEU cc_start: 0.8563 (tp) cc_final: 0.8318 (tt) REVERT: A 337 GLU cc_start: 0.7788 (tp30) cc_final: 0.7463 (tp30) REVERT: A 354 GLU cc_start: 0.8181 (tt0) cc_final: 0.7847 (tt0) REVERT: A 377 LEU cc_start: 0.8638 (tp) cc_final: 0.8322 (mp) REVERT: A 383 MET cc_start: 0.6812 (mmm) cc_final: 0.6375 (mmm) REVERT: A 411 SER cc_start: 0.8431 (p) cc_final: 0.8187 (p) REVERT: A 487 SER cc_start: 0.8205 (t) cc_final: 0.7924 (m) REVERT: A 511 MET cc_start: 0.8842 (tmm) cc_final: 0.8486 (ttp) REVERT: A 577 ASP cc_start: 0.8201 (m-30) cc_final: 0.7834 (m-30) REVERT: A 608 LEU cc_start: 0.8633 (tp) cc_final: 0.8426 (tt) REVERT: A 634 SER cc_start: 0.8888 (m) cc_final: 0.8630 (t) REVERT: A 647 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8361 (mtmm) REVERT: A 697 MET cc_start: 0.6443 (mmm) cc_final: 0.5708 (mmm) REVERT: A 820 LYS cc_start: 0.8085 (mmmt) cc_final: 0.7824 (mmmt) REVERT: A 828 LYS cc_start: 0.8373 (mmmm) cc_final: 0.8129 (mmmm) REVERT: A 841 LYS cc_start: 0.8960 (mtpt) cc_final: 0.8600 (mtpt) REVERT: A 853 ILE cc_start: 0.9053 (tp) cc_final: 0.8751 (tp) REVERT: A 884 LEU cc_start: 0.8504 (mm) cc_final: 0.8254 (mm) REVERT: A 887 ARG cc_start: 0.8397 (tpp80) cc_final: 0.8153 (ttm-80) REVERT: A 910 ARG cc_start: 0.8511 (ttp-170) cc_final: 0.7929 (ttp-170) REVERT: A 911 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8294 (mm-30) REVERT: A 931 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7887 (mm-30) REVERT: A 937 LYS cc_start: 0.8688 (mttm) cc_final: 0.8421 (mttm) REVERT: A 942 MET cc_start: 0.8628 (tpp) cc_final: 0.8214 (tpt) REVERT: A 994 GLU cc_start: 0.7672 (pm20) cc_final: 0.7198 (pm20) REVERT: A 1006 VAL cc_start: 0.8383 (m) cc_final: 0.8130 (p) REVERT: A 1035 TYR cc_start: 0.8196 (m-80) cc_final: 0.7559 (m-80) REVERT: A 1044 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7414 (mt-10) REVERT: A 1060 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7261 (mm-30) REVERT: A 1087 GLU cc_start: 0.7552 (tt0) cc_final: 0.7191 (tp30) REVERT: A 1104 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7450 (tpp) REVERT: A 1112 TRP cc_start: 0.7547 (m100) cc_final: 0.7103 (m100) REVERT: A 1116 LYS cc_start: 0.8511 (mttt) cc_final: 0.7998 (mttt) REVERT: A 1120 HIS cc_start: 0.8839 (t-90) cc_final: 0.8584 (t-90) REVERT: A 1136 PHE cc_start: 0.6733 (t80) cc_final: 0.6432 (t80) REVERT: A 1139 ASP cc_start: 0.7660 (m-30) cc_final: 0.7308 (m-30) REVERT: A 1173 LYS cc_start: 0.7581 (mtpp) cc_final: 0.7167 (mtpp) REVERT: A 1190 ARG cc_start: 0.7919 (mmm-85) cc_final: 0.7577 (mmm-85) REVERT: A 1220 ASN cc_start: 0.7992 (m-40) cc_final: 0.7556 (m110) REVERT: B 116 VAL cc_start: 0.8630 (t) cc_final: 0.8342 (m) REVERT: B 134 ASP cc_start: 0.8163 (t0) cc_final: 0.7811 (t70) REVERT: B 149 GLU cc_start: 0.7888 (tp30) cc_final: 0.7537 (tm-30) REVERT: B 155 ASP cc_start: 0.8149 (t0) cc_final: 0.7722 (t0) REVERT: B 233 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7600 (tm-30) REVERT: B 265 VAL cc_start: 0.8695 (t) cc_final: 0.8399 (p) REVERT: B 337 GLU cc_start: 0.7784 (tp30) cc_final: 0.7445 (tp30) REVERT: B 375 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8351 (mtpp) REVERT: B 419 TRP cc_start: 0.8078 (p-90) cc_final: 0.7843 (p-90) REVERT: B 487 SER cc_start: 0.8359 (t) cc_final: 0.8059 (p) REVERT: B 511 MET cc_start: 0.8820 (tmm) cc_final: 0.8461 (ttp) REVERT: B 531 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6906 (tm-30) REVERT: B 554 GLU cc_start: 0.8197 (tp30) cc_final: 0.7757 (tp30) REVERT: B 580 GLU cc_start: 0.7996 (tp30) cc_final: 0.7637 (tp30) REVERT: B 584 LEU cc_start: 0.8702 (mm) cc_final: 0.8381 (mm) REVERT: B 588 LYS cc_start: 0.8565 (tppt) cc_final: 0.8312 (tttm) REVERT: B 598 PHE cc_start: 0.8864 (t80) cc_final: 0.8446 (t80) REVERT: B 634 SER cc_start: 0.8931 (m) cc_final: 0.8546 (t) REVERT: B 697 MET cc_start: 0.5780 (mmm) cc_final: 0.5138 (mmm) REVERT: B 736 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.7962 (t0) REVERT: B 820 LYS cc_start: 0.7991 (mmmt) cc_final: 0.7751 (mmmt) REVERT: B 852 LYS cc_start: 0.8571 (mttp) cc_final: 0.8075 (mtpt) REVERT: B 853 ILE cc_start: 0.9013 (tp) cc_final: 0.8730 (tt) REVERT: B 859 ASP cc_start: 0.8015 (p0) cc_final: 0.7717 (p0) REVERT: B 872 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7525 (mm-30) REVERT: B 877 GLN cc_start: 0.8612 (tt0) cc_final: 0.8397 (tt0) REVERT: B 887 ARG cc_start: 0.8293 (tpp80) cc_final: 0.7902 (ttm-80) REVERT: B 926 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7854 (mm-30) REVERT: B 954 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7487 (mm-30) REVERT: B 958 LYS cc_start: 0.8902 (ttpt) cc_final: 0.8499 (ttmm) REVERT: B 968 LYS cc_start: 0.8571 (mtpp) cc_final: 0.8239 (mmmm) REVERT: B 978 SER cc_start: 0.8593 (t) cc_final: 0.8083 (p) REVERT: B 994 GLU cc_start: 0.7618 (pm20) cc_final: 0.7189 (pm20) REVERT: B 1003 SER cc_start: 0.8355 (t) cc_final: 0.8036 (m) REVERT: B 1035 TYR cc_start: 0.8104 (m-80) cc_final: 0.7591 (m-80) REVERT: B 1075 ILE cc_start: 0.8929 (mt) cc_final: 0.8547 (tt) REVERT: B 1088 TYR cc_start: 0.7344 (t80) cc_final: 0.6966 (t80) REVERT: B 1118 LYS cc_start: 0.8633 (mtpp) cc_final: 0.8371 (mtmm) REVERT: B 1121 LEU cc_start: 0.8985 (mm) cc_final: 0.8741 (mt) REVERT: B 1122 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7682 (mm-30) REVERT: B 1136 PHE cc_start: 0.6752 (t80) cc_final: 0.6368 (t80) REVERT: B 1162 ARG cc_start: 0.5749 (OUTLIER) cc_final: 0.5090 (tpm-80) REVERT: B 1212 ILE cc_start: 0.5381 (OUTLIER) cc_final: 0.4942 (mp) outliers start: 74 outliers final: 50 residues processed: 564 average time/residue: 0.1390 time to fit residues: 114.0717 Evaluate side-chains 584 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 527 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 407 SER Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET 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 647 LYS 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 979 LEU 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 B residue 123 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 412 ARG 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 736 ASN Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 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 1199 LEU Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 205 optimal weight: 0.0000 chunk 60 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.142652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.119644 restraints weight = 25089.380| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.05 r_work: 0.3410 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16740 Z= 0.197 Angle : 0.695 15.943 22706 Z= 0.339 Chirality : 0.043 0.184 2734 Planarity : 0.005 0.061 2796 Dihedral : 5.803 59.230 2276 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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 are not related in a simple way. whole: 1.44 (0.19), residues: 2050 helix: 1.95 (0.14), residues: 1452 sheet: -2.03 (0.57), residues: 86 loop : -1.43 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1053 TYR 0.013 0.001 TYR B1035 PHE 0.024 0.002 PHE A 972 TRP 0.014 0.001 TRP B 962 HIS 0.005 0.001 HIS B 914 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 (16740) covalent geometry : angle 0.69482 / 0.34 (22706) hydrogen bonds : bond 0.05067 / 3.46 ( 1163) hydrogen bonds : angle 4.27034 / 3.09 ( 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 605 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 538 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8726 (mm) cc_final: 0.8354 (mt) REVERT: A 116 VAL cc_start: 0.8697 (t) cc_final: 0.8416 (t) REVERT: A 163 PHE cc_start: 0.8421 (t80) cc_final: 0.8208 (t80) REVERT: A 174 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8246 (tt) REVERT: A 176 VAL cc_start: 0.8925 (p) cc_final: 0.8696 (t) REVERT: A 184 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8429 (tt) REVERT: A 266 LEU cc_start: 0.8375 (tp) cc_final: 0.8126 (tt) REVERT: A 269 LEU cc_start: 0.8608 (tp) cc_final: 0.8407 (tt) REVERT: A 337 GLU cc_start: 0.7825 (tp30) cc_final: 0.7500 (tp30) REVERT: A 346 GLU cc_start: 0.7811 (tt0) cc_final: 0.7563 (tt0) REVERT: A 354 GLU cc_start: 0.8185 (tt0) cc_final: 0.7854 (tt0) REVERT: A 377 LEU cc_start: 0.8676 (tp) cc_final: 0.8378 (mp) REVERT: A 383 MET cc_start: 0.7006 (mmm) cc_final: 0.6566 (mmm) REVERT: A 411 SER cc_start: 0.8509 (p) cc_final: 0.8241 (p) REVERT: A 487 SER cc_start: 0.8186 (t) cc_final: 0.7883 (p) REVERT: A 511 MET cc_start: 0.8835 (tmm) cc_final: 0.8525 (ttp) REVERT: A 577 ASP cc_start: 0.8233 (m-30) cc_final: 0.7874 (m-30) REVERT: A 586 MET cc_start: 0.8274 (ttm) cc_final: 0.8051 (tpp) REVERT: A 634 SER cc_start: 0.8869 (m) cc_final: 0.8614 (t) REVERT: A 697 MET cc_start: 0.6434 (mmm) cc_final: 0.5714 (mmm) REVERT: A 815 LYS cc_start: 0.8981 (tttt) cc_final: 0.8718 (ttmm) REVERT: A 820 LYS cc_start: 0.8188 (mmmt) cc_final: 0.7923 (mmmt) REVERT: A 841 LYS cc_start: 0.8953 (mtpt) cc_final: 0.8587 (mtpt) REVERT: A 853 ILE cc_start: 0.9062 (tp) cc_final: 0.8332 (tp) REVERT: A 884 LEU cc_start: 0.8550 (mm) cc_final: 0.8276 (mt) REVERT: A 887 ARG cc_start: 0.8429 (tpp80) cc_final: 0.8134 (ttm-80) REVERT: A 910 ARG cc_start: 0.8533 (ttp-170) cc_final: 0.7957 (ttp-170) REVERT: A 911 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8294 (mm-30) REVERT: A 931 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7887 (mm-30) REVERT: A 937 LYS cc_start: 0.8726 (mttm) cc_final: 0.8503 (mttm) REVERT: A 942 MET cc_start: 0.8616 (tpp) cc_final: 0.8222 (tpt) REVERT: A 989 VAL cc_start: 0.7567 (t) cc_final: 0.7349 (t) REVERT: A 994 GLU cc_start: 0.7691 (pm20) cc_final: 0.7230 (pm20) REVERT: A 1006 VAL cc_start: 0.8417 (m) cc_final: 0.8161 (t) REVERT: A 1035 TYR cc_start: 0.8319 (m-80) cc_final: 0.7828 (m-80) REVERT: A 1044 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7377 (mt-10) REVERT: A 1060 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7456 (mm-30) REVERT: A 1104 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7508 (tpp) REVERT: A 1112 TRP cc_start: 0.7576 (m100) cc_final: 0.7152 (m100) REVERT: A 1116 LYS cc_start: 0.8507 (mttt) cc_final: 0.8019 (mttt) REVERT: A 1122 GLU cc_start: 0.8196 (tp30) cc_final: 0.7820 (tm-30) REVERT: A 1136 PHE cc_start: 0.6768 (t80) cc_final: 0.6547 (t80) REVERT: A 1139 ASP cc_start: 0.7677 (m-30) cc_final: 0.7278 (m-30) REVERT: A 1173 LYS cc_start: 0.7521 (mtpp) cc_final: 0.7037 (mtpp) REVERT: A 1190 ARG cc_start: 0.7946 (mmm-85) cc_final: 0.7569 (mmm-85) REVERT: A 1220 ASN cc_start: 0.7912 (m-40) cc_final: 0.7624 (m110) REVERT: B 116 VAL cc_start: 0.8676 (t) cc_final: 0.8384 (m) REVERT: B 134 ASP cc_start: 0.8157 (t0) cc_final: 0.7814 (t70) REVERT: B 149 GLU cc_start: 0.7873 (tp30) cc_final: 0.7545 (tm-30) REVERT: B 155 ASP cc_start: 0.8149 (t0) cc_final: 0.7728 (t0) REVERT: B 233 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7635 (tm-30) REVERT: B 265 VAL cc_start: 0.8708 (t) cc_final: 0.8415 (p) REVERT: B 337 GLU cc_start: 0.7811 (tp30) cc_final: 0.7459 (tp30) REVERT: B 375 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8382 (mtpp) REVERT: B 385 TRP cc_start: 0.8368 (m100) cc_final: 0.8139 (m100) REVERT: B 419 TRP cc_start: 0.8085 (p-90) cc_final: 0.7857 (p-90) REVERT: B 487 SER cc_start: 0.8379 (t) cc_final: 0.8076 (p) REVERT: B 511 MET cc_start: 0.8832 (tmm) cc_final: 0.8521 (ttp) REVERT: B 531 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7006 (tm-30) REVERT: B 554 GLU cc_start: 0.8217 (tp30) cc_final: 0.7760 (tp30) REVERT: B 580 GLU cc_start: 0.8040 (tp30) cc_final: 0.7672 (tp30) REVERT: B 584 LEU cc_start: 0.8733 (mm) cc_final: 0.8386 (mm) REVERT: B 647 LYS cc_start: 0.8499 (mmtp) cc_final: 0.8107 (mtmm) REVERT: B 697 MET cc_start: 0.5761 (mmm) cc_final: 0.5120 (mmm) REVERT: B 736 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.7953 (t0) REVERT: B 815 LYS cc_start: 0.9055 (tttt) cc_final: 0.8711 (tptm) REVERT: B 820 LYS cc_start: 0.8114 (mmmt) cc_final: 0.7873 (mmmt) REVERT: B 852 LYS cc_start: 0.8624 (mttp) cc_final: 0.8147 (mtpt) REVERT: B 853 ILE cc_start: 0.9038 (tp) cc_final: 0.8697 (tt) REVERT: B 859 ASP cc_start: 0.8041 (p0) cc_final: 0.7740 (p0) REVERT: B 877 GLN cc_start: 0.8590 (tt0) cc_final: 0.8364 (tt0) REVERT: B 887 ARG cc_start: 0.8381 (tpp80) cc_final: 0.7995 (ttm-80) REVERT: B 926 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7824 (mm-30) REVERT: B 942 MET cc_start: 0.8184 (tpp) cc_final: 0.7867 (tpp) REVERT: B 954 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7471 (mm-30) REVERT: B 958 LYS cc_start: 0.8883 (ttpt) cc_final: 0.8422 (ttmm) REVERT: B 968 LYS cc_start: 0.8606 (mtpp) cc_final: 0.8302 (mmmm) REVERT: B 970 ILE cc_start: 0.8642 (mt) cc_final: 0.8399 (tt) REVERT: B 978 SER cc_start: 0.8517 (t) cc_final: 0.8026 (p) REVERT: B 994 GLU cc_start: 0.7629 (pm20) cc_final: 0.7208 (pm20) REVERT: B 1003 SER cc_start: 0.8510 (t) cc_final: 0.8227 (m) REVERT: B 1006 VAL cc_start: 0.8463 (m) cc_final: 0.8208 (t) REVERT: B 1035 TYR cc_start: 0.8271 (m-80) cc_final: 0.7828 (m-80) REVERT: B 1075 ILE cc_start: 0.8940 (mt) cc_final: 0.8568 (tt) REVERT: B 1118 LYS cc_start: 0.8603 (mtpp) cc_final: 0.8340 (mtmm) REVERT: B 1121 LEU cc_start: 0.8999 (mm) cc_final: 0.8729 (mt) REVERT: B 1122 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7724 (mm-30) REVERT: B 1162 ARG cc_start: 0.5761 (OUTLIER) cc_final: 0.5104 (tpm-80) REVERT: B 1212 ILE cc_start: 0.5468 (OUTLIER) cc_final: 0.5022 (mp) outliers start: 67 outliers final: 53 residues processed: 571 average time/residue: 0.1290 time to fit residues: 107.5793 Evaluate side-chains 588 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 528 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 174 LEU 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 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 443 GLU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 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 963 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1069 THR 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 B residue 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 412 ARG 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 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 1100 THR Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1154 ASN Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1199 LEU Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 178 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 204 optimal weight: 0.1980 chunk 92 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 959 ASN B 981 HIS ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1220 ASN 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 = 0.144151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.121272 restraints weight = 25227.447| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.07 r_work: 0.3417 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3705 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= 0.153 Angle : 0.690 15.692 22706 Z= 0.334 Chirality : 0.043 0.169 2734 Planarity : 0.005 0.119 2796 Dihedral : 5.668 58.447 2274 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.29 % Allowed : 24.72 % Favored : 71.99 % 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 are not related in a simple way. whole: 1.49 (0.19), residues: 2050 helix: 1.98 (0.14), residues: 1454 sheet: -1.95 (0.58), residues: 86 loop : -1.42 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1053 TYR 0.011 0.001 TYR A1009 PHE 0.024 0.001 PHE A 972 TRP 0.014 0.001 TRP B 962 HIS 0.005 0.001 HIS B 981 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (16740) covalent geometry : angle 0.69025 / 0.33 (22706) hydrogen bonds : bond 0.04797 / 3.26 ( 1163) hydrogen bonds : angle 4.25246 / 3.08 ( 3459) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4957.99 seconds wall clock time: 85 minutes 32.29 seconds (5132.29 seconds total)