Starting phenix.real_space_refine on Tue Aug 6 12:50:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xq7_38568/08_2024/8xq7_38568.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xq7_38568/08_2024/8xq7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xq7_38568/08_2024/8xq7_38568.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xq7_38568/08_2024/8xq7_38568.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xq7_38568/08_2024/8xq7_38568.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xq7_38568/08_2024/8xq7_38568.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 88 5.16 5 C 10694 2.51 5 N 2724 2.21 5 O 2922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 984": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16430 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8193 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 33, 'TRANS': 1007} Chain breaks: 7 Chain: "B" Number of atoms: 8193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8193 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 33, 'TRANS': 1007} Chain breaks: 7 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 9.20, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 6.51 Conformation dependent library (CDL) restraints added in 3.3 seconds 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3924 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 10 sheets defined 74.0% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 75 through 95 removed outlier: 4.281A pdb=" N VAL A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.813A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.822A pdb=" N HIS A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 removed outlier: 3.534A pdb=" N SER A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 207 removed outlier: 3.797A pdb=" N ALA A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 253 Processing helix chain 'A' and resid 260 through 292 Proline residue: A 276 - end of helix removed outlier: 3.850A pdb=" N HIS A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 317 removed outlier: 3.892A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 removed outlier: 3.686A pdb=" N ALA A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 376 through 379 removed outlier: 3.982A pdb=" N ALA A 379 " --> pdb=" O ALA A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 379' Processing helix chain 'A' and resid 381 through 412 Proline residue: A 408 - end of helix removed outlier: 4.041A pdb=" N ARG A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.672A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 481 removed outlier: 4.309A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 removed outlier: 4.012A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 Processing helix chain 'A' and resid 548 through 558 Processing helix chain 'A' and resid 571 through 601 Processing helix chain 'A' and resid 604 through 621 Processing helix chain 'A' and resid 627 through 633 removed outlier: 3.882A pdb=" N LEU A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 652 removed outlier: 3.854A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 699 Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 727 through 753 Processing helix chain 'A' and resid 762 through 777 Processing helix chain 'A' and resid 799 through 853 removed outlier: 4.120A pdb=" N LEU A 805 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A 806 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET A 810 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 811 " --> pdb=" O GLY A 807 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Proline residue: A 819 - end of helix Processing helix chain 'A' and resid 853 through 858 removed outlier: 3.865A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.702A pdb=" N HIS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.691A pdb=" N ASN A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 959 removed outlier: 3.683A pdb=" N LEU A 957 " --> pdb=" O PRO A 953 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 958 " --> pdb=" O GLU A 954 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 976 Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1069 through 1080 Processing helix chain 'A' and resid 1085 through 1107 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1123 removed outlier: 3.700A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1133 removed outlier: 4.044A pdb=" N SER A1132 " --> pdb=" O ASP A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1210 removed outlier: 4.144A pdb=" N SER A1210 " --> pdb=" O SER A1207 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 95 removed outlier: 4.273A pdb=" N VAL B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 120 removed outlier: 3.813A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.748A pdb=" N HIS B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 153 Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.529A pdb=" N SER B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 189 Processing helix chain 'B' and resid 194 through 207 removed outlier: 3.755A pdb=" N ALA B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 220 Processing helix chain 'B' and resid 223 through 253 Processing helix chain 'B' and resid 260 through 292 Proline residue: B 276 - end of helix removed outlier: 3.819A pdb=" N HIS B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 317 removed outlier: 3.901A pdb=" N GLU B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.673A pdb=" N ALA B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 375 Processing helix chain 'B' and resid 381 through 412 Proline residue: B 408 - end of helix removed outlier: 4.081A pdb=" N ARG B 412 " --> pdb=" O PRO B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.658A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 481 removed outlier: 4.347A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 513 Processing helix chain 'B' and resid 522 through 530 Processing helix chain 'B' and resid 548 through 558 Processing helix chain 'B' and resid 571 through 600 Processing helix chain 'B' and resid 604 through 621 removed outlier: 3.621A pdb=" N GLU B 621 " --> pdb=" O VAL B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 633 removed outlier: 3.878A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 652 removed outlier: 3.865A pdb=" N TRP B 643 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 699 Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 727 through 753 Processing helix chain 'B' and resid 762 through 777 Processing helix chain 'B' and resid 799 through 853 removed outlier: 4.215A pdb=" N LEU B 805 " --> pdb=" O LEU B 801 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 806 " --> pdb=" O PHE B 802 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET B 810 " --> pdb=" O ARG B 806 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 811 " --> pdb=" O GLY B 807 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS B 815 " --> pdb=" O LEU B 811 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA B 816 " --> pdb=" O ARG B 812 " (cutoff:3.500A) Proline residue: B 819 - end of helix Processing helix chain 'B' and resid 853 through 858 removed outlier: 3.873A pdb=" N MET B 857 " --> pdb=" O ILE B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 3.716A pdb=" N HIS B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.684A pdb=" N ASN B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 959 removed outlier: 3.679A pdb=" N LEU B 957 " --> pdb=" O PRO B 953 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 958 " --> pdb=" O GLU B 954 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 976 Processing helix chain 'B' and resid 1043 through 1050 Processing helix chain 'B' and resid 1069 through 1080 Processing helix chain 'B' and resid 1085 through 1107 Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1113 through 1122 Processing helix chain 'B' and resid 1128 through 1133 removed outlier: 3.872A pdb=" N SER B1132 " --> pdb=" O ASP B1128 " (cutoff:3.500A) Processing helix chain 'B' and resid 1206 through 1210 removed outlier: 4.183A pdb=" N SER B1210 " --> pdb=" O SER B1207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1041 through 1042 removed outlier: 6.412A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1032 through 1034 Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 3.680A pdb=" N VAL A1188 " --> pdb=" O TYR A1125 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP A1144 " --> pdb=" O VAL A1189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137 Processing sheet with id=AA5, first strand: chain 'A' and resid 1203 through 1204 removed outlier: 3.583A pdb=" N ASP A1204 " --> pdb=" O SER A1213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A1213 " --> pdb=" O ASP A1204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 1041 through 1042 removed outlier: 6.413A pdb=" N GLN B1064 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1032 through 1034 Processing sheet with id=AA8, first strand: chain 'B' and resid 1125 through 1126 removed outlier: 3.652A pdb=" N VAL B1188 " --> pdb=" O TYR B1125 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP B1144 " --> pdb=" O VAL B1189 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL B1145 " --> pdb=" O ILE B1167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1136 through 1137 Processing sheet with id=AB1, first strand: chain 'B' and resid 1203 through 1204 removed outlier: 3.570A pdb=" N ASP B1204 " --> pdb=" O SER B1213 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B1213 " --> pdb=" O ASP B1204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 1163 hydrogen bonds defined for protein. 3459 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.61 Time building geometry restraints manager: 7.19 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: 99.92 - 107.06: 442 107.06 - 114.19: 10072 114.19 - 121.32: 8329 121.32 - 128.45: 3732 128.45 - 135.59: 131 Bond angle restraints: 22706 Sorted by residual: angle pdb=" C3' CMP B2001 " pdb=" O3' CMP B2001 " pdb=" P CMP B2001 " ideal model delta sigma weight residual 120.50 105.13 15.37 3.00e+00 1.11e-01 2.62e+01 angle pdb=" C3' CMP A2001 " pdb=" O3' CMP A2001 " pdb=" P CMP A2001 " ideal model delta sigma weight residual 120.50 105.70 14.80 3.00e+00 1.11e-01 2.43e+01 angle pdb=" C ASP B 129 " pdb=" N VAL B 130 " pdb=" CA VAL B 130 " ideal model delta sigma weight residual 122.97 118.37 4.60 9.80e-01 1.04e+00 2.20e+01 angle pdb=" C ASP A 129 " pdb=" N VAL A 130 " pdb=" CA VAL A 130 " ideal model delta sigma weight residual 123.08 118.44 4.64 1.01e+00 9.80e-01 2.11e+01 angle pdb=" C THR A1061 " pdb=" N THR A1062 " pdb=" CA THR A1062 " ideal model delta sigma weight residual 122.82 128.93 -6.11 1.42e+00 4.96e-01 1.85e+01 ... (remaining 22701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.43: 9698 27.43 - 54.87: 293 54.87 - 82.30: 33 82.30 - 109.73: 0 109.73 - 137.17: 2 Dihedral angle restraints: 10026 sinusoidal: 3982 harmonic: 6044 Sorted by residual: dihedral pdb=" CA GLU A 621 " pdb=" C GLU A 621 " pdb=" N LYS A 622 " pdb=" CA LYS A 622 " ideal model delta harmonic sigma weight residual 180.00 147.83 32.17 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA TYR A1083 " pdb=" C TYR A1083 " pdb=" N PRO A1084 " pdb=" CA PRO A1084 " ideal model delta harmonic sigma weight residual 180.00 153.63 26.37 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ALA A1180 " pdb=" C ALA A1180 " pdb=" N THR A1181 " pdb=" CA THR A1181 " ideal model delta harmonic sigma weight residual -180.00 -153.78 -26.22 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 10023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2422 0.072 - 0.144: 272 0.144 - 0.216: 35 0.216 - 0.288: 1 0.288 - 0.360: 4 Chirality restraints: 2734 Sorted by residual: chirality pdb=" CB ILE B 742 " pdb=" CA ILE B 742 " pdb=" CG1 ILE B 742 " pdb=" CG2 ILE B 742 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CB ILE A 742 " pdb=" CA ILE A 742 " pdb=" CG1 ILE A 742 " pdb=" CG2 ILE A 742 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CB ILE B 751 " pdb=" CA ILE B 751 " pdb=" CG1 ILE B 751 " pdb=" CG2 ILE B 751 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 2731 not shown) Planarity restraints: 2796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 693 " -0.063 5.00e-02 4.00e+02 9.49e-02 1.44e+01 pdb=" N PRO A 694 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO A 694 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 694 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 693 " 0.063 5.00e-02 4.00e+02 9.47e-02 1.44e+01 pdb=" N PRO B 694 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 694 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 694 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A1083 " -0.049 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO A1084 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A1084 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A1084 " -0.040 5.00e-02 4.00e+02 ... (remaining 2793 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3672 2.79 - 3.32: 15591 3.32 - 3.84: 27753 3.84 - 4.37: 30681 4.37 - 4.90: 55050 Nonbonded interactions: 132747 Sorted by model distance: nonbonded pdb=" O MET A1045 " pdb=" OG1 THR A1049 " model vdw 2.261 3.040 nonbonded pdb=" O ILE A 469 " pdb=" OG1 THR A 473 " model vdw 2.271 3.040 nonbonded pdb=" O ILE B 469 " pdb=" OG1 THR B 473 " model vdw 2.272 3.040 nonbonded pdb=" O ALA A 307 " pdb=" OG1 THR A 311 " model vdw 2.297 3.040 nonbonded pdb=" O ALA B 307 " pdb=" OG1 THR B 311 " model vdw 2.301 3.040 ... (remaining 132742 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 46.230 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 16740 Z= 0.294 Angle : 0.793 15.366 22706 Z= 0.438 Chirality : 0.049 0.360 2734 Planarity : 0.007 0.095 2796 Dihedral : 13.363 137.168 6102 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.64 % Allowed : 9.10 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.16), residues: 2050 helix: -0.41 (0.12), residues: 1454 sheet: -1.45 (0.72), residues: 50 loop : -2.03 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 962 HIS 0.002 0.001 HIS B1133 PHE 0.031 0.002 PHE B 766 TYR 0.012 0.001 TYR A1153 ARG 0.002 0.000 ARG A 431 *********************** 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 fitting. rotamer outliers: 101 poor density : 641 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8548 (mm) cc_final: 0.8158 (mt) REVERT: A 116 VAL cc_start: 0.8685 (t) cc_final: 0.8434 (t) REVERT: A 174 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8129 (tt) REVERT: A 195 PHE cc_start: 0.8027 (t80) cc_final: 0.7772 (t80) REVERT: A 196 SER cc_start: 0.8164 (p) cc_final: 0.7946 (p) REVERT: A 233 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7533 (tm-30) REVERT: A 237 ASN cc_start: 0.8352 (t0) cc_final: 0.8114 (t0) REVERT: A 269 LEU cc_start: 0.8440 (tp) cc_final: 0.8020 (tt) REVERT: A 280 TYR cc_start: 0.8508 (t80) cc_final: 0.8178 (t80) REVERT: A 300 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7753 (mt-10) REVERT: A 337 GLU cc_start: 0.7859 (tp30) cc_final: 0.7515 (tp30) REVERT: A 346 GLU cc_start: 0.7810 (tt0) cc_final: 0.7570 (tt0) REVERT: A 354 GLU cc_start: 0.8365 (tt0) cc_final: 0.8049 (tt0) REVERT: A 366 MET cc_start: 0.8634 (mmm) cc_final: 0.8237 (mmt) REVERT: A 375 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8489 (ttpp) REVERT: A 377 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8111 (mp) REVERT: A 383 MET cc_start: 0.7130 (mmm) cc_final: 0.6550 (mmm) REVERT: A 385 TRP cc_start: 0.8545 (m100) cc_final: 0.8299 (m100) REVERT: A 387 TYR cc_start: 0.8505 (m-10) cc_final: 0.8206 (m-10) REVERT: A 443 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7819 (tm-30) REVERT: A 486 ILE cc_start: 0.8745 (mp) cc_final: 0.8514 (mm) REVERT: A 487 SER cc_start: 0.8314 (t) cc_final: 0.8005 (p) REVERT: A 511 MET cc_start: 0.8838 (tmm) cc_final: 0.8281 (tmm) REVERT: A 531 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6956 (tm-30) REVERT: A 554 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7700 (tp30) REVERT: A 578 MET cc_start: 0.8583 (mtp) cc_final: 0.8375 (mtp) REVERT: A 579 MET cc_start: 0.8146 (tmm) cc_final: 0.7900 (tpp) REVERT: A 581 GLU cc_start: 0.8381 (tp30) cc_final: 0.7910 (tp30) REVERT: A 588 LYS cc_start: 0.8632 (tppt) cc_final: 0.8208 (tppt) REVERT: A 602 MET cc_start: 0.7830 (mpp) cc_final: 0.7513 (mpp) REVERT: A 613 GLN cc_start: 0.8161 (tt0) cc_final: 0.7959 (tt0) REVERT: A 632 LYS cc_start: 0.8288 (ttpt) cc_final: 0.7807 (ttmm) REVERT: A 637 ILE cc_start: 0.8689 (tp) cc_final: 0.8473 (tp) REVERT: A 645 LYS cc_start: 0.8512 (tttp) cc_final: 0.8227 (tttm) REVERT: A 647 LYS cc_start: 0.8690 (mmtp) cc_final: 0.8413 (mmtm) REVERT: A 697 MET cc_start: 0.6212 (mmm) cc_final: 0.5610 (mmm) REVERT: A 736 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8365 (p0) REVERT: A 810 MET cc_start: 0.6702 (ptt) cc_final: 0.6469 (ptt) REVERT: A 815 LYS cc_start: 0.8997 (tttt) cc_final: 0.8730 (tppp) REVERT: A 820 LYS cc_start: 0.8276 (mmmt) cc_final: 0.8008 (mmmt) REVERT: A 841 LYS cc_start: 0.8558 (mtpt) cc_final: 0.8334 (mtpt) REVERT: A 864 LEU cc_start: 0.8487 (tp) cc_final: 0.8185 (tp) REVERT: A 878 VAL cc_start: 0.8796 (t) cc_final: 0.8571 (t) REVERT: A 881 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7929 (tp30) REVERT: A 923 ASP cc_start: 0.7690 (p0) cc_final: 0.7367 (p0) REVERT: A 942 MET cc_start: 0.8604 (tpp) cc_final: 0.8373 (tpt) REVERT: A 958 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8670 (ttpt) REVERT: A 969 LEU cc_start: 0.9015 (tp) cc_final: 0.8801 (tt) REVERT: A 983 ASP cc_start: 0.7981 (t0) cc_final: 0.7630 (p0) REVERT: A 994 GLU cc_start: 0.7968 (pm20) cc_final: 0.7671 (pm20) REVERT: A 1003 SER cc_start: 0.8567 (t) cc_final: 0.8358 (m) REVERT: A 1041 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8168 (p) REVERT: A 1060 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7386 (mm-30) REVERT: A 1063 VAL cc_start: 0.8648 (t) cc_final: 0.8397 (p) REVERT: A 1098 ILE cc_start: 0.8952 (tt) cc_final: 0.8624 (tp) REVERT: A 1104 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7519 (tpt) REVERT: A 1121 LEU cc_start: 0.8818 (mm) cc_final: 0.8579 (mt) REVERT: A 1122 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7614 (tp30) REVERT: A 1125 TYR cc_start: 0.8329 (p90) cc_final: 0.8075 (p90) REVERT: A 1167 ILE cc_start: 0.8205 (mm) cc_final: 0.7968 (mt) REVERT: A 1212 ILE cc_start: 0.5567 (OUTLIER) cc_final: 0.5083 (mp) REVERT: B 112 ILE cc_start: 0.8445 (mm) cc_final: 0.8102 (mt) REVERT: B 154 MET cc_start: 0.8619 (tpp) cc_final: 0.8361 (tpp) REVERT: B 174 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8264 (tt) REVERT: B 196 SER cc_start: 0.8313 (p) cc_final: 0.8086 (p) REVERT: B 250 LYS cc_start: 0.8477 (mttt) cc_final: 0.8223 (mttm) REVERT: B 263 GLN cc_start: 0.8384 (mt0) cc_final: 0.8079 (mt0) REVERT: B 266 LEU cc_start: 0.8479 (tp) cc_final: 0.8243 (tt) REVERT: B 267 TYR cc_start: 0.8510 (t80) cc_final: 0.8054 (t80) REVERT: B 300 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7889 (mt-10) REVERT: B 321 VAL cc_start: 0.7524 (OUTLIER) cc_final: 0.7252 (m) REVERT: B 337 GLU cc_start: 0.7909 (tp30) cc_final: 0.7571 (tp30) REVERT: B 375 LYS cc_start: 0.8644 (tppp) cc_final: 0.8173 (mtpp) REVERT: B 385 TRP cc_start: 0.8468 (m100) cc_final: 0.8259 (m100) REVERT: B 419 TRP cc_start: 0.8107 (p-90) cc_final: 0.7806 (p-90) REVERT: B 486 ILE cc_start: 0.8816 (mp) cc_final: 0.8573 (mm) REVERT: B 487 SER cc_start: 0.8439 (t) cc_final: 0.8126 (p) REVERT: B 511 MET cc_start: 0.8885 (tmm) cc_final: 0.8326 (tmm) REVERT: B 515 ASP cc_start: 0.8642 (t0) cc_final: 0.8374 (t70) REVERT: B 531 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6958 (tm-30) REVERT: B 579 MET cc_start: 0.8082 (tmm) cc_final: 0.7734 (tpp) REVERT: B 588 LYS cc_start: 0.8638 (tppt) cc_final: 0.8310 (tttm) REVERT: B 637 ILE cc_start: 0.8845 (tp) cc_final: 0.8636 (tp) REVERT: B 697 MET cc_start: 0.5687 (mmm) cc_final: 0.5073 (mmm) REVERT: B 736 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8214 (p0) REVERT: B 808 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7848 (pt) REVERT: B 810 MET cc_start: 0.6738 (ptt) cc_final: 0.6503 (ptt) REVERT: B 820 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7939 (mmmt) REVERT: B 825 VAL cc_start: 0.8758 (t) cc_final: 0.8499 (p) REVERT: B 852 LYS cc_start: 0.8359 (mttp) cc_final: 0.7895 (ttmm) REVERT: B 931 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7613 (mt-10) REVERT: B 942 MET cc_start: 0.8568 (tpp) cc_final: 0.8346 (tpt) REVERT: B 954 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7619 (mm-30) REVERT: B 958 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8505 (ttmm) REVERT: B 968 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8334 (mmmm) REVERT: B 972 PHE cc_start: 0.8730 (t80) cc_final: 0.8302 (t80) REVERT: B 994 GLU cc_start: 0.7893 (pm20) cc_final: 0.7551 (pm20) REVERT: B 1003 SER cc_start: 0.8594 (t) cc_final: 0.8283 (m) REVERT: B 1005 LEU cc_start: 0.8453 (tp) cc_final: 0.8219 (tt) REVERT: B 1041 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8208 (p) REVERT: B 1051 LYS cc_start: 0.8297 (pttt) cc_final: 0.7963 (pttt) REVERT: B 1060 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7583 (mm-30) REVERT: B 1098 ILE cc_start: 0.8925 (tt) cc_final: 0.8592 (tp) REVERT: B 1104 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7343 (tpp) REVERT: B 1105 GLU cc_start: 0.7634 (tp30) cc_final: 0.7410 (tp30) REVERT: B 1118 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8258 (mtmm) REVERT: B 1121 LEU cc_start: 0.8978 (mm) cc_final: 0.8758 (mt) REVERT: B 1122 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7538 (mm-30) REVERT: B 1125 TYR cc_start: 0.8278 (p90) cc_final: 0.8049 (p90) REVERT: B 1162 ARG cc_start: 0.5414 (OUTLIER) cc_final: 0.5070 (tpm-80) REVERT: B 1179 THR cc_start: 0.5317 (OUTLIER) cc_final: 0.5027 (p) REVERT: B 1212 ILE cc_start: 0.5617 (OUTLIER) cc_final: 0.5323 (mp) outliers start: 101 outliers final: 37 residues processed: 709 average time/residue: 0.3166 time to fit residues: 322.2531 Evaluate side-chains 595 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 540 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 MET Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1158 ARG Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1041 VAL Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1156 HIS Chi-restraints excluded: chain B residue 1158 ARG Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.5980 chunk 157 optimal weight: 0.1980 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 163 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 121 optimal weight: 0.7980 chunk 188 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN A 295 ASN A 421 ASN A 600 HIS A 736 ASN A 831 ASN A 943 ASN A 959 ASN A 981 HIS B 421 ASN ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN B1191 ASN B1220 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16740 Z= 0.203 Angle : 0.638 17.165 22706 Z= 0.321 Chirality : 0.041 0.200 2734 Planarity : 0.005 0.072 2796 Dihedral : 8.896 132.734 2343 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.02 % Allowed : 17.24 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.18), residues: 2050 helix: 0.99 (0.13), residues: 1466 sheet: -3.08 (0.47), residues: 102 loop : -1.76 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1112 HIS 0.007 0.001 HIS A 981 PHE 0.021 0.001 PHE A 972 TYR 0.017 0.001 TYR B 415 ARG 0.009 0.001 ARG A 609 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 563 time to evaluate : 1.900 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: 0.8678 (mm) cc_final: 0.8243 (mt) REVERT: A 116 VAL cc_start: 0.8769 (t) cc_final: 0.8499 (t) REVERT: A 149 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7648 (tm-30) REVERT: A 176 VAL cc_start: 0.8861 (p) cc_final: 0.8599 (t) REVERT: A 225 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7673 (tp40) REVERT: A 233 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7683 (tm-30) REVERT: A 266 LEU cc_start: 0.8464 (tp) cc_final: 0.8228 (tt) REVERT: A 269 LEU cc_start: 0.8508 (tp) cc_final: 0.8213 (tt) REVERT: A 300 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7823 (mt-10) REVERT: A 316 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7905 (m-30) REVERT: A 337 GLU cc_start: 0.7838 (tp30) cc_final: 0.7490 (tp30) REVERT: A 346 GLU cc_start: 0.7816 (tt0) cc_final: 0.7540 (tt0) REVERT: A 354 GLU cc_start: 0.8282 (tt0) cc_final: 0.7973 (tt0) REVERT: A 366 MET cc_start: 0.8576 (mmm) cc_final: 0.8138 (mmt) REVERT: A 375 LYS cc_start: 0.8758 (tppp) cc_final: 0.8456 (ttpp) REVERT: A 383 MET cc_start: 0.7226 (mmm) cc_final: 0.6650 (mmm) REVERT: A 385 TRP cc_start: 0.8528 (m100) cc_final: 0.8069 (m100) REVERT: A 387 TYR cc_start: 0.8574 (m-10) cc_final: 0.8131 (m-10) REVERT: A 443 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 486 ILE cc_start: 0.8743 (mp) cc_final: 0.8522 (mm) REVERT: A 487 SER cc_start: 0.8390 (t) cc_final: 0.8074 (p) REVERT: A 511 MET cc_start: 0.8902 (tmm) cc_final: 0.8657 (tmm) REVERT: A 516 ARG cc_start: 0.8681 (ttp-110) cc_final: 0.8412 (ttp-110) REVERT: A 531 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6998 (tm-30) REVERT: A 578 MET cc_start: 0.8625 (mtp) cc_final: 0.8366 (mtp) REVERT: A 579 MET cc_start: 0.8102 (tmm) cc_final: 0.7768 (tpp) REVERT: A 580 GLU cc_start: 0.8364 (tp30) cc_final: 0.7956 (tp30) REVERT: A 602 MET cc_start: 0.7841 (mpp) cc_final: 0.7490 (mpp) REVERT: A 609 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.8224 (ttp-110) REVERT: A 632 LYS cc_start: 0.8336 (ttpt) cc_final: 0.8076 (ttmm) REVERT: A 647 LYS cc_start: 0.8748 (mmtp) cc_final: 0.8467 (mmtm) REVERT: A 697 MET cc_start: 0.6371 (mmm) cc_final: 0.5776 (mmm) REVERT: A 815 LYS cc_start: 0.9007 (tttt) cc_final: 0.8651 (tppp) REVERT: A 820 LYS cc_start: 0.8312 (mmmt) cc_final: 0.8022 (mmmt) REVERT: A 841 LYS cc_start: 0.8585 (mtpt) cc_final: 0.8382 (mtpt) REVERT: A 853 ILE cc_start: 0.8695 (tp) cc_final: 0.8406 (tt) REVERT: A 864 LEU cc_start: 0.8553 (tp) cc_final: 0.8339 (tp) REVERT: A 897 LYS cc_start: 0.8981 (mttp) cc_final: 0.8697 (mmtp) REVERT: A 911 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8175 (mm-30) REVERT: A 926 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7808 (mm-30) REVERT: A 942 MET cc_start: 0.8600 (tpp) cc_final: 0.8377 (tpt) REVERT: A 972 PHE cc_start: 0.8578 (t80) cc_final: 0.8378 (t80) REVERT: A 983 ASP cc_start: 0.7987 (t0) cc_final: 0.7716 (p0) REVERT: A 994 GLU cc_start: 0.7949 (pm20) cc_final: 0.7606 (pm20) REVERT: A 1008 LEU cc_start: 0.8168 (mp) cc_final: 0.7766 (tp) REVERT: A 1033 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7619 (mp0) REVERT: A 1044 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7652 (mt-10) REVERT: A 1060 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7519 (mm-30) REVERT: A 1066 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: A 1080 PHE cc_start: 0.8050 (m-80) cc_final: 0.7408 (m-80) REVERT: A 1104 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7524 (tpp) REVERT: A 1121 LEU cc_start: 0.8886 (mm) cc_final: 0.8634 (mt) REVERT: A 1122 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7778 (tp30) REVERT: A 1190 ARG cc_start: 0.8143 (mmm-85) cc_final: 0.7639 (mmm-85) REVERT: A 1212 ILE cc_start: 0.5465 (OUTLIER) cc_final: 0.4943 (mp) REVERT: A 1220 ASN cc_start: 0.7985 (m-40) cc_final: 0.7779 (m-40) REVERT: B 149 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7606 (tm-30) REVERT: B 250 LYS cc_start: 0.8492 (mttt) cc_final: 0.8200 (mttm) REVERT: B 300 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7878 (mt-10) REVERT: B 337 GLU cc_start: 0.7929 (tp30) cc_final: 0.7564 (tp30) REVERT: B 375 LYS cc_start: 0.8730 (tppp) cc_final: 0.8173 (mtpp) REVERT: B 383 MET cc_start: 0.7315 (tpp) cc_final: 0.6773 (mmm) REVERT: B 385 TRP cc_start: 0.8452 (m100) cc_final: 0.8140 (m100) REVERT: B 419 TRP cc_start: 0.8134 (p-90) cc_final: 0.7771 (p-90) REVERT: B 443 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7676 (tm-30) REVERT: B 487 SER cc_start: 0.8492 (t) cc_final: 0.8212 (p) REVERT: B 511 MET cc_start: 0.8915 (tmm) cc_final: 0.8690 (tmm) REVERT: B 531 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7018 (tm-30) REVERT: B 578 MET cc_start: 0.8684 (mtp) cc_final: 0.8344 (mtp) REVERT: B 579 MET cc_start: 0.7993 (tmm) cc_final: 0.7585 (tpp) REVERT: B 588 LYS cc_start: 0.8588 (tppt) cc_final: 0.8303 (tttm) REVERT: B 647 LYS cc_start: 0.8644 (mmtm) cc_final: 0.8399 (mmtp) REVERT: B 697 MET cc_start: 0.5767 (mmm) cc_final: 0.5177 (mmm) REVERT: B 736 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8067 (t0) REVERT: B 808 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7970 (pt) REVERT: B 810 MET cc_start: 0.6994 (ptt) cc_final: 0.6783 (ptt) REVERT: B 820 LYS cc_start: 0.8213 (mmmt) cc_final: 0.7967 (mmmt) REVERT: B 825 VAL cc_start: 0.8753 (t) cc_final: 0.8453 (p) REVERT: B 852 LYS cc_start: 0.8400 (mttp) cc_final: 0.7990 (ttmm) REVERT: B 926 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7815 (mm-30) REVERT: B 931 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7642 (mt-10) REVERT: B 942 MET cc_start: 0.8600 (tpp) cc_final: 0.8395 (tpt) REVERT: B 947 SER cc_start: 0.7887 (t) cc_final: 0.7672 (t) REVERT: B 954 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7644 (mm-30) REVERT: B 958 LYS cc_start: 0.8898 (ttpt) cc_final: 0.8502 (ttmm) REVERT: B 968 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8413 (mmmm) REVERT: B 993 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6709 (m-30) REVERT: B 994 GLU cc_start: 0.7936 (pm20) cc_final: 0.7641 (pm20) REVERT: B 996 ASP cc_start: 0.7326 (p0) cc_final: 0.7057 (p0) REVERT: B 1003 SER cc_start: 0.8636 (t) cc_final: 0.8338 (m) REVERT: B 1005 LEU cc_start: 0.8483 (tp) cc_final: 0.8219 (tp) REVERT: B 1060 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7643 (mm-30) REVERT: B 1073 MET cc_start: 0.8594 (tpp) cc_final: 0.8131 (tpp) REVERT: B 1098 ILE cc_start: 0.8933 (tt) cc_final: 0.8582 (tp) REVERT: B 1104 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7395 (tpt) REVERT: B 1118 LYS cc_start: 0.8658 (mtpp) cc_final: 0.8321 (mtmm) REVERT: B 1121 LEU cc_start: 0.9010 (mm) cc_final: 0.8730 (mt) REVERT: B 1122 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7701 (tp30) REVERT: B 1125 TYR cc_start: 0.8349 (p90) cc_final: 0.8102 (p90) REVERT: B 1126 LEU cc_start: 0.8429 (mt) cc_final: 0.7970 (pt) REVERT: B 1127 VAL cc_start: 0.8719 (m) cc_final: 0.8509 (p) REVERT: B 1143 GLU cc_start: 0.7866 (tt0) cc_final: 0.7092 (tt0) REVERT: B 1162 ARG cc_start: 0.5724 (OUTLIER) cc_final: 0.5147 (tpm-80) REVERT: B 1179 THR cc_start: 0.5523 (OUTLIER) cc_final: 0.5237 (p) REVERT: B 1190 ARG cc_start: 0.8091 (mmm-85) cc_final: 0.7675 (mmm-85) REVERT: B 1212 ILE cc_start: 0.5452 (OUTLIER) cc_final: 0.5165 (mp) outliers start: 90 outliers final: 42 residues processed: 617 average time/residue: 0.3195 time to fit residues: 280.6616 Evaluate side-chains 586 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 530 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 981 HIS Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1104 MET Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1158 ARG Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 865 ARG Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1154 ASN Chi-restraints excluded: chain B residue 1156 HIS Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1199 LEU Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 189 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 chunk 168 optimal weight: 10.0000 chunk 187 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 151 optimal weight: 0.0040 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2506 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= 0.195 Angle : 0.622 17.057 22706 Z= 0.309 Chirality : 0.041 0.185 2734 Planarity : 0.005 0.065 2796 Dihedral : 7.802 133.461 2297 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.02 % Allowed : 19.14 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 2050 helix: 1.52 (0.14), residues: 1454 sheet: -3.28 (0.48), residues: 82 loop : -1.69 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1112 HIS 0.008 0.001 HIS A1120 PHE 0.016 0.001 PHE B 766 TYR 0.011 0.001 TYR B 415 ARG 0.008 0.001 ARG A1185 *********************** 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 643 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 553 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8699 (mm) cc_final: 0.8286 (mt) REVERT: A 116 VAL cc_start: 0.8789 (t) cc_final: 0.8494 (t) REVERT: A 149 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7579 (tm-30) REVERT: A 176 VAL cc_start: 0.8828 (p) cc_final: 0.8569 (t) REVERT: A 233 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7640 (tm-30) REVERT: A 266 LEU cc_start: 0.8460 (tp) cc_final: 0.8222 (tt) REVERT: A 269 LEU cc_start: 0.8525 (tp) cc_final: 0.8251 (tt) REVERT: A 300 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7931 (mt-10) REVERT: A 316 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7873 (m-30) REVERT: A 337 GLU cc_start: 0.7835 (tp30) cc_final: 0.7488 (tp30) REVERT: A 346 GLU cc_start: 0.7801 (tt0) cc_final: 0.7515 (tt0) REVERT: A 354 GLU cc_start: 0.8286 (tt0) cc_final: 0.7950 (tt0) REVERT: A 375 LYS cc_start: 0.8746 (tppp) cc_final: 0.8516 (ttpp) REVERT: A 383 MET cc_start: 0.7171 (mmm) cc_final: 0.6597 (mmm) REVERT: A 385 TRP cc_start: 0.8483 (m100) cc_final: 0.8080 (m100) REVERT: A 387 TYR cc_start: 0.8545 (m-10) cc_final: 0.8049 (m-10) REVERT: A 419 TRP cc_start: 0.8180 (p-90) cc_final: 0.7939 (p-90) REVERT: A 486 ILE cc_start: 0.8782 (mp) cc_final: 0.8546 (mm) REVERT: A 487 SER cc_start: 0.8386 (t) cc_final: 0.8054 (p) REVERT: A 531 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: A 578 MET cc_start: 0.8603 (mtp) cc_final: 0.8385 (mtp) REVERT: A 579 MET cc_start: 0.8060 (tmm) cc_final: 0.7723 (tpp) REVERT: A 580 GLU cc_start: 0.8373 (tp30) cc_final: 0.7952 (tp30) REVERT: A 599 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: A 602 MET cc_start: 0.7842 (mpp) cc_final: 0.7511 (mpp) REVERT: A 632 LYS cc_start: 0.8260 (ttpt) cc_final: 0.7990 (ttmm) REVERT: A 634 SER cc_start: 0.8890 (m) cc_final: 0.8605 (t) REVERT: A 647 LYS cc_start: 0.8746 (mmtp) cc_final: 0.8487 (mmtm) REVERT: A 697 MET cc_start: 0.6391 (mmm) cc_final: 0.5792 (mmm) REVERT: A 815 LYS cc_start: 0.9032 (tttt) cc_final: 0.8668 (tppp) REVERT: A 820 LYS cc_start: 0.8281 (mmmt) cc_final: 0.8001 (mmmt) REVERT: A 926 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7890 (mm-30) REVERT: A 942 MET cc_start: 0.8618 (tpp) cc_final: 0.8375 (tpt) REVERT: A 972 PHE cc_start: 0.8611 (t80) cc_final: 0.8300 (t80) REVERT: A 983 ASP cc_start: 0.7999 (t0) cc_final: 0.7620 (p0) REVERT: A 994 GLU cc_start: 0.7921 (pm20) cc_final: 0.7557 (pm20) REVERT: A 1008 LEU cc_start: 0.8145 (mp) cc_final: 0.7802 (tp) REVERT: A 1044 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7588 (mt-10) REVERT: A 1060 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7560 (mm-30) REVERT: A 1061 THR cc_start: 0.7793 (OUTLIER) cc_final: 0.7552 (p) REVERT: A 1066 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: A 1072 ASP cc_start: 0.7625 (m-30) cc_final: 0.7357 (m-30) REVERT: A 1080 PHE cc_start: 0.8050 (m-80) cc_final: 0.7488 (m-80) REVERT: A 1104 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7420 (tpp) REVERT: A 1112 TRP cc_start: 0.7862 (m100) cc_final: 0.7502 (m100) REVERT: A 1116 LYS cc_start: 0.8514 (mttt) cc_final: 0.7774 (mttt) REVERT: A 1121 LEU cc_start: 0.8923 (mm) cc_final: 0.8646 (mt) REVERT: A 1122 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7814 (tp30) REVERT: A 1173 LYS cc_start: 0.7393 (ttpp) cc_final: 0.6967 (ptmm) REVERT: A 1190 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7757 (mmm-85) REVERT: A 1212 ILE cc_start: 0.5429 (OUTLIER) cc_final: 0.4904 (mp) REVERT: B 134 ASP cc_start: 0.8030 (t0) cc_final: 0.7677 (t70) REVERT: B 149 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7555 (tm-30) REVERT: B 337 GLU cc_start: 0.7911 (tp30) cc_final: 0.7547 (tp30) REVERT: B 375 LYS cc_start: 0.8749 (tppp) cc_final: 0.8218 (mtpp) REVERT: B 383 MET cc_start: 0.7257 (tpp) cc_final: 0.6722 (mmm) REVERT: B 385 TRP cc_start: 0.8427 (m100) cc_final: 0.8105 (m100) REVERT: B 487 SER cc_start: 0.8474 (t) cc_final: 0.8186 (p) REVERT: B 511 MET cc_start: 0.8920 (tmm) cc_final: 0.8489 (tmm) REVERT: B 520 ASP cc_start: 0.8554 (p0) cc_final: 0.8257 (p0) REVERT: B 531 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7044 (tm-30) REVERT: B 578 MET cc_start: 0.8703 (mtp) cc_final: 0.8354 (mtp) REVERT: B 579 MET cc_start: 0.7963 (tmm) cc_final: 0.7747 (tpp) REVERT: B 581 GLU cc_start: 0.8460 (tp30) cc_final: 0.8162 (tp30) REVERT: B 588 LYS cc_start: 0.8550 (tppt) cc_final: 0.8301 (tttm) REVERT: B 697 MET cc_start: 0.5775 (mmm) cc_final: 0.5153 (mmm) REVERT: B 736 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.7982 (t0) REVERT: B 808 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7992 (pp) REVERT: B 810 MET cc_start: 0.7002 (ptt) cc_final: 0.6797 (ptt) REVERT: B 815 LYS cc_start: 0.9122 (tttt) cc_final: 0.8669 (tppp) REVERT: B 820 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7946 (mmmt) REVERT: B 825 VAL cc_start: 0.8767 (t) cc_final: 0.8445 (p) REVERT: B 832 GLN cc_start: 0.8448 (tt0) cc_final: 0.8184 (tp-100) REVERT: B 852 LYS cc_start: 0.8402 (mttp) cc_final: 0.7966 (ttmm) REVERT: B 859 ASP cc_start: 0.7954 (p0) cc_final: 0.7602 (p0) REVERT: B 877 GLN cc_start: 0.8681 (tt0) cc_final: 0.8394 (tt0) REVERT: B 926 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7819 (mm-30) REVERT: B 931 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7665 (mt-10) REVERT: B 942 MET cc_start: 0.8579 (tpp) cc_final: 0.8375 (tpt) REVERT: B 947 SER cc_start: 0.7937 (t) cc_final: 0.7720 (t) REVERT: B 954 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7598 (mm-30) REVERT: B 958 LYS cc_start: 0.8908 (ttpt) cc_final: 0.8501 (ttmm) REVERT: B 968 LYS cc_start: 0.8708 (mtpp) cc_final: 0.8388 (mmmm) REVERT: B 993 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.6777 (m-30) REVERT: B 994 GLU cc_start: 0.7944 (pm20) cc_final: 0.7552 (pm20) REVERT: B 996 ASP cc_start: 0.7347 (p0) cc_final: 0.7144 (p0) REVERT: B 1005 LEU cc_start: 0.8454 (tp) cc_final: 0.8234 (tt) REVERT: B 1060 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7479 (mm-30) REVERT: B 1066 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.7763 (m-80) REVERT: B 1098 ILE cc_start: 0.8936 (tt) cc_final: 0.8576 (tp) REVERT: B 1104 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7338 (tpt) REVERT: B 1118 LYS cc_start: 0.8656 (mtpp) cc_final: 0.8330 (mtmm) REVERT: B 1121 LEU cc_start: 0.9006 (mm) cc_final: 0.8729 (mt) REVERT: B 1122 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7580 (mm-30) REVERT: B 1126 LEU cc_start: 0.8299 (mt) cc_final: 0.7874 (pt) REVERT: B 1144 ASP cc_start: 0.7047 (m-30) cc_final: 0.6804 (m-30) REVERT: B 1162 ARG cc_start: 0.5679 (OUTLIER) cc_final: 0.5107 (tpm-80) REVERT: B 1179 THR cc_start: 0.5324 (OUTLIER) cc_final: 0.5065 (p) REVERT: B 1190 ARG cc_start: 0.7923 (mmm-85) cc_final: 0.7640 (mmm-85) REVERT: B 1212 ILE cc_start: 0.5487 (OUTLIER) cc_final: 0.5194 (mp) outliers start: 90 outliers final: 48 residues processed: 602 average time/residue: 0.3262 time to fit residues: 280.0044 Evaluate side-chains 595 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 532 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 591 LYS 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 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 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 103 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 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 864 LEU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1127 VAL 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 186 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 189 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 54 optimal weight: 0.0670 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS B 165 GLN B 597 GLN B1220 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2796 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= 0.214 Angle : 0.624 17.050 22706 Z= 0.310 Chirality : 0.041 0.173 2734 Planarity : 0.004 0.063 2796 Dihedral : 7.502 133.328 2291 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.19 % Allowed : 20.09 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.19), residues: 2050 helix: 1.76 (0.14), residues: 1452 sheet: -2.53 (0.49), residues: 92 loop : -1.68 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1112 HIS 0.006 0.001 HIS A 981 PHE 0.022 0.001 PHE B 680 TYR 0.010 0.001 TYR B 191 ARG 0.008 0.000 ARG B1185 *********************** 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 639 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 546 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8688 (mm) cc_final: 0.8286 (mt) REVERT: A 116 VAL cc_start: 0.8705 (t) cc_final: 0.8427 (t) REVERT: A 149 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7566 (tm-30) REVERT: A 163 PHE cc_start: 0.8357 (t80) cc_final: 0.8071 (t80) REVERT: A 176 VAL cc_start: 0.8779 (p) cc_final: 0.8568 (t) REVERT: A 199 MET cc_start: 0.8608 (mmm) cc_final: 0.8141 (tpp) REVERT: A 225 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7543 (tp40) REVERT: A 233 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7649 (tm-30) REVERT: A 266 LEU cc_start: 0.8449 (tp) cc_final: 0.8209 (tt) REVERT: A 269 LEU cc_start: 0.8591 (tp) cc_final: 0.8322 (tt) REVERT: A 316 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: A 337 GLU cc_start: 0.7847 (tp30) cc_final: 0.7484 (tp30) REVERT: A 346 GLU cc_start: 0.7816 (tt0) cc_final: 0.7542 (tt0) REVERT: A 354 GLU cc_start: 0.8303 (tt0) cc_final: 0.7953 (tt0) REVERT: A 375 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8569 (ttpp) REVERT: A 383 MET cc_start: 0.7117 (mmm) cc_final: 0.6542 (mmm) REVERT: A 419 TRP cc_start: 0.8155 (p-90) cc_final: 0.7949 (p-90) REVERT: A 486 ILE cc_start: 0.8790 (mp) cc_final: 0.8546 (mm) REVERT: A 487 SER cc_start: 0.8318 (t) cc_final: 0.7980 (p) REVERT: A 499 ARG cc_start: 0.8478 (ttp-170) cc_final: 0.8242 (mtp-110) REVERT: A 511 MET cc_start: 0.8748 (tmm) cc_final: 0.8427 (ttp) REVERT: A 531 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7022 (tm-30) REVERT: A 578 MET cc_start: 0.8531 (mtp) cc_final: 0.8316 (mtp) REVERT: A 579 MET cc_start: 0.8093 (tmm) cc_final: 0.7789 (tpp) REVERT: A 580 GLU cc_start: 0.8364 (tp30) cc_final: 0.7908 (tp30) REVERT: A 602 MET cc_start: 0.7846 (mpp) cc_final: 0.7520 (mpp) REVERT: A 632 LYS cc_start: 0.8248 (ttpt) cc_final: 0.7994 (ttmm) REVERT: A 647 LYS cc_start: 0.8771 (mmtp) cc_final: 0.8510 (mmtm) REVERT: A 697 MET cc_start: 0.6421 (mmm) cc_final: 0.5789 (mmm) REVERT: A 815 LYS cc_start: 0.9000 (tttt) cc_final: 0.8619 (tppp) REVERT: A 820 LYS cc_start: 0.8299 (mmmt) cc_final: 0.8019 (mmmt) REVERT: A 841 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8441 (mtpt) REVERT: A 897 LYS cc_start: 0.8918 (mttm) cc_final: 0.8672 (mmtp) REVERT: A 937 LYS cc_start: 0.8712 (mttm) cc_final: 0.8316 (mttm) REVERT: A 942 MET cc_start: 0.8648 (tpp) cc_final: 0.8432 (tpt) REVERT: A 983 ASP cc_start: 0.7971 (t0) cc_final: 0.7742 (p0) REVERT: A 990 ARG cc_start: 0.8054 (tpp80) cc_final: 0.7750 (tpp80) REVERT: A 994 GLU cc_start: 0.7961 (pm20) cc_final: 0.7629 (pm20) REVERT: A 1006 VAL cc_start: 0.8458 (m) cc_final: 0.8142 (t) REVERT: A 1008 LEU cc_start: 0.8153 (mp) cc_final: 0.7829 (tp) REVERT: A 1044 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7524 (mt-10) REVERT: A 1060 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7585 (mm-30) REVERT: A 1061 THR cc_start: 0.7830 (OUTLIER) cc_final: 0.7583 (p) REVERT: A 1066 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7707 (m-80) REVERT: A 1072 ASP cc_start: 0.7688 (m-30) cc_final: 0.7427 (m-30) REVERT: A 1073 MET cc_start: 0.8781 (tpp) cc_final: 0.8576 (tpp) REVERT: A 1080 PHE cc_start: 0.8041 (m-80) cc_final: 0.7564 (m-80) REVERT: A 1104 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7462 (tpp) REVERT: A 1116 LYS cc_start: 0.8518 (mttt) cc_final: 0.7562 (mttt) REVERT: A 1121 LEU cc_start: 0.8925 (mm) cc_final: 0.8670 (mt) REVERT: A 1122 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7846 (tp30) REVERT: A 1139 ASP cc_start: 0.7571 (m-30) cc_final: 0.7281 (m-30) REVERT: A 1173 LYS cc_start: 0.7425 (ttpp) cc_final: 0.7088 (ptmm) REVERT: A 1190 ARG cc_start: 0.8096 (mmm-85) cc_final: 0.7689 (mmm-85) REVERT: A 1198 ILE cc_start: 0.5704 (OUTLIER) cc_final: 0.5476 (pp) REVERT: A 1199 LEU cc_start: 0.7913 (tp) cc_final: 0.7511 (tt) REVERT: A 1212 ILE cc_start: 0.5455 (OUTLIER) cc_final: 0.4900 (mp) REVERT: B 116 VAL cc_start: 0.8566 (t) cc_final: 0.8229 (m) REVERT: B 134 ASP cc_start: 0.8033 (t0) cc_final: 0.7651 (t70) REVERT: B 149 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7907 (tp30) REVERT: B 337 GLU cc_start: 0.7918 (tp30) cc_final: 0.7538 (tp30) REVERT: B 375 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8350 (mtpp) REVERT: B 383 MET cc_start: 0.7290 (tpp) cc_final: 0.6714 (mmm) REVERT: B 385 TRP cc_start: 0.8437 (m100) cc_final: 0.8165 (m100) REVERT: B 419 TRP cc_start: 0.8130 (p-90) cc_final: 0.7798 (p-90) REVERT: B 443 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7892 (tm-30) REVERT: B 487 SER cc_start: 0.8496 (t) cc_final: 0.8195 (p) REVERT: B 511 MET cc_start: 0.8902 (tmm) cc_final: 0.8435 (ttp) REVERT: B 581 GLU cc_start: 0.8372 (tp30) cc_final: 0.8005 (tp30) REVERT: B 588 LYS cc_start: 0.8550 (tppt) cc_final: 0.8288 (tttm) REVERT: B 697 MET cc_start: 0.5776 (mmm) cc_final: 0.5130 (mmm) REVERT: B 736 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8026 (t0) REVERT: B 808 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.8002 (pp) REVERT: B 810 MET cc_start: 0.7015 (ptt) cc_final: 0.6810 (ptt) REVERT: B 815 LYS cc_start: 0.9074 (tttt) cc_final: 0.8605 (tppp) REVERT: B 820 LYS cc_start: 0.8210 (mmmt) cc_final: 0.7958 (mmmt) REVERT: B 832 GLN cc_start: 0.8436 (tt0) cc_final: 0.8173 (tp-100) REVERT: B 852 LYS cc_start: 0.8484 (mttp) cc_final: 0.8111 (mtpt) REVERT: B 856 ARG cc_start: 0.8080 (ttp80) cc_final: 0.7767 (ttp80) REVERT: B 859 ASP cc_start: 0.7974 (p0) cc_final: 0.7676 (p0) REVERT: B 877 GLN cc_start: 0.8681 (tt0) cc_final: 0.8391 (tt0) REVERT: B 942 MET cc_start: 0.8554 (tpp) cc_final: 0.8261 (tpp) REVERT: B 947 SER cc_start: 0.7973 (t) cc_final: 0.7749 (t) REVERT: B 954 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7625 (mm-30) REVERT: B 958 LYS cc_start: 0.8921 (ttpt) cc_final: 0.8543 (ttmm) REVERT: B 968 LYS cc_start: 0.8698 (mtpp) cc_final: 0.8368 (mmmm) REVERT: B 993 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.6908 (m-30) REVERT: B 994 GLU cc_start: 0.7932 (pm20) cc_final: 0.7529 (pm20) REVERT: B 1003 SER cc_start: 0.8373 (t) cc_final: 0.7956 (m) REVERT: B 1005 LEU cc_start: 0.8496 (tp) cc_final: 0.8231 (tt) REVERT: B 1066 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: B 1075 ILE cc_start: 0.8990 (mm) cc_final: 0.8695 (tt) REVERT: B 1098 ILE cc_start: 0.8948 (tt) cc_final: 0.8576 (tp) REVERT: B 1118 LYS cc_start: 0.8634 (mtpp) cc_final: 0.8334 (mtmm) REVERT: B 1121 LEU cc_start: 0.9032 (mm) cc_final: 0.8761 (mt) REVERT: B 1122 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7851 (tp30) REVERT: B 1144 ASP cc_start: 0.7056 (m-30) cc_final: 0.6814 (m-30) REVERT: B 1162 ARG cc_start: 0.5761 (OUTLIER) cc_final: 0.5156 (tpm-80) REVERT: B 1179 THR cc_start: 0.5270 (OUTLIER) cc_final: 0.5020 (p) REVERT: B 1212 ILE cc_start: 0.5361 (OUTLIER) cc_final: 0.5007 (mp) outliers start: 93 outliers final: 54 residues processed: 597 average time/residue: 0.3247 time to fit residues: 277.6692 Evaluate side-chains 600 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 530 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 316 ASP 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 424 ILE Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 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 624 GLN 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 1147 LEU Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1158 ARG Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 532 ILE 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 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 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 1127 VAL Chi-restraints excluded: chain B residue 1154 ASN Chi-restraints excluded: chain B residue 1156 HIS Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 0.3980 chunk 114 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS B 165 GLN B1220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3026 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= 0.200 Angle : 0.626 16.880 22706 Z= 0.309 Chirality : 0.041 0.171 2734 Planarity : 0.004 0.062 2796 Dihedral : 7.333 133.289 2288 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.30 % Allowed : 19.75 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.19), residues: 2050 helix: 1.88 (0.14), residues: 1450 sheet: -2.36 (0.50), residues: 92 loop : -1.68 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1112 HIS 0.005 0.001 HIS A 981 PHE 0.020 0.001 PHE B 680 TYR 0.014 0.001 TYR B 415 ARG 0.008 0.000 ARG B1185 *********************** 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 637 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 542 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8675 (mm) cc_final: 0.8293 (mt) REVERT: A 116 VAL cc_start: 0.8676 (t) cc_final: 0.8421 (t) REVERT: A 149 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7551 (tm-30) REVERT: A 163 PHE cc_start: 0.8365 (t80) cc_final: 0.8052 (t80) REVERT: A 176 VAL cc_start: 0.8784 (p) cc_final: 0.8558 (t) REVERT: A 225 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7488 (tp40) REVERT: A 233 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7583 (tm-30) REVERT: A 266 LEU cc_start: 0.8423 (tp) cc_final: 0.8183 (tt) REVERT: A 269 LEU cc_start: 0.8573 (tp) cc_final: 0.8307 (tt) REVERT: A 337 GLU cc_start: 0.7835 (tp30) cc_final: 0.7471 (tp30) REVERT: A 338 LYS cc_start: 0.8675 (mtmm) cc_final: 0.7976 (mtmm) REVERT: A 346 GLU cc_start: 0.7808 (tt0) cc_final: 0.7448 (tt0) REVERT: A 354 GLU cc_start: 0.8284 (tt0) cc_final: 0.7938 (tt0) REVERT: A 383 MET cc_start: 0.7024 (mmm) cc_final: 0.6446 (mmm) REVERT: A 387 TYR cc_start: 0.8509 (m-10) cc_final: 0.8054 (m-10) REVERT: A 419 TRP cc_start: 0.8129 (p-90) cc_final: 0.7919 (p-90) REVERT: A 486 ILE cc_start: 0.8763 (mp) cc_final: 0.8479 (mm) REVERT: A 487 SER cc_start: 0.8306 (t) cc_final: 0.8003 (m) REVERT: A 499 ARG cc_start: 0.8486 (ttp-170) cc_final: 0.8237 (mtp-110) REVERT: A 511 MET cc_start: 0.8766 (tmm) cc_final: 0.8401 (ttp) REVERT: A 531 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7020 (tm-30) REVERT: A 578 MET cc_start: 0.8525 (mtp) cc_final: 0.8302 (mtp) REVERT: A 579 MET cc_start: 0.8030 (tmm) cc_final: 0.7734 (tpp) REVERT: A 580 GLU cc_start: 0.8347 (tp30) cc_final: 0.7869 (tp30) REVERT: A 602 MET cc_start: 0.7831 (mpp) cc_final: 0.7499 (mpp) REVERT: A 632 LYS cc_start: 0.8225 (ttpt) cc_final: 0.7960 (ttmm) REVERT: A 634 SER cc_start: 0.8883 (m) cc_final: 0.8601 (t) REVERT: A 647 LYS cc_start: 0.8768 (mmtp) cc_final: 0.8518 (mmtm) REVERT: A 697 MET cc_start: 0.6404 (mmm) cc_final: 0.5789 (mmm) REVERT: A 815 LYS cc_start: 0.8987 (tttt) cc_final: 0.8631 (tppp) REVERT: A 820 LYS cc_start: 0.8260 (mmmt) cc_final: 0.7982 (mmmt) REVERT: A 841 LYS cc_start: 0.8825 (mtpt) cc_final: 0.8435 (mtpt) REVERT: A 884 LEU cc_start: 0.8494 (mm) cc_final: 0.8227 (mm) REVERT: A 897 LYS cc_start: 0.8922 (mttm) cc_final: 0.8685 (mmtp) REVERT: A 937 LYS cc_start: 0.8707 (mttm) cc_final: 0.8321 (mmtp) REVERT: A 942 MET cc_start: 0.8631 (tpp) cc_final: 0.8222 (tpt) REVERT: A 990 ARG cc_start: 0.8110 (tpp80) cc_final: 0.7795 (tpp80) REVERT: A 994 GLU cc_start: 0.7973 (pm20) cc_final: 0.7630 (pm20) REVERT: A 1005 LEU cc_start: 0.8363 (tp) cc_final: 0.8140 (tp) REVERT: A 1006 VAL cc_start: 0.8465 (m) cc_final: 0.8168 (t) REVERT: A 1008 LEU cc_start: 0.8149 (mp) cc_final: 0.7821 (tp) REVERT: A 1044 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7535 (mt-10) REVERT: A 1060 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7562 (mm-30) REVERT: A 1061 THR cc_start: 0.7771 (OUTLIER) cc_final: 0.7531 (p) REVERT: A 1066 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7839 (m-80) REVERT: A 1072 ASP cc_start: 0.7742 (m-30) cc_final: 0.7495 (m-30) REVERT: A 1080 PHE cc_start: 0.8021 (m-80) cc_final: 0.7550 (m-80) REVERT: A 1104 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7438 (tpp) REVERT: A 1121 LEU cc_start: 0.8972 (mm) cc_final: 0.8745 (mt) REVERT: A 1122 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7835 (tp30) REVERT: A 1139 ASP cc_start: 0.7568 (m-30) cc_final: 0.7322 (m-30) REVERT: A 1173 LYS cc_start: 0.7437 (ttpp) cc_final: 0.7220 (ptmm) REVERT: A 1190 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7714 (mmm-85) REVERT: A 1198 ILE cc_start: 0.5719 (OUTLIER) cc_final: 0.5501 (pp) REVERT: A 1199 LEU cc_start: 0.7921 (tp) cc_final: 0.7528 (tt) REVERT: A 1212 ILE cc_start: 0.5411 (OUTLIER) cc_final: 0.4836 (mp) REVERT: B 103 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8318 (p) REVERT: B 116 VAL cc_start: 0.8565 (t) cc_final: 0.8232 (m) REVERT: B 134 ASP cc_start: 0.8029 (t0) cc_final: 0.7643 (t70) REVERT: B 149 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7561 (tm-30) REVERT: B 155 ASP cc_start: 0.8192 (t0) cc_final: 0.7944 (t0) REVERT: B 265 VAL cc_start: 0.8649 (t) cc_final: 0.8363 (p) REVERT: B 337 GLU cc_start: 0.7926 (tp30) cc_final: 0.7534 (tp30) REVERT: B 375 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8365 (mtpp) REVERT: B 407 SER cc_start: 0.8691 (t) cc_final: 0.8463 (p) REVERT: B 419 TRP cc_start: 0.8116 (p-90) cc_final: 0.7792 (p-90) REVERT: B 443 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7924 (tm-30) REVERT: B 487 SER cc_start: 0.8491 (t) cc_final: 0.8187 (p) REVERT: B 511 MET cc_start: 0.8865 (tmm) cc_final: 0.8453 (ttp) REVERT: B 579 MET cc_start: 0.8456 (tpp) cc_final: 0.8085 (tpp) REVERT: B 581 GLU cc_start: 0.8291 (tp30) cc_final: 0.7967 (tp30) REVERT: B 588 LYS cc_start: 0.8549 (tppt) cc_final: 0.8293 (tttm) REVERT: B 621 GLU cc_start: 0.7708 (pp20) cc_final: 0.7435 (pm20) REVERT: B 634 SER cc_start: 0.8938 (m) cc_final: 0.8541 (t) REVERT: B 697 MET cc_start: 0.5773 (mmm) cc_final: 0.5132 (mmm) REVERT: B 736 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8005 (t0) REVERT: B 815 LYS cc_start: 0.9069 (tttt) cc_final: 0.8586 (tppp) REVERT: B 820 LYS cc_start: 0.8194 (mmmt) cc_final: 0.7945 (mmmt) REVERT: B 852 LYS cc_start: 0.8474 (mttp) cc_final: 0.8098 (mtpt) REVERT: B 853 ILE cc_start: 0.8847 (tp) cc_final: 0.8531 (tt) REVERT: B 859 ASP cc_start: 0.7970 (p0) cc_final: 0.7696 (p0) REVERT: B 877 GLN cc_start: 0.8667 (tt0) cc_final: 0.8462 (tt0) REVERT: B 942 MET cc_start: 0.8554 (tpp) cc_final: 0.8284 (tpp) REVERT: B 954 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7652 (mm-30) REVERT: B 958 LYS cc_start: 0.8892 (ttpt) cc_final: 0.8507 (ttmm) REVERT: B 968 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8358 (mmmm) REVERT: B 993 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.6902 (m-30) REVERT: B 994 GLU cc_start: 0.7930 (pm20) cc_final: 0.7506 (pm20) REVERT: B 1003 SER cc_start: 0.8396 (t) cc_final: 0.7977 (m) REVERT: B 1005 LEU cc_start: 0.8493 (tp) cc_final: 0.8229 (tt) REVERT: B 1044 GLU cc_start: 0.7782 (mp0) cc_final: 0.7569 (mp0) REVERT: B 1066 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: B 1075 ILE cc_start: 0.8965 (mm) cc_final: 0.8664 (tt) REVERT: B 1098 ILE cc_start: 0.8940 (tt) cc_final: 0.8565 (tp) REVERT: B 1118 LYS cc_start: 0.8626 (mtpp) cc_final: 0.8334 (mtmm) REVERT: B 1121 LEU cc_start: 0.9032 (mm) cc_final: 0.8768 (mt) REVERT: B 1122 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7986 (tp30) REVERT: B 1136 PHE cc_start: 0.6836 (t80) cc_final: 0.6483 (t80) REVERT: B 1144 ASP cc_start: 0.7080 (m-30) cc_final: 0.6858 (m-30) REVERT: B 1162 ARG cc_start: 0.5763 (OUTLIER) cc_final: 0.5124 (tpm-80) REVERT: B 1179 THR cc_start: 0.5146 (OUTLIER) cc_final: 0.4922 (p) REVERT: B 1212 ILE cc_start: 0.5370 (OUTLIER) cc_final: 0.5016 (mp) outliers start: 95 outliers final: 59 residues processed: 592 average time/residue: 0.3177 time to fit residues: 268.1669 Evaluate side-chains 610 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 537 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 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 872 GLU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 981 HIS Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 MET Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1158 ARG Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 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 925 MET Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1154 ASN Chi-restraints excluded: chain B residue 1156 HIS Chi-restraints excluded: chain B residue 1162 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 0.5980 chunk 181 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 118 optimal weight: 0.0370 chunk 49 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 600 HIS A 981 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16740 Z= 0.225 Angle : 0.638 16.827 22706 Z= 0.316 Chirality : 0.042 0.170 2734 Planarity : 0.004 0.061 2796 Dihedral : 7.247 133.475 2282 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.13 % Allowed : 20.42 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.19), residues: 2050 helix: 1.90 (0.14), residues: 1454 sheet: -2.28 (0.50), residues: 96 loop : -1.63 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1112 HIS 0.003 0.001 HIS A 981 PHE 0.018 0.001 PHE A1136 TYR 0.012 0.001 TYR B 415 ARG 0.009 0.000 ARG B1185 *********************** 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 fitting. rotamer outliers: 92 poor density : 541 time to evaluate : 1.821 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: 0.8684 (mm) cc_final: 0.8302 (mt) REVERT: A 116 VAL cc_start: 0.8673 (t) cc_final: 0.8426 (t) REVERT: A 149 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7548 (tm-30) REVERT: A 163 PHE cc_start: 0.8385 (t80) cc_final: 0.8135 (t80) REVERT: A 176 VAL cc_start: 0.8792 (p) cc_final: 0.8573 (t) REVERT: A 233 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7554 (tm-30) REVERT: A 266 LEU cc_start: 0.8405 (tp) cc_final: 0.8182 (tt) REVERT: A 269 LEU cc_start: 0.8581 (tp) cc_final: 0.8350 (tt) REVERT: A 280 TYR cc_start: 0.8457 (t80) cc_final: 0.8148 (t80) REVERT: A 337 GLU cc_start: 0.7843 (tp30) cc_final: 0.7480 (tp30) REVERT: A 346 GLU cc_start: 0.7785 (tt0) cc_final: 0.7377 (tt0) REVERT: A 354 GLU cc_start: 0.8280 (tt0) cc_final: 0.7928 (tt0) REVERT: A 375 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8453 (ttpp) REVERT: A 383 MET cc_start: 0.7050 (mmm) cc_final: 0.6442 (mmm) REVERT: A 486 ILE cc_start: 0.8780 (mp) cc_final: 0.8499 (mm) REVERT: A 487 SER cc_start: 0.8305 (t) cc_final: 0.7960 (p) REVERT: A 511 MET cc_start: 0.8777 (tmm) cc_final: 0.8431 (ttp) REVERT: A 531 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7043 (tm-30) REVERT: A 578 MET cc_start: 0.8528 (mtp) cc_final: 0.8322 (mtp) REVERT: A 579 MET cc_start: 0.8027 (tmm) cc_final: 0.7720 (tpp) REVERT: A 580 GLU cc_start: 0.8359 (tp30) cc_final: 0.7874 (tp30) REVERT: A 599 GLU cc_start: 0.7694 (mp0) cc_final: 0.7447 (mp0) REVERT: A 632 LYS cc_start: 0.8229 (ttpt) cc_final: 0.7973 (ttmm) REVERT: A 634 SER cc_start: 0.8868 (m) cc_final: 0.8586 (t) REVERT: A 647 LYS cc_start: 0.8775 (mmtp) cc_final: 0.8568 (mmtp) REVERT: A 697 MET cc_start: 0.6437 (mmm) cc_final: 0.5806 (mmm) REVERT: A 820 LYS cc_start: 0.8244 (mmmt) cc_final: 0.7972 (mmmt) REVERT: A 828 LYS cc_start: 0.8360 (mmmm) cc_final: 0.8095 (mmmm) REVERT: A 841 LYS cc_start: 0.8824 (mtpt) cc_final: 0.8456 (mtpt) REVERT: A 884 LEU cc_start: 0.8490 (mm) cc_final: 0.8197 (mm) REVERT: A 937 LYS cc_start: 0.8699 (mttm) cc_final: 0.8487 (mttm) REVERT: A 942 MET cc_start: 0.8652 (tpp) cc_final: 0.8206 (tpt) REVERT: A 989 VAL cc_start: 0.7895 (t) cc_final: 0.7580 (t) REVERT: A 990 ARG cc_start: 0.8115 (tpp80) cc_final: 0.7629 (tpp80) REVERT: A 994 GLU cc_start: 0.7966 (pm20) cc_final: 0.7628 (pm20) REVERT: A 1005 LEU cc_start: 0.8405 (tp) cc_final: 0.8168 (tp) REVERT: A 1006 VAL cc_start: 0.8463 (m) cc_final: 0.8175 (t) REVERT: A 1008 LEU cc_start: 0.8160 (mp) cc_final: 0.7834 (tp) REVERT: A 1044 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7524 (mt-10) REVERT: A 1060 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7538 (mm-30) REVERT: A 1061 THR cc_start: 0.7750 (OUTLIER) cc_final: 0.7489 (p) REVERT: A 1072 ASP cc_start: 0.7778 (m-30) cc_final: 0.7521 (m-30) REVERT: A 1080 PHE cc_start: 0.8008 (m-80) cc_final: 0.7563 (m-80) REVERT: A 1087 GLU cc_start: 0.7513 (tm-30) cc_final: 0.6895 (tm-30) REVERT: A 1104 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7620 (tpp) REVERT: A 1113 THR cc_start: 0.8190 (p) cc_final: 0.7934 (t) REVERT: A 1121 LEU cc_start: 0.8993 (mm) cc_final: 0.8774 (mt) REVERT: A 1139 ASP cc_start: 0.7532 (m-30) cc_final: 0.7217 (m-30) REVERT: A 1185 ARG cc_start: 0.6940 (mmt-90) cc_final: 0.6579 (mmt180) REVERT: A 1190 ARG cc_start: 0.8066 (mmm-85) cc_final: 0.7696 (mmm-85) REVERT: A 1198 ILE cc_start: 0.5715 (OUTLIER) cc_final: 0.5495 (pp) REVERT: A 1199 LEU cc_start: 0.7955 (tp) cc_final: 0.7553 (tt) REVERT: A 1212 ILE cc_start: 0.5424 (OUTLIER) cc_final: 0.4817 (mp) REVERT: B 103 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8304 (p) REVERT: B 134 ASP cc_start: 0.8034 (t0) cc_final: 0.7684 (t70) REVERT: B 149 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7582 (tm-30) REVERT: B 155 ASP cc_start: 0.8179 (t0) cc_final: 0.7724 (t0) REVERT: B 265 VAL cc_start: 0.8654 (t) cc_final: 0.8372 (p) REVERT: B 337 GLU cc_start: 0.7924 (tp30) cc_final: 0.7551 (tp30) REVERT: B 375 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8394 (mtpp) REVERT: B 407 SER cc_start: 0.8708 (t) cc_final: 0.8466 (p) REVERT: B 419 TRP cc_start: 0.8117 (p-90) cc_final: 0.7824 (p-90) REVERT: B 425 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8431 (ttp) REVERT: B 443 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7930 (tm-30) REVERT: B 487 SER cc_start: 0.8465 (t) cc_final: 0.8176 (p) REVERT: B 511 MET cc_start: 0.8873 (tmm) cc_final: 0.8472 (ttp) REVERT: B 579 MET cc_start: 0.8435 (tpp) cc_final: 0.8220 (mmm) REVERT: B 581 GLU cc_start: 0.8325 (tp30) cc_final: 0.8003 (tp30) REVERT: B 584 LEU cc_start: 0.8825 (mm) cc_final: 0.8622 (mm) REVERT: B 588 LYS cc_start: 0.8542 (tppt) cc_final: 0.8292 (tttm) REVERT: B 621 GLU cc_start: 0.7760 (pp20) cc_final: 0.7458 (pm20) REVERT: B 697 MET cc_start: 0.5783 (mmm) cc_final: 0.5142 (mmm) REVERT: B 736 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8002 (t0) REVERT: B 820 LYS cc_start: 0.8194 (mmmt) cc_final: 0.7947 (mmmt) REVERT: B 852 LYS cc_start: 0.8508 (mttp) cc_final: 0.8034 (mtpt) REVERT: B 853 ILE cc_start: 0.8884 (tp) cc_final: 0.8563 (tt) REVERT: B 859 ASP cc_start: 0.7974 (p0) cc_final: 0.7668 (p0) REVERT: B 877 GLN cc_start: 0.8598 (tt0) cc_final: 0.8368 (tt0) REVERT: B 942 MET cc_start: 0.8552 (tpp) cc_final: 0.8305 (tpp) REVERT: B 954 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7670 (mm-30) REVERT: B 958 LYS cc_start: 0.8886 (ttpt) cc_final: 0.8499 (ttmm) REVERT: B 968 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8350 (mmmm) REVERT: B 993 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.6910 (m-30) REVERT: B 994 GLU cc_start: 0.7918 (pm20) cc_final: 0.7360 (pm20) REVERT: B 998 LEU cc_start: 0.8629 (mt) cc_final: 0.8413 (mm) REVERT: B 1003 SER cc_start: 0.8420 (t) cc_final: 0.8005 (m) REVERT: B 1005 LEU cc_start: 0.8482 (tp) cc_final: 0.8219 (tt) REVERT: B 1044 GLU cc_start: 0.7673 (mp0) cc_final: 0.7458 (mp0) REVERT: B 1066 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.8281 (m-80) REVERT: B 1098 ILE cc_start: 0.8945 (tt) cc_final: 0.8739 (tt) REVERT: B 1118 LYS cc_start: 0.8634 (mtpp) cc_final: 0.8344 (mtmm) REVERT: B 1121 LEU cc_start: 0.9027 (mm) cc_final: 0.8769 (mt) REVERT: B 1122 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7675 (mm-30) REVERT: B 1136 PHE cc_start: 0.6865 (t80) cc_final: 0.6486 (t80) REVERT: B 1162 ARG cc_start: 0.5767 (OUTLIER) cc_final: 0.5135 (tpm-80) REVERT: B 1179 THR cc_start: 0.5041 (OUTLIER) cc_final: 0.4839 (p) REVERT: B 1212 ILE cc_start: 0.5421 (OUTLIER) cc_final: 0.5034 (mp) REVERT: B 1221 MET cc_start: 0.7926 (mmt) cc_final: 0.7618 (mmt) outliers start: 92 outliers final: 65 residues processed: 584 average time/residue: 0.3208 time to fit residues: 268.7532 Evaluate side-chains 605 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 526 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 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 628 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 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 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 1198 ILE Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 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 355 MET Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 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 865 ARG Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 125 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 92 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN B 165 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3314 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= 0.212 Angle : 0.639 16.726 22706 Z= 0.316 Chirality : 0.041 0.169 2734 Planarity : 0.004 0.061 2796 Dihedral : 7.128 132.598 2280 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.08 % Allowed : 20.70 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.19), residues: 2050 helix: 1.96 (0.14), residues: 1454 sheet: -2.25 (0.51), residues: 96 loop : -1.61 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1112 HIS 0.002 0.001 HIS B 981 PHE 0.017 0.001 PHE A1136 TYR 0.010 0.001 TYR B 415 ARG 0.009 0.000 ARG A1053 *********************** 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 629 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 538 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8053 (mt) REVERT: A 112 ILE cc_start: 0.8685 (mm) cc_final: 0.8310 (mt) REVERT: A 116 VAL cc_start: 0.8667 (t) cc_final: 0.8423 (t) REVERT: A 163 PHE cc_start: 0.8413 (t80) cc_final: 0.8193 (t80) REVERT: A 176 VAL cc_start: 0.8782 (p) cc_final: 0.8569 (t) REVERT: A 195 PHE cc_start: 0.7998 (t80) cc_final: 0.7782 (t80) REVERT: A 266 LEU cc_start: 0.8411 (tp) cc_final: 0.8181 (tt) REVERT: A 269 LEU cc_start: 0.8582 (tp) cc_final: 0.8365 (tt) REVERT: A 280 TYR cc_start: 0.8438 (t80) cc_final: 0.8135 (t80) REVERT: A 337 GLU cc_start: 0.7861 (tp30) cc_final: 0.7484 (tp30) REVERT: A 346 GLU cc_start: 0.7768 (tt0) cc_final: 0.7506 (tt0) REVERT: A 354 GLU cc_start: 0.8273 (tt0) cc_final: 0.7917 (tt0) REVERT: A 375 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8552 (ttpp) REVERT: A 377 LEU cc_start: 0.8653 (tp) cc_final: 0.8334 (mp) REVERT: A 383 MET cc_start: 0.6950 (mmm) cc_final: 0.6430 (mmm) REVERT: A 387 TYR cc_start: 0.8530 (m-10) cc_final: 0.8133 (m-10) REVERT: A 411 SER cc_start: 0.8430 (p) cc_final: 0.8120 (p) REVERT: A 487 SER cc_start: 0.8331 (t) cc_final: 0.8032 (m) REVERT: A 511 MET cc_start: 0.8776 (tmm) cc_final: 0.8409 (ttp) REVERT: A 578 MET cc_start: 0.8495 (mtp) cc_final: 0.8279 (mtp) REVERT: A 579 MET cc_start: 0.8002 (tmm) cc_final: 0.7719 (tpp) REVERT: A 632 LYS cc_start: 0.8209 (ttpt) cc_final: 0.7954 (ttmm) REVERT: A 634 SER cc_start: 0.8842 (m) cc_final: 0.8562 (t) REVERT: A 697 MET cc_start: 0.6414 (mmm) cc_final: 0.5714 (mmm) REVERT: A 815 LYS cc_start: 0.8990 (tttt) cc_final: 0.8628 (tppp) REVERT: A 820 LYS cc_start: 0.8235 (mmmt) cc_final: 0.7964 (mmmt) REVERT: A 841 LYS cc_start: 0.8821 (mtpt) cc_final: 0.8447 (mtpt) REVERT: A 853 ILE cc_start: 0.8603 (tp) cc_final: 0.8335 (tp) REVERT: A 884 LEU cc_start: 0.8485 (mm) cc_final: 0.8175 (mm) REVERT: A 911 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8312 (mm-30) REVERT: A 937 LYS cc_start: 0.8699 (mttm) cc_final: 0.8488 (mttm) REVERT: A 942 MET cc_start: 0.8657 (tpp) cc_final: 0.8231 (tpt) REVERT: A 989 VAL cc_start: 0.7614 (t) cc_final: 0.7315 (t) REVERT: A 994 GLU cc_start: 0.7932 (pm20) cc_final: 0.7606 (pm20) REVERT: A 1006 VAL cc_start: 0.8406 (m) cc_final: 0.8173 (t) REVERT: A 1008 LEU cc_start: 0.8178 (mp) cc_final: 0.7904 (mm) REVERT: A 1035 TYR cc_start: 0.8143 (m-80) cc_final: 0.7585 (m-80) REVERT: A 1044 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7490 (mt-10) REVERT: A 1057 VAL cc_start: 0.8896 (t) cc_final: 0.8675 (m) REVERT: A 1060 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7393 (mm-30) REVERT: A 1061 THR cc_start: 0.7692 (OUTLIER) cc_final: 0.7437 (p) REVERT: A 1072 ASP cc_start: 0.7803 (m-30) cc_final: 0.7551 (m-30) REVERT: A 1080 PHE cc_start: 0.7991 (m-80) cc_final: 0.7604 (m-80) REVERT: A 1087 GLU cc_start: 0.7554 (tm-30) cc_final: 0.6960 (tt0) REVERT: A 1104 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7464 (tpp) REVERT: A 1139 ASP cc_start: 0.7546 (m-30) cc_final: 0.7263 (m-30) REVERT: A 1185 ARG cc_start: 0.6810 (mmt-90) cc_final: 0.6577 (mmt180) REVERT: A 1190 ARG cc_start: 0.8043 (mmm-85) cc_final: 0.7670 (mmm-85) REVERT: A 1198 ILE cc_start: 0.5714 (OUTLIER) cc_final: 0.5504 (pp) REVERT: A 1199 LEU cc_start: 0.7959 (tp) cc_final: 0.7576 (tt) REVERT: B 103 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8299 (p) REVERT: B 116 VAL cc_start: 0.8554 (t) cc_final: 0.8245 (m) REVERT: B 134 ASP cc_start: 0.8022 (t0) cc_final: 0.7681 (t70) REVERT: B 149 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7552 (tm-30) REVERT: B 155 ASP cc_start: 0.8144 (t0) cc_final: 0.7687 (t0) REVERT: B 205 MET cc_start: 0.8353 (mmp) cc_final: 0.7896 (mmp) REVERT: B 265 VAL cc_start: 0.8651 (t) cc_final: 0.8371 (p) REVERT: B 337 GLU cc_start: 0.7910 (tp30) cc_final: 0.7515 (tp30) REVERT: B 375 LYS cc_start: 0.8757 (tppp) cc_final: 0.8454 (mtpp) REVERT: B 407 SER cc_start: 0.8728 (t) cc_final: 0.8474 (p) REVERT: B 419 TRP cc_start: 0.8099 (p-90) cc_final: 0.7814 (p-90) REVERT: B 425 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8496 (ttp) REVERT: B 487 SER cc_start: 0.8480 (t) cc_final: 0.8212 (p) REVERT: B 511 MET cc_start: 0.8854 (tmm) cc_final: 0.8434 (ttp) REVERT: B 579 MET cc_start: 0.8416 (tpp) cc_final: 0.8194 (mmm) REVERT: B 581 GLU cc_start: 0.8294 (tp30) cc_final: 0.7972 (tp30) REVERT: B 584 LEU cc_start: 0.8806 (mm) cc_final: 0.8589 (mm) REVERT: B 588 LYS cc_start: 0.8525 (tppt) cc_final: 0.8275 (tttm) REVERT: B 598 PHE cc_start: 0.8870 (t80) cc_final: 0.8389 (t80) REVERT: B 697 MET cc_start: 0.5765 (mmm) cc_final: 0.5106 (mmm) REVERT: B 736 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8034 (t0) REVERT: B 815 LYS cc_start: 0.9033 (tttt) cc_final: 0.8647 (tttm) REVERT: B 820 LYS cc_start: 0.8199 (mmmt) cc_final: 0.7945 (mmmt) REVERT: B 852 LYS cc_start: 0.8535 (mttp) cc_final: 0.8042 (mtpt) REVERT: B 853 ILE cc_start: 0.8904 (tp) cc_final: 0.8585 (tt) REVERT: B 859 ASP cc_start: 0.7950 (p0) cc_final: 0.7653 (p0) REVERT: B 877 GLN cc_start: 0.8555 (tt0) cc_final: 0.8323 (tt0) REVERT: B 910 ARG cc_start: 0.8621 (ttp-170) cc_final: 0.8393 (ttm110) REVERT: B 942 MET cc_start: 0.8536 (tpp) cc_final: 0.8311 (tpp) REVERT: B 954 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7680 (mm-30) REVERT: B 958 LYS cc_start: 0.8880 (ttpt) cc_final: 0.8486 (ttmm) REVERT: B 968 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8349 (mmmm) REVERT: B 993 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.6953 (m-30) REVERT: B 994 GLU cc_start: 0.7887 (pm20) cc_final: 0.7423 (pm20) REVERT: B 1003 SER cc_start: 0.8419 (t) cc_final: 0.8091 (m) REVERT: B 1005 LEU cc_start: 0.8473 (tp) cc_final: 0.8230 (tt) REVERT: B 1035 TYR cc_start: 0.8081 (m-80) cc_final: 0.7825 (m-80) REVERT: B 1044 GLU cc_start: 0.7596 (mp0) cc_final: 0.7388 (mp0) REVERT: B 1060 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7204 (mm-30) REVERT: B 1118 LYS cc_start: 0.8628 (mtpp) cc_final: 0.8330 (mtmm) REVERT: B 1121 LEU cc_start: 0.9021 (mm) cc_final: 0.8776 (mt) REVERT: B 1136 PHE cc_start: 0.6859 (t80) cc_final: 0.6483 (t80) REVERT: B 1162 ARG cc_start: 0.5770 (OUTLIER) cc_final: 0.5121 (tpm-80) REVERT: B 1212 ILE cc_start: 0.5408 (OUTLIER) cc_final: 0.5001 (mp) REVERT: B 1221 MET cc_start: 0.7919 (mmt) cc_final: 0.7565 (mmt) outliers start: 91 outliers final: 63 residues processed: 581 average time/residue: 0.3236 time to fit residues: 268.0598 Evaluate side-chains 597 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 523 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 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 628 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 915 GLU 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 1050 LYS Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 MET Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1158 ARG Chi-restraints excluded: chain A residue 1198 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 196 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 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 1162 ARG Chi-restraints excluded: chain B residue 1212 ILE Chi-restraints excluded: chain B residue 1222 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 18 optimal weight: 0.1980 chunk 157 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 959 ASN B1156 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3457 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= 0.210 Angle : 0.653 16.667 22706 Z= 0.322 Chirality : 0.042 0.169 2734 Planarity : 0.005 0.061 2796 Dihedral : 6.954 135.872 2273 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.85 % Allowed : 21.54 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.19), residues: 2050 helix: 1.99 (0.14), residues: 1458 sheet: -2.56 (0.48), residues: 106 loop : -1.52 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1112 HIS 0.003 0.001 HIS B 981 PHE 0.020 0.001 PHE A1136 TYR 0.016 0.001 TYR A1009 ARG 0.008 0.000 ARG B1053 *********************** 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 612 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 525 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8063 (mt) REVERT: A 112 ILE cc_start: 0.8678 (mm) cc_final: 0.8307 (mt) REVERT: A 116 VAL cc_start: 0.8657 (t) cc_final: 0.8416 (t) REVERT: A 163 PHE cc_start: 0.8414 (t80) cc_final: 0.8158 (t80) REVERT: A 176 VAL cc_start: 0.8780 (p) cc_final: 0.8559 (t) REVERT: A 199 MET cc_start: 0.8533 (mmm) cc_final: 0.7989 (tpp) REVERT: A 266 LEU cc_start: 0.8401 (tp) cc_final: 0.8166 (tt) REVERT: A 269 LEU cc_start: 0.8578 (tp) cc_final: 0.8367 (tt) REVERT: A 280 TYR cc_start: 0.8425 (t80) cc_final: 0.8123 (t80) REVERT: A 337 GLU cc_start: 0.7862 (tp30) cc_final: 0.7496 (tp30) REVERT: A 346 GLU cc_start: 0.7753 (tt0) cc_final: 0.7486 (tt0) REVERT: A 354 GLU cc_start: 0.8276 (tt0) cc_final: 0.7927 (tt0) REVERT: A 377 LEU cc_start: 0.8682 (tp) cc_final: 0.8366 (mp) REVERT: A 383 MET cc_start: 0.6922 (mmm) cc_final: 0.6399 (mmm) REVERT: A 387 TYR cc_start: 0.8549 (m-10) cc_final: 0.8135 (m-10) REVERT: A 411 SER cc_start: 0.8442 (p) cc_final: 0.8141 (p) REVERT: A 486 ILE cc_start: 0.8867 (mm) cc_final: 0.8620 (mp) REVERT: A 487 SER cc_start: 0.8312 (t) cc_final: 0.8027 (m) REVERT: A 511 MET cc_start: 0.8722 (tmm) cc_final: 0.8326 (ttp) REVERT: A 578 MET cc_start: 0.8504 (mtp) cc_final: 0.8193 (mtp) REVERT: A 579 MET cc_start: 0.7985 (tmm) cc_final: 0.7693 (tpp) REVERT: A 581 GLU cc_start: 0.8238 (tp30) cc_final: 0.7930 (tp30) REVERT: A 632 LYS cc_start: 0.8168 (ttpt) cc_final: 0.7938 (ttmm) REVERT: A 634 SER cc_start: 0.8830 (m) cc_final: 0.8558 (t) REVERT: A 697 MET cc_start: 0.6377 (mmm) cc_final: 0.5649 (mmm) REVERT: A 815 LYS cc_start: 0.8986 (tttt) cc_final: 0.8624 (tppp) REVERT: A 820 LYS cc_start: 0.8225 (mmmt) cc_final: 0.7958 (mmmt) REVERT: A 828 LYS cc_start: 0.8339 (mmmm) cc_final: 0.8074 (mmmm) REVERT: A 841 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8445 (mtpt) REVERT: A 853 ILE cc_start: 0.8635 (tp) cc_final: 0.8357 (tp) REVERT: A 884 LEU cc_start: 0.8471 (mm) cc_final: 0.8159 (mt) REVERT: A 910 ARG cc_start: 0.8535 (ttp-170) cc_final: 0.7946 (ttp-170) REVERT: A 911 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8314 (mm-30) REVERT: A 937 LYS cc_start: 0.8710 (mttm) cc_final: 0.8506 (mttm) REVERT: A 942 MET cc_start: 0.8645 (tpp) cc_final: 0.8233 (tpt) REVERT: A 989 VAL cc_start: 0.7642 (t) cc_final: 0.7343 (t) REVERT: A 994 GLU cc_start: 0.7897 (pm20) cc_final: 0.7416 (pm20) REVERT: A 1006 VAL cc_start: 0.8402 (m) cc_final: 0.8111 (p) REVERT: A 1035 TYR cc_start: 0.8127 (m-80) cc_final: 0.7684 (m-80) REVERT: A 1044 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7443 (mt-10) REVERT: A 1060 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7386 (mm-30) REVERT: A 1061 THR cc_start: 0.7700 (OUTLIER) cc_final: 0.7451 (p) REVERT: A 1072 ASP cc_start: 0.7789 (m-30) cc_final: 0.7539 (m-30) REVERT: A 1080 PHE cc_start: 0.7986 (m-80) cc_final: 0.7605 (m-80) REVERT: A 1087 GLU cc_start: 0.7619 (tm-30) cc_final: 0.6998 (tt0) REVERT: A 1104 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7462 (tpp) REVERT: A 1139 ASP cc_start: 0.7676 (m-30) cc_final: 0.7323 (m-30) REVERT: A 1185 ARG cc_start: 0.6765 (mmt-90) cc_final: 0.6558 (mmt180) REVERT: A 1190 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7657 (mmm-85) REVERT: A 1198 ILE cc_start: 0.5673 (OUTLIER) cc_final: 0.5445 (pp) REVERT: A 1199 LEU cc_start: 0.7904 (tp) cc_final: 0.7526 (tt) REVERT: B 103 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8216 (p) REVERT: B 116 VAL cc_start: 0.8559 (t) cc_final: 0.8234 (m) REVERT: B 134 ASP cc_start: 0.8006 (t0) cc_final: 0.7728 (t70) REVERT: B 149 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7541 (tm-30) REVERT: B 155 ASP cc_start: 0.8138 (t0) cc_final: 0.7684 (t0) REVERT: B 199 MET cc_start: 0.8661 (mmm) cc_final: 0.8428 (tpp) REVERT: B 205 MET cc_start: 0.8344 (mmp) cc_final: 0.7877 (mmp) REVERT: B 265 VAL cc_start: 0.8698 (t) cc_final: 0.8392 (p) REVERT: B 337 GLU cc_start: 0.7910 (tp30) cc_final: 0.7514 (tp30) REVERT: B 407 SER cc_start: 0.8738 (t) cc_final: 0.8485 (p) REVERT: B 419 TRP cc_start: 0.8089 (p-90) cc_final: 0.7813 (p-90) REVERT: B 487 SER cc_start: 0.8477 (t) cc_final: 0.8201 (p) REVERT: B 511 MET cc_start: 0.8842 (tmm) cc_final: 0.8464 (ttp) REVERT: B 579 MET cc_start: 0.8409 (tpp) cc_final: 0.8190 (mmm) REVERT: B 581 GLU cc_start: 0.8273 (tp30) cc_final: 0.7963 (tp30) REVERT: B 584 LEU cc_start: 0.8771 (mm) cc_final: 0.8555 (mm) REVERT: B 588 LYS cc_start: 0.8520 (tppt) cc_final: 0.8273 (tttm) REVERT: B 598 PHE cc_start: 0.8861 (t80) cc_final: 0.8376 (t80) REVERT: B 644 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8344 (mp) REVERT: B 697 MET cc_start: 0.5778 (mmm) cc_final: 0.5103 (mmm) REVERT: B 736 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.8031 (t0) REVERT: B 815 LYS cc_start: 0.9019 (tttt) cc_final: 0.8649 (tttm) REVERT: B 820 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7930 (mmmt) REVERT: B 852 LYS cc_start: 0.8531 (mttp) cc_final: 0.8047 (mtpt) REVERT: B 853 ILE cc_start: 0.8915 (tp) cc_final: 0.8631 (tt) REVERT: B 856 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7815 (ttp80) REVERT: B 859 ASP cc_start: 0.7953 (p0) cc_final: 0.7659 (p0) REVERT: B 910 ARG cc_start: 0.8613 (ttp-170) cc_final: 0.8389 (ttm110) REVERT: B 942 MET cc_start: 0.8526 (tpp) cc_final: 0.8310 (tpp) REVERT: B 954 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7706 (mm-30) REVERT: B 958 LYS cc_start: 0.8873 (ttpt) cc_final: 0.8448 (ttmm) REVERT: B 968 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8363 (mmmm) REVERT: B 993 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6977 (m-30) REVERT: B 994 GLU cc_start: 0.7860 (pm20) cc_final: 0.7407 (pm20) REVERT: B 1003 SER cc_start: 0.8419 (t) cc_final: 0.8097 (m) REVERT: B 1005 LEU cc_start: 0.8470 (tp) cc_final: 0.8234 (tt) REVERT: B 1008 LEU cc_start: 0.7827 (mp) cc_final: 0.7600 (mm) REVERT: B 1035 TYR cc_start: 0.8102 (m-80) cc_final: 0.7773 (m-80) REVERT: B 1053 ARG cc_start: 0.7602 (mtt-85) cc_final: 0.7346 (mtt90) REVERT: B 1075 ILE cc_start: 0.8993 (mt) cc_final: 0.8709 (tt) REVERT: B 1118 LYS cc_start: 0.8600 (mtpp) cc_final: 0.8324 (mtmm) REVERT: B 1136 PHE cc_start: 0.6849 (t80) cc_final: 0.6542 (t80) REVERT: B 1156 HIS cc_start: 0.7927 (OUTLIER) cc_final: 0.7499 (p90) REVERT: B 1162 ARG cc_start: 0.5769 (OUTLIER) cc_final: 0.5119 (tpm-80) REVERT: B 1212 ILE cc_start: 0.5408 (OUTLIER) cc_final: 0.4991 (mp) REVERT: B 1221 MET cc_start: 0.7953 (mmt) cc_final: 0.7388 (mmt) outliers start: 87 outliers final: 62 residues processed: 566 average time/residue: 0.3289 time to fit residues: 266.6947 Evaluate side-chains 596 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 523 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 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 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 835 LEU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 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 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 1198 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 196 SER 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 355 MET Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 736 ASN 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 Chi-restraints excluded: chain B residue 1222 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 0.2980 chunk 192 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 186 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 168 optimal weight: 0.4980 chunk 176 optimal weight: 2.9990 chunk 122 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN B 132 HIS ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16740 Z= 0.196 Angle : 0.656 16.518 22706 Z= 0.323 Chirality : 0.042 0.168 2734 Planarity : 0.005 0.061 2796 Dihedral : 6.934 135.619 2273 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.46 % Allowed : 22.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.19), residues: 2050 helix: 2.04 (0.14), residues: 1458 sheet: -2.43 (0.49), residues: 106 loop : -1.53 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1112 HIS 0.012 0.001 HIS B1156 PHE 0.022 0.001 PHE A1136 TYR 0.013 0.001 TYR A1009 ARG 0.007 0.000 ARG A1053 *********************** 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 605 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 525 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8053 (mt) REVERT: A 112 ILE cc_start: 0.8665 (mm) cc_final: 0.8292 (mt) REVERT: A 116 VAL cc_start: 0.8580 (t) cc_final: 0.8319 (t) REVERT: A 163 PHE cc_start: 0.8422 (t80) cc_final: 0.8200 (t80) REVERT: A 176 VAL cc_start: 0.8761 (p) cc_final: 0.8530 (t) REVERT: A 199 MET cc_start: 0.8519 (mmm) cc_final: 0.8070 (tpp) REVERT: A 266 LEU cc_start: 0.8395 (tp) cc_final: 0.8158 (tt) REVERT: A 269 LEU cc_start: 0.8566 (tp) cc_final: 0.8354 (tt) REVERT: A 280 TYR cc_start: 0.8419 (t80) cc_final: 0.8123 (t80) REVERT: A 337 GLU cc_start: 0.7855 (tp30) cc_final: 0.7508 (tp30) REVERT: A 346 GLU cc_start: 0.7750 (tt0) cc_final: 0.7463 (tt0) REVERT: A 354 GLU cc_start: 0.8275 (tt0) cc_final: 0.7917 (tt0) REVERT: A 377 LEU cc_start: 0.8667 (tp) cc_final: 0.8363 (mp) REVERT: A 383 MET cc_start: 0.6882 (mmm) cc_final: 0.6359 (mmm) REVERT: A 387 TYR cc_start: 0.8519 (m-10) cc_final: 0.8085 (m-10) REVERT: A 411 SER cc_start: 0.8431 (p) cc_final: 0.8137 (p) REVERT: A 486 ILE cc_start: 0.8867 (mm) cc_final: 0.8617 (mp) REVERT: A 487 SER cc_start: 0.8312 (t) cc_final: 0.8030 (m) REVERT: A 511 MET cc_start: 0.8719 (tmm) cc_final: 0.8322 (ttp) REVERT: A 578 MET cc_start: 0.8476 (mtp) cc_final: 0.8214 (mtp) REVERT: A 581 GLU cc_start: 0.8221 (tp30) cc_final: 0.7931 (tp30) REVERT: A 634 SER cc_start: 0.8826 (m) cc_final: 0.8553 (t) REVERT: A 647 LYS cc_start: 0.8684 (mmtp) cc_final: 0.8323 (mtmm) REVERT: A 697 MET cc_start: 0.6382 (mmm) cc_final: 0.5647 (mmm) REVERT: A 815 LYS cc_start: 0.8988 (tttt) cc_final: 0.8626 (tppp) REVERT: A 820 LYS cc_start: 0.8105 (mmmt) cc_final: 0.7845 (mmmt) REVERT: A 841 LYS cc_start: 0.8816 (mtpt) cc_final: 0.8448 (mtpt) REVERT: A 853 ILE cc_start: 0.8653 (tp) cc_final: 0.8384 (tp) REVERT: A 884 LEU cc_start: 0.8464 (mm) cc_final: 0.8171 (mt) REVERT: A 910 ARG cc_start: 0.8531 (ttp-170) cc_final: 0.7918 (ttp-170) REVERT: A 911 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8308 (mm-30) REVERT: A 931 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7858 (mm-30) REVERT: A 937 LYS cc_start: 0.8711 (mttm) cc_final: 0.8473 (mttm) REVERT: A 942 MET cc_start: 0.8625 (tpp) cc_final: 0.8219 (tpt) REVERT: A 989 VAL cc_start: 0.7590 (t) cc_final: 0.7328 (t) REVERT: A 994 GLU cc_start: 0.7882 (pm20) cc_final: 0.7373 (pm20) REVERT: A 1006 VAL cc_start: 0.8393 (m) cc_final: 0.8141 (t) REVERT: A 1035 TYR cc_start: 0.8064 (m-80) cc_final: 0.7676 (m-80) REVERT: A 1044 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7381 (mt-10) REVERT: A 1060 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7344 (mm-30) REVERT: A 1061 THR cc_start: 0.7659 (OUTLIER) cc_final: 0.7403 (p) REVERT: A 1072 ASP cc_start: 0.7776 (m-30) cc_final: 0.7514 (m-30) REVERT: A 1080 PHE cc_start: 0.7956 (m-80) cc_final: 0.7618 (m-80) REVERT: A 1087 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7034 (tt0) REVERT: A 1104 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7449 (tpp) REVERT: A 1139 ASP cc_start: 0.7660 (m-30) cc_final: 0.7352 (m-30) REVERT: A 1173 LYS cc_start: 0.7670 (pttp) cc_final: 0.7435 (pttp) REVERT: A 1190 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7610 (mmm-85) REVERT: A 1198 ILE cc_start: 0.5688 (OUTLIER) cc_final: 0.5486 (pp) REVERT: A 1199 LEU cc_start: 0.7882 (tp) cc_final: 0.7509 (tt) REVERT: B 116 VAL cc_start: 0.8553 (t) cc_final: 0.8222 (m) REVERT: B 134 ASP cc_start: 0.7994 (t0) cc_final: 0.7665 (t70) REVERT: B 149 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7529 (tm-30) REVERT: B 155 ASP cc_start: 0.8134 (t0) cc_final: 0.7701 (t0) REVERT: B 199 MET cc_start: 0.8677 (mmm) cc_final: 0.8451 (tpp) REVERT: B 205 MET cc_start: 0.8329 (mmp) cc_final: 0.7884 (mmp) REVERT: B 265 VAL cc_start: 0.8689 (t) cc_final: 0.8379 (p) REVERT: B 337 GLU cc_start: 0.7903 (tp30) cc_final: 0.7504 (tp30) REVERT: B 375 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8482 (mtpp) REVERT: B 407 SER cc_start: 0.8745 (t) cc_final: 0.8490 (p) REVERT: B 419 TRP cc_start: 0.8088 (p-90) cc_final: 0.7850 (p-90) REVERT: B 487 SER cc_start: 0.8469 (t) cc_final: 0.8204 (p) REVERT: B 511 MET cc_start: 0.8843 (tmm) cc_final: 0.8467 (ttp) REVERT: B 579 MET cc_start: 0.8396 (tpp) cc_final: 0.8180 (mmm) REVERT: B 581 GLU cc_start: 0.8257 (tp30) cc_final: 0.7956 (tp30) REVERT: B 584 LEU cc_start: 0.8748 (mm) cc_final: 0.8520 (mm) REVERT: B 588 LYS cc_start: 0.8524 (tppt) cc_final: 0.8274 (tttm) REVERT: B 598 PHE cc_start: 0.8841 (t80) cc_final: 0.8392 (t80) REVERT: B 644 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8277 (mp) REVERT: B 697 MET cc_start: 0.5764 (mmm) cc_final: 0.5092 (mmm) REVERT: B 736 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.8019 (t0) REVERT: B 815 LYS cc_start: 0.9015 (tttt) cc_final: 0.8649 (tttm) REVERT: B 820 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7923 (mmmt) REVERT: B 852 LYS cc_start: 0.8530 (mttp) cc_final: 0.8048 (mtpt) REVERT: B 853 ILE cc_start: 0.8919 (tp) cc_final: 0.8640 (tt) REVERT: B 856 ARG cc_start: 0.8098 (ttp80) cc_final: 0.7864 (ttp80) REVERT: B 859 ASP cc_start: 0.7948 (p0) cc_final: 0.7650 (p0) REVERT: B 877 GLN cc_start: 0.8612 (tt0) cc_final: 0.8243 (tt0) REVERT: B 910 ARG cc_start: 0.8606 (ttp-170) cc_final: 0.8401 (ttm110) REVERT: B 942 MET cc_start: 0.8514 (tpp) cc_final: 0.8292 (tpp) REVERT: B 954 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7703 (mm-30) REVERT: B 958 LYS cc_start: 0.8877 (ttpt) cc_final: 0.8453 (ttmm) REVERT: B 968 LYS cc_start: 0.8659 (mtpp) cc_final: 0.8350 (mmmm) REVERT: B 972 PHE cc_start: 0.8872 (t80) cc_final: 0.8661 (t80) REVERT: B 993 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.6832 (m-30) REVERT: B 994 GLU cc_start: 0.7883 (pm20) cc_final: 0.7432 (pm20) REVERT: B 1003 SER cc_start: 0.8402 (t) cc_final: 0.8041 (m) REVERT: B 1005 LEU cc_start: 0.8460 (tp) cc_final: 0.8232 (tt) REVERT: B 1033 GLU cc_start: 0.7755 (tp30) cc_final: 0.7500 (tp30) REVERT: B 1035 TYR cc_start: 0.8199 (m-80) cc_final: 0.7739 (m-80) REVERT: B 1053 ARG cc_start: 0.7710 (mtt-85) cc_final: 0.7470 (mtt90) REVERT: B 1060 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7314 (mm-30) REVERT: B 1087 GLU cc_start: 0.7667 (tt0) cc_final: 0.7327 (tt0) REVERT: B 1118 LYS cc_start: 0.8593 (mtpp) cc_final: 0.8314 (mtmm) REVERT: B 1136 PHE cc_start: 0.6835 (t80) cc_final: 0.6566 (t80) REVERT: B 1162 ARG cc_start: 0.5759 (OUTLIER) cc_final: 0.5117 (tpm-80) REVERT: B 1212 ILE cc_start: 0.5424 (OUTLIER) cc_final: 0.4978 (mp) outliers start: 80 outliers final: 62 residues processed: 561 average time/residue: 0.3216 time to fit residues: 257.0256 Evaluate side-chains 585 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 514 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 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 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 852 LYS Chi-restraints excluded: chain A residue 915 GLU 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 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 1198 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 196 SER 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 355 MET Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1154 ASN Chi-restraints excluded: chain B residue 1158 ARG 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 197 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 207 optimal weight: 0.0470 chunk 190 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16740 Z= 0.207 Angle : 0.664 16.404 22706 Z= 0.328 Chirality : 0.042 0.173 2734 Planarity : 0.005 0.104 2796 Dihedral : 6.931 134.805 2273 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.07 % Allowed : 22.82 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.19), residues: 2050 helix: 2.03 (0.14), residues: 1458 sheet: -2.39 (0.49), residues: 106 loop : -1.50 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1112 HIS 0.004 0.001 HIS B 981 PHE 0.022 0.001 PHE A1136 TYR 0.012 0.001 TYR A1009 ARG 0.008 0.000 ARG A 609 ********************** 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 584 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 511 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8043 (mt) REVERT: A 112 ILE cc_start: 0.8659 (mm) cc_final: 0.8281 (mt) REVERT: A 116 VAL cc_start: 0.8566 (t) cc_final: 0.8316 (t) REVERT: A 163 PHE cc_start: 0.8421 (t80) cc_final: 0.8199 (t80) REVERT: A 176 VAL cc_start: 0.8764 (p) cc_final: 0.8542 (t) REVERT: A 266 LEU cc_start: 0.8397 (tp) cc_final: 0.8158 (tt) REVERT: A 269 LEU cc_start: 0.8565 (tp) cc_final: 0.8347 (tt) REVERT: A 280 TYR cc_start: 0.8415 (t80) cc_final: 0.8109 (t80) REVERT: A 337 GLU cc_start: 0.7859 (tp30) cc_final: 0.7515 (tp30) REVERT: A 346 GLU cc_start: 0.7754 (tt0) cc_final: 0.7470 (tt0) REVERT: A 354 GLU cc_start: 0.8272 (tt0) cc_final: 0.7912 (tt0) REVERT: A 375 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8422 (ptpp) REVERT: A 383 MET cc_start: 0.6865 (mmm) cc_final: 0.6379 (mmm) REVERT: A 411 SER cc_start: 0.8465 (p) cc_final: 0.8160 (p) REVERT: A 486 ILE cc_start: 0.8867 (mm) cc_final: 0.8622 (mp) REVERT: A 487 SER cc_start: 0.8315 (t) cc_final: 0.8035 (m) REVERT: A 490 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8264 (tttt) REVERT: A 511 MET cc_start: 0.8725 (tmm) cc_final: 0.8325 (ttp) REVERT: A 578 MET cc_start: 0.8528 (mtp) cc_final: 0.8289 (mtp) REVERT: A 579 MET cc_start: 0.8214 (tmm) cc_final: 0.7864 (tmm) REVERT: A 581 GLU cc_start: 0.8203 (tp30) cc_final: 0.7900 (tp30) REVERT: A 588 LYS cc_start: 0.8350 (tppt) cc_final: 0.8124 (ttmm) REVERT: A 634 SER cc_start: 0.8817 (m) cc_final: 0.8551 (t) REVERT: A 697 MET cc_start: 0.6377 (mmm) cc_final: 0.5635 (mmm) REVERT: A 815 LYS cc_start: 0.8983 (tttt) cc_final: 0.8709 (tppt) REVERT: A 820 LYS cc_start: 0.8115 (mmmt) cc_final: 0.7860 (mmmt) REVERT: A 841 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8457 (ttmm) REVERT: A 853 ILE cc_start: 0.8663 (tp) cc_final: 0.8290 (tp) REVERT: A 884 LEU cc_start: 0.8466 (mm) cc_final: 0.8185 (mt) REVERT: A 910 ARG cc_start: 0.8532 (ttp-170) cc_final: 0.7899 (ttp-170) REVERT: A 911 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8307 (mm-30) REVERT: A 931 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7851 (mm-30) REVERT: A 942 MET cc_start: 0.8629 (tpp) cc_final: 0.8404 (tpt) REVERT: A 989 VAL cc_start: 0.7599 (t) cc_final: 0.7353 (t) REVERT: A 994 GLU cc_start: 0.7865 (pm20) cc_final: 0.7460 (pm20) REVERT: A 1006 VAL cc_start: 0.8390 (m) cc_final: 0.8139 (t) REVERT: A 1044 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7360 (mt-10) REVERT: A 1060 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7440 (mm-30) REVERT: A 1072 ASP cc_start: 0.7765 (m-30) cc_final: 0.7494 (m-30) REVERT: A 1080 PHE cc_start: 0.7961 (m-80) cc_final: 0.7624 (m-80) REVERT: A 1087 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7219 (tp30) REVERT: A 1104 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.6988 (tmt) REVERT: A 1139 ASP cc_start: 0.7652 (m-30) cc_final: 0.7327 (m-30) REVERT: A 1173 LYS cc_start: 0.7705 (pttp) cc_final: 0.7328 (pptt) REVERT: A 1190 ARG cc_start: 0.8010 (mmm-85) cc_final: 0.7604 (mmm-85) REVERT: A 1199 LEU cc_start: 0.7865 (tp) cc_final: 0.7491 (tt) REVERT: B 116 VAL cc_start: 0.8545 (t) cc_final: 0.8227 (m) REVERT: B 134 ASP cc_start: 0.7994 (t0) cc_final: 0.7659 (t70) REVERT: B 149 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7522 (tm-30) REVERT: B 155 ASP cc_start: 0.8126 (t0) cc_final: 0.7690 (t0) REVERT: B 199 MET cc_start: 0.8684 (mmm) cc_final: 0.8456 (tpp) REVERT: B 205 MET cc_start: 0.8350 (mmp) cc_final: 0.7892 (mmp) REVERT: B 265 VAL cc_start: 0.8676 (t) cc_final: 0.8375 (p) REVERT: B 337 GLU cc_start: 0.7909 (tp30) cc_final: 0.7509 (tp30) REVERT: B 375 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8459 (mtmm) REVERT: B 407 SER cc_start: 0.8748 (t) cc_final: 0.8483 (p) REVERT: B 419 TRP cc_start: 0.8091 (p-90) cc_final: 0.7852 (p-90) REVERT: B 487 SER cc_start: 0.8469 (t) cc_final: 0.8220 (p) REVERT: B 511 MET cc_start: 0.8838 (tmm) cc_final: 0.8419 (ttp) REVERT: B 554 GLU cc_start: 0.8142 (tp30) cc_final: 0.7761 (tp30) REVERT: B 579 MET cc_start: 0.8389 (tpp) cc_final: 0.8176 (mmm) REVERT: B 581 GLU cc_start: 0.8258 (tp30) cc_final: 0.7956 (tp30) REVERT: B 584 LEU cc_start: 0.8745 (mm) cc_final: 0.8498 (mm) REVERT: B 588 LYS cc_start: 0.8524 (tppt) cc_final: 0.8276 (tttm) REVERT: B 598 PHE cc_start: 0.8842 (t80) cc_final: 0.8420 (t80) REVERT: B 644 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8203 (mp) REVERT: B 647 LYS cc_start: 0.8633 (mmtm) cc_final: 0.8162 (mtmm) REVERT: B 697 MET cc_start: 0.5741 (mmm) cc_final: 0.5097 (mmm) REVERT: B 736 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8019 (t0) REVERT: B 815 LYS cc_start: 0.9007 (tttt) cc_final: 0.8648 (tttm) REVERT: B 820 LYS cc_start: 0.8171 (mmmt) cc_final: 0.7935 (mmmt) REVERT: B 852 LYS cc_start: 0.8535 (mttp) cc_final: 0.8044 (mtpt) REVERT: B 853 ILE cc_start: 0.8938 (tp) cc_final: 0.8663 (tt) REVERT: B 856 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7873 (ttp80) REVERT: B 859 ASP cc_start: 0.7945 (p0) cc_final: 0.7649 (p0) REVERT: B 877 GLN cc_start: 0.8612 (tt0) cc_final: 0.8242 (tt0) REVERT: B 910 ARG cc_start: 0.8627 (ttp-170) cc_final: 0.8391 (ttm110) REVERT: B 942 MET cc_start: 0.8505 (tpp) cc_final: 0.8288 (tpp) REVERT: B 954 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7719 (mm-30) REVERT: B 958 LYS cc_start: 0.8878 (ttpt) cc_final: 0.8398 (ttmm) REVERT: B 968 LYS cc_start: 0.8652 (mtpp) cc_final: 0.8299 (mmmm) REVERT: B 969 LEU cc_start: 0.8981 (tp) cc_final: 0.8711 (tt) REVERT: B 970 ILE cc_start: 0.8645 (mt) cc_final: 0.8398 (tt) REVERT: B 993 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.6817 (m-30) REVERT: B 994 GLU cc_start: 0.7890 (pm20) cc_final: 0.7438 (pm20) REVERT: B 1005 LEU cc_start: 0.8423 (tp) cc_final: 0.8189 (tt) REVERT: B 1033 GLU cc_start: 0.7751 (tp30) cc_final: 0.7487 (tp30) REVERT: B 1035 TYR cc_start: 0.8154 (m-80) cc_final: 0.7709 (m-80) REVERT: B 1053 ARG cc_start: 0.7741 (mtt-85) cc_final: 0.7481 (mtt90) REVERT: B 1118 LYS cc_start: 0.8594 (mtpp) cc_final: 0.8315 (mtmm) REVERT: B 1136 PHE cc_start: 0.6802 (t80) cc_final: 0.6549 (t80) REVERT: B 1162 ARG cc_start: 0.5739 (OUTLIER) cc_final: 0.5092 (tpm-80) REVERT: B 1212 ILE cc_start: 0.5426 (OUTLIER) cc_final: 0.4982 (mp) outliers start: 73 outliers final: 59 residues processed: 543 average time/residue: 0.3171 time to fit residues: 247.1424 Evaluate side-chains 572 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 503 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 419 TRP 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 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 915 GLU 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 1087 GLU 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 B residue 137 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 196 SER 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 355 MET Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 563 LYS Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 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 Chi-restraints excluded: chain B residue 1222 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 152 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 165 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 145 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 614 HIS B1220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.143393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.120125 restraints weight = 25113.583| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.06 r_work: 0.3405 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16740 Z= 0.213 Angle : 0.663 16.343 22706 Z= 0.328 Chirality : 0.042 0.171 2734 Planarity : 0.005 0.061 2796 Dihedral : 6.892 134.399 2272 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.85 % Allowed : 23.55 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.19), residues: 2050 helix: 2.03 (0.14), residues: 1460 sheet: -1.88 (0.54), residues: 96 loop : -1.63 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1112 HIS 0.004 0.001 HIS B 981 PHE 0.022 0.001 PHE A1136 TYR 0.012 0.001 TYR A1009 ARG 0.008 0.000 ARG A 609 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5071.35 seconds wall clock time: 89 minutes 46.39 seconds (5386.39 seconds total)