Starting phenix.real_space_refine on Sun Mar 17 12:46:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2y_13784/03_2024/7q2y_13784_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2y_13784/03_2024/7q2y_13784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2y_13784/03_2024/7q2y_13784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2y_13784/03_2024/7q2y_13784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2y_13784/03_2024/7q2y_13784_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2y_13784/03_2024/7q2y_13784_updated.pdb" } resolution = 3.0 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= 0.006 sd= 0.055 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: 8 Type Number sf(0) Gaussians P 60 5.49 5 Mg 2 5.21 5 S 91 5.16 5 Be 2 3.05 5 C 11115 2.51 5 N 2975 2.21 5 O 3503 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1327": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17754 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3413 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 12, 'TRANS': 418} Chain breaks: 1 Chain: "B" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3102 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 375} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2251 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 279} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 7776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7776 Classifications: {'peptide': 976} Link IDs: {'PTRANS': 24, 'TRANS': 951} Chain breaks: 10 Chain: "F" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 588 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "G" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 560 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.31, per 1000 atoms: 0.52 Number of scatterers: 17754 At special positions: 0 Unit cell: (118.77, 145.52, 163.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 91 16.00 P 60 15.00 Mg 2 11.99 F 6 9.00 O 3503 8.00 N 2975 7.00 C 11115 6.00 Be 2 4.00 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: 6.99 Conformation dependent library (CDL) restraints added in 2.8 seconds 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3976 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 8 sheets defined 60.7% alpha, 6.8% beta 26 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 7.56 Creating SS restraints... Processing helix chain 'A' and resid 38 through 49 removed outlier: 3.587A pdb=" N LEU A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 158 through 166 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 175 through 201 removed outlier: 3.675A pdb=" N LYS A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 227 removed outlier: 3.650A pdb=" N MET A 216 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 977 Processing helix chain 'A' and resid 986 through 1047 removed outlier: 3.966A pdb=" N GLU A1027 " --> pdb=" O GLU A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1086 through 1103 Processing helix chain 'A' and resid 1120 through 1132 Processing helix chain 'A' and resid 1146 through 1149 No H-bonds generated for 'chain 'A' and resid 1146 through 1149' Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 206 through 209 Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 279 through 289 Processing helix chain 'B' and resid 323 through 331 Processing helix chain 'B' and resid 333 through 349 Proline residue: B 338 - end of helix removed outlier: 3.805A pdb=" N ASN B 349 " --> pdb=" O GLN B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1247 through 1286 Processing helix chain 'B' and resid 1301 through 1304 No H-bonds generated for 'chain 'B' and resid 1301 through 1304' Processing helix chain 'B' and resid 1325 through 1342 Processing helix chain 'B' and resid 1359 through 1371 Processing helix chain 'B' and resid 1385 through 1389 Processing helix chain 'C' and resid 23 through 39 Processing helix chain 'C' and resid 54 through 58 Processing helix chain 'C' and resid 72 through 104 Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 276 through 287 Processing helix chain 'C' and resid 300 through 311 removed outlier: 4.004A pdb=" N GLU C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 322 removed outlier: 3.723A pdb=" N GLU C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 667 Processing helix chain 'C' and resid 692 through 701 removed outlier: 3.553A pdb=" N LYS C 701 " --> pdb=" O GLN C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 710 removed outlier: 3.506A pdb=" N ASP C 710 " --> pdb=" O ASP C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 726 Processing helix chain 'D' and resid 7 through 15 Processing helix chain 'D' and resid 27 through 38 Processing helix chain 'D' and resid 51 through 61 removed outlier: 3.889A pdb=" N ASP D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 91 removed outlier: 3.645A pdb=" N THR D 71 " --> pdb=" O PRO D 67 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 130 removed outlier: 4.909A pdb=" N GLU D 129 " --> pdb=" O PHE D 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 130 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 175 Processing helix chain 'D' and resid 186 through 204 Proline residue: D 199 - end of helix Processing helix chain 'D' and resid 207 through 211 Processing helix chain 'D' and resid 213 through 229 Processing helix chain 'D' and resid 233 through 246 Processing helix chain 'D' and resid 251 through 265 Processing helix chain 'D' and resid 269 through 280 Processing helix chain 'D' and resid 289 through 304 Processing helix chain 'D' and resid 306 through 321 removed outlier: 3.792A pdb=" N ARG D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN D 312 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR D 318 " --> pdb=" O ASN D 314 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU D 320 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASN D 321 " --> pdb=" O ILE D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 342 Processing helix chain 'D' and resid 346 through 367 removed outlier: 7.052A pdb=" N GLN D 354 " --> pdb=" O GLU D 350 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLN D 355 " --> pdb=" O HIS D 351 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 387 Processing helix chain 'D' and resid 393 through 408 removed outlier: 5.180A pdb=" N GLN D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 427 Processing helix chain 'D' and resid 441 through 454 Processing helix chain 'D' and resid 518 through 550 Processing helix chain 'D' and resid 556 through 571 Processing helix chain 'D' and resid 577 through 587 Processing helix chain 'D' and resid 600 through 612 Processing helix chain 'D' and resid 621 through 637 Processing helix chain 'D' and resid 641 through 657 removed outlier: 3.611A pdb=" N GLN D 649 " --> pdb=" O ALA D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 675 removed outlier: 4.030A pdb=" N ALA D 675 " --> pdb=" O ILE D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 713 Processing helix chain 'D' and resid 716 through 719 No H-bonds generated for 'chain 'D' and resid 716 through 719' Processing helix chain 'D' and resid 722 through 728 Processing helix chain 'D' and resid 732 through 736 Processing helix chain 'D' and resid 738 through 751 Processing helix chain 'D' and resid 765 through 780 Processing helix chain 'D' and resid 786 through 802 removed outlier: 3.636A pdb=" N TYR D 789 " --> pdb=" O ASN D 786 " (cutoff:3.500A) Proline residue: D 790 - end of helix removed outlier: 4.027A pdb=" N GLU D 793 " --> pdb=" O PRO D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 806 through 820 Processing helix chain 'D' and resid 839 through 873 Processing helix chain 'D' and resid 910 through 927 removed outlier: 5.094A pdb=" N LEU D 925 " --> pdb=" O LYS D 921 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU D 926 " --> pdb=" O GLU D 922 " (cutoff:3.500A) Processing helix chain 'D' and resid 934 through 945 Proline residue: D 938 - end of helix Processing helix chain 'D' and resid 947 through 950 No H-bonds generated for 'chain 'D' and resid 947 through 950' Processing helix chain 'D' and resid 953 through 967 Processing helix chain 'D' and resid 971 through 987 Proline residue: D 979 - end of helix Processing helix chain 'D' and resid 991 through 1006 Processing helix chain 'D' and resid 1009 through 1011 No H-bonds generated for 'chain 'D' and resid 1009 through 1011' Processing helix chain 'D' and resid 1015 through 1023 Processing helix chain 'D' and resid 1028 through 1044 Processing helix chain 'D' and resid 1053 through 1061 removed outlier: 4.087A pdb=" N LYS D1058 " --> pdb=" O GLY D1054 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N CYS D1059 " --> pdb=" O GLU D1055 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU D1060 " --> pdb=" O MET D1056 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASP D1061 " --> pdb=" O ALA D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1068 through 1077 Processing helix chain 'D' and resid 1084 through 1099 removed outlier: 4.645A pdb=" N ILE D1090 " --> pdb=" O TYR D1086 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASP D1091 " --> pdb=" O ASN D1087 " (cutoff:3.500A) Processing helix chain 'D' and resid 1104 through 1117 removed outlier: 3.681A pdb=" N PHE D1117 " --> pdb=" O PHE D1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 1121 through 1137 Processing helix chain 'D' and resid 1142 through 1153 Processing helix chain 'D' and resid 1159 through 1165 Processing sheet with id= A, first strand: chain 'A' and resid 18 through 20 removed outlier: 3.688A pdb=" N GLU A 5 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR A 115 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1165 through 1169 Processing sheet with id= C, first strand: chain 'A' and resid 1051 through 1056 removed outlier: 4.775A pdb=" N VAL A1071 " --> pdb=" O LYS A1078 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 170 through 173 removed outlier: 6.893A pdb=" N HIS B 235 " --> pdb=" O ASN B 157 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU B 159 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA B 233 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU B 161 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER B 231 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR B 270 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 1403 through 1410 removed outlier: 3.809A pdb=" N GLN B1393 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE B1378 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL B 183 " --> pdb=" O PHE B1378 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL B1380 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N GLY B 185 " --> pdb=" O VAL B1380 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 239 through 241 Processing sheet with id= G, first strand: chain 'B' and resid 1290 through 1295 Processing sheet with id= H, first strand: chain 'C' and resid 730 through 733 958 hydrogen bonds defined for protein. 2718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 6.56 Time building geometry restraints manager: 7.59 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: 5063 1.34 - 1.45: 2699 1.45 - 1.57: 10090 1.57 - 1.69: 116 1.69 - 1.81: 153 Bond restraints: 18121 Sorted by residual: bond pdb=" BE BEF A2002 " pdb=" F2 BEF A2002 " ideal model delta sigma weight residual 1.476 1.559 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" BE BEF B2002 " pdb=" F2 BEF B2002 " ideal model delta sigma weight residual 1.476 1.559 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" BE BEF B2002 " pdb=" F3 BEF B2002 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" BE BEF A2002 " pdb=" F3 BEF A2002 " ideal model delta sigma weight residual 1.476 1.545 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" N LEU D 179 " pdb=" CA LEU D 179 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.15e-02 7.56e+03 8.99e+00 ... (remaining 18116 not shown) Histogram of bond angle deviations from ideal: 97.63 - 105.33: 431 105.33 - 113.03: 10174 113.03 - 120.72: 8530 120.72 - 128.42: 5378 128.42 - 136.12: 126 Bond angle restraints: 24639 Sorted by residual: angle pdb=" N GLU D 364 " pdb=" CA GLU D 364 " pdb=" CB GLU D 364 " ideal model delta sigma weight residual 110.16 116.53 -6.37 1.48e+00 4.57e-01 1.85e+01 angle pdb=" N GLU D 114 " pdb=" CA GLU D 114 " pdb=" CB GLU D 114 " ideal model delta sigma weight residual 110.12 116.21 -6.09 1.47e+00 4.63e-01 1.72e+01 angle pdb=" F2 BEF B2002 " pdb=" BE BEF B2002 " pdb=" F3 BEF B2002 " ideal model delta sigma weight residual 119.96 107.55 12.41 3.00e+00 1.11e-01 1.71e+01 angle pdb=" F2 BEF A2002 " pdb=" BE BEF A2002 " pdb=" F3 BEF A2002 " ideal model delta sigma weight residual 119.96 107.65 12.31 3.00e+00 1.11e-01 1.68e+01 angle pdb=" C LYS D1058 " pdb=" N CYS D1059 " pdb=" CA CYS D1059 " ideal model delta sigma weight residual 122.56 115.88 6.68 1.72e+00 3.38e-01 1.51e+01 ... (remaining 24634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 10672 35.30 - 70.61: 350 70.61 - 105.91: 17 105.91 - 141.22: 3 141.22 - 176.52: 2 Dihedral angle restraints: 11044 sinusoidal: 4963 harmonic: 6081 Sorted by residual: dihedral pdb=" CD ARG A 215 " pdb=" NE ARG A 215 " pdb=" CZ ARG A 215 " pdb=" NH1 ARG A 215 " ideal model delta sinusoidal sigma weight residual 0.00 -75.53 75.53 1 1.00e+01 1.00e-02 7.20e+01 dihedral pdb=" O1B ADP B2001 " pdb=" O3A ADP B2001 " pdb=" PB ADP B2001 " pdb=" PA ADP B2001 " ideal model delta sinusoidal sigma weight residual -60.00 75.18 -135.18 1 2.00e+01 2.50e-03 4.10e+01 dihedral pdb=" C5' ADP B2001 " pdb=" O5' ADP B2001 " pdb=" PA ADP B2001 " pdb=" O2A ADP B2001 " ideal model delta sinusoidal sigma weight residual 300.00 175.18 124.83 1 2.00e+01 2.50e-03 3.77e+01 ... (remaining 11041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2218 0.042 - 0.085: 494 0.085 - 0.127: 145 0.127 - 0.170: 13 0.170 - 0.212: 3 Chirality restraints: 2873 Sorted by residual: chirality pdb=" CA GLU A 219 " pdb=" N GLU A 219 " pdb=" C GLU A 219 " pdb=" CB GLU A 219 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ARG A 215 " pdb=" N ARG A 215 " pdb=" C ARG A 215 " pdb=" CB ARG A 215 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB THR D1076 " pdb=" CA THR D1076 " pdb=" OG1 THR D1076 " pdb=" CG2 THR D1076 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.21e-01 ... (remaining 2870 not shown) Planarity restraints: 2905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 215 " -1.058 9.50e-02 1.11e+02 4.74e-01 1.36e+02 pdb=" NE ARG A 215 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 215 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 215 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 215 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D1072 " 0.472 9.50e-02 1.11e+02 2.12e-01 2.74e+01 pdb=" NE ARG D1072 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG D1072 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D1072 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D1072 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 697 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.83e+00 pdb=" C LYS D 697 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS D 697 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU D 698 " 0.016 2.00e-02 2.50e+03 ... (remaining 2902 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 177 2.62 - 3.19: 15970 3.19 - 3.76: 28335 3.76 - 4.33: 37666 4.33 - 4.90: 61681 Nonbonded interactions: 143829 Sorted by model distance: nonbonded pdb=" F3 BEF B2002 " pdb="MG MG B2003 " model vdw 2.047 2.120 nonbonded pdb=" O2B ADP A2001 " pdb="MG MG A2003 " model vdw 2.049 2.170 nonbonded pdb=" OE1 GLN A 147 " pdb="MG MG A2003 " model vdw 2.084 2.170 nonbonded pdb=" OG SER A 39 " pdb="MG MG A2003 " model vdw 2.100 2.170 nonbonded pdb=" O1B ADP B2001 " pdb="MG MG B2003 " model vdw 2.122 2.170 ... (remaining 143824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.970 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 51.020 Find NCS groups from input model: 0.420 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:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 18121 Z= 0.176 Angle : 0.613 12.413 24639 Z= 0.343 Chirality : 0.040 0.212 2873 Planarity : 0.010 0.474 2905 Dihedral : 16.399 176.524 7068 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.64 % Favored : 96.31 % Rotamer: Outliers : 0.42 % Allowed : 0.85 % Favored : 98.73 % 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: 2.39 (0.19), residues: 2032 helix: 2.63 (0.15), residues: 1286 sheet: 1.51 (0.40), residues: 175 loop : -0.97 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D1144 HIS 0.002 0.000 HIS D 435 PHE 0.022 0.001 PHE A1149 TYR 0.014 0.001 TYR B 326 ARG 0.010 0.001 ARG D 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 521 time to evaluate : 1.945 Fit side-chains REVERT: A 17 ARG cc_start: 0.8213 (ttt-90) cc_final: 0.7890 (ttt180) REVERT: A 62 LEU cc_start: 0.8573 (mt) cc_final: 0.8372 (mt) REVERT: A 90 ASN cc_start: 0.6826 (t0) cc_final: 0.6574 (t0) REVERT: A 155 ASN cc_start: 0.7897 (m110) cc_final: 0.7637 (m-40) REVERT: A 212 ASN cc_start: 0.7450 (m-40) cc_final: 0.7243 (m-40) REVERT: A 1075 ASN cc_start: 0.7744 (m110) cc_final: 0.7536 (m-40) REVERT: B 170 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7756 (ttmm) REVERT: B 208 LYS cc_start: 0.8215 (mmmm) cc_final: 0.7969 (mmmm) REVERT: B 215 SER cc_start: 0.7359 (t) cc_final: 0.7002 (p) REVERT: B 216 ASP cc_start: 0.6752 (m-30) cc_final: 0.6523 (m-30) REVERT: B 276 GLU cc_start: 0.7489 (tp30) cc_final: 0.7197 (mm-30) REVERT: B 1271 PHE cc_start: 0.7754 (t80) cc_final: 0.7371 (t80) REVERT: B 1281 MET cc_start: 0.8207 (tpp) cc_final: 0.7958 (tpp) REVERT: B 1292 GLU cc_start: 0.5937 (tt0) cc_final: 0.5664 (tt0) REVERT: B 1358 ASP cc_start: 0.6313 (t70) cc_final: 0.6042 (t70) REVERT: C 56 TYR cc_start: 0.8020 (m-10) cc_final: 0.7759 (m-10) REVERT: C 73 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7405 (mp10) REVERT: C 213 THR cc_start: 0.7873 (p) cc_final: 0.7604 (p) REVERT: C 664 GLU cc_start: 0.7276 (tp30) cc_final: 0.6397 (tp30) REVERT: D 62 PHE cc_start: 0.5735 (m-10) cc_final: 0.5476 (m-10) REVERT: D 120 GLN cc_start: 0.8233 (tm130) cc_final: 0.7829 (tm-30) REVERT: D 163 GLN cc_start: 0.7949 (pt0) cc_final: 0.7415 (pm20) REVERT: D 166 ASN cc_start: 0.7658 (m110) cc_final: 0.7113 (m110) REVERT: D 203 LEU cc_start: 0.7754 (tp) cc_final: 0.7483 (tm) REVERT: D 259 LYS cc_start: 0.7998 (tttm) cc_final: 0.7553 (tttp) REVERT: D 263 ASP cc_start: 0.6258 (m-30) cc_final: 0.5761 (m-30) REVERT: D 264 GLU cc_start: 0.6234 (mp0) cc_final: 0.5743 (mp0) REVERT: D 303 GLU cc_start: 0.6871 (tm-30) cc_final: 0.6505 (tm-30) REVERT: D 364 GLU cc_start: 0.6781 (mp0) cc_final: 0.6267 (mp0) REVERT: D 398 LYS cc_start: 0.7796 (tptm) cc_final: 0.7588 (tppp) REVERT: D 424 LYS cc_start: 0.7706 (ttmm) cc_final: 0.7422 (ttmm) REVERT: D 573 ASP cc_start: 0.6367 (m-30) cc_final: 0.6133 (m-30) REVERT: D 655 TYR cc_start: 0.8274 (t80) cc_final: 0.8037 (t80) REVERT: D 714 ASP cc_start: 0.6194 (m-30) cc_final: 0.5897 (m-30) REVERT: D 872 LYS cc_start: 0.7893 (tttm) cc_final: 0.7548 (tppp) REVERT: D 972 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7785 (mtpp) REVERT: D 1070 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7631 (mmt) REVERT: D 1075 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6689 (m-80) outliers start: 8 outliers final: 2 residues processed: 524 average time/residue: 1.3157 time to fit residues: 765.0597 Evaluate side-chains 474 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 469 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain D residue 1070 MET Chi-restraints excluded: chain D residue 1075 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9980 chunk 159 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 107 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 100 optimal weight: 0.0970 chunk 122 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 100 GLN A 193 GLN B 171 GLN B 193 ASN B 266 ASN B1319 ASN B1361 ASN B1385 ASN D 111 HIS ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN D1010 ASN D1065 GLN D1128 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18121 Z= 0.176 Angle : 0.541 7.548 24639 Z= 0.284 Chirality : 0.039 0.160 2873 Planarity : 0.004 0.041 2905 Dihedral : 16.898 176.709 2884 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.59 % Favored : 96.36 % Rotamer: Outliers : 2.55 % Allowed : 14.01 % Favored : 83.44 % 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: 2.45 (0.19), residues: 2032 helix: 2.63 (0.14), residues: 1288 sheet: 1.59 (0.41), residues: 175 loop : -0.83 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 108 HIS 0.005 0.001 HIS D 111 PHE 0.023 0.001 PHE B1388 TYR 0.024 0.001 TYR D 776 ARG 0.010 0.001 ARG D 871 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 481 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.8112 (p) REVERT: A 90 ASN cc_start: 0.6841 (t0) cc_final: 0.6544 (t0) REVERT: A 155 ASN cc_start: 0.8013 (m110) cc_final: 0.7767 (m-40) REVERT: A 166 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6568 (mt-10) REVERT: A 213 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6929 (mt-10) REVERT: A 228 GLU cc_start: 0.5689 (OUTLIER) cc_final: 0.5296 (mp0) REVERT: A 1027 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6648 (tm-30) REVERT: B 170 LYS cc_start: 0.8014 (ttmm) cc_final: 0.7768 (ttmm) REVERT: B 208 LYS cc_start: 0.8196 (mmmm) cc_final: 0.7980 (mmmm) REVERT: B 239 VAL cc_start: 0.8437 (p) cc_final: 0.8155 (t) REVERT: B 1271 PHE cc_start: 0.7810 (t80) cc_final: 0.7417 (t80) REVERT: B 1281 MET cc_start: 0.8246 (tpp) cc_final: 0.7947 (tpp) REVERT: B 1358 ASP cc_start: 0.6361 (t70) cc_final: 0.6134 (t70) REVERT: B 1360 ARG cc_start: 0.7347 (mtp-110) cc_final: 0.6970 (mtp180) REVERT: C 56 TYR cc_start: 0.8051 (m-10) cc_final: 0.7791 (m-10) REVERT: C 63 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6637 (pp) REVERT: C 73 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7463 (mp10) REVERT: C 664 GLU cc_start: 0.7253 (tp30) cc_final: 0.7018 (tp30) REVERT: D 62 PHE cc_start: 0.5806 (m-10) cc_final: 0.5581 (m-10) REVERT: D 120 GLN cc_start: 0.8249 (tm130) cc_final: 0.7877 (tm-30) REVERT: D 163 GLN cc_start: 0.7994 (pt0) cc_final: 0.7507 (pt0) REVERT: D 166 ASN cc_start: 0.7734 (m110) cc_final: 0.7320 (m110) REVERT: D 203 LEU cc_start: 0.7938 (tp) cc_final: 0.7703 (tm) REVERT: D 213 SER cc_start: 0.7211 (p) cc_final: 0.6986 (m) REVERT: D 264 GLU cc_start: 0.6531 (mp0) cc_final: 0.6121 (mp0) REVERT: D 303 GLU cc_start: 0.6707 (tm-30) cc_final: 0.6415 (tm-30) REVERT: D 331 VAL cc_start: 0.8178 (t) cc_final: 0.7797 (t) REVERT: D 364 GLU cc_start: 0.6877 (mp0) cc_final: 0.6409 (mp0) REVERT: D 365 GLU cc_start: 0.6734 (tm-30) cc_final: 0.6267 (tm-30) REVERT: D 424 LYS cc_start: 0.7875 (ttmm) cc_final: 0.7603 (ttmm) REVERT: D 556 ARG cc_start: 0.7695 (tmm160) cc_final: 0.7476 (ttp-110) REVERT: D 573 ASP cc_start: 0.6618 (m-30) cc_final: 0.6390 (m-30) REVERT: D 578 GLU cc_start: 0.6617 (mm-30) cc_final: 0.6400 (mm-30) REVERT: D 787 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6737 (mm-30) REVERT: D 813 LEU cc_start: 0.7855 (tt) cc_final: 0.7608 (tp) REVERT: D 861 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8050 (mp) REVERT: D 941 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6825 (mt-10) REVERT: D 972 LYS cc_start: 0.8100 (mtpt) cc_final: 0.7805 (mtpp) REVERT: D 1025 ASP cc_start: 0.7723 (t70) cc_final: 0.7222 (m-30) REVERT: D 1075 PHE cc_start: 0.7088 (OUTLIER) cc_final: 0.6877 (m-80) outliers start: 48 outliers final: 11 residues processed: 491 average time/residue: 1.3633 time to fit residues: 741.4555 Evaluate side-chains 485 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 468 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain B residue 1354 ASP Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 1075 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 0.9990 chunk 59 optimal weight: 0.0870 chunk 158 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 206 optimal weight: 50.0000 chunk 170 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 65 optimal weight: 30.0000 chunk 153 optimal weight: 5.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 63 GLN A 100 GLN A 193 GLN B 171 GLN B 266 ASN B1375 ASN B1385 ASN B1386 ASN D 111 HIS D 120 GLN D 249 HIS ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 HIS D 845 GLN D1010 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18121 Z= 0.238 Angle : 0.555 6.555 24639 Z= 0.290 Chirality : 0.040 0.268 2873 Planarity : 0.004 0.045 2905 Dihedral : 17.061 178.429 2876 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.69 % Favored : 96.26 % Rotamer: Outliers : 3.82 % Allowed : 16.56 % Favored : 79.62 % 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: 2.26 (0.19), residues: 2032 helix: 2.49 (0.14), residues: 1281 sheet: 1.53 (0.42), residues: 170 loop : -0.86 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 108 HIS 0.009 0.001 HIS D 111 PHE 0.025 0.002 PHE B1388 TYR 0.022 0.002 TYR D 776 ARG 0.007 0.001 ARG D 871 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 504 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.8024 (t) REVERT: A 20 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7481 (mt) REVERT: A 53 SER cc_start: 0.8372 (t) cc_final: 0.7847 (p) REVERT: A 90 ASN cc_start: 0.6832 (t0) cc_final: 0.6535 (t0) REVERT: A 112 THR cc_start: 0.6473 (p) cc_final: 0.6153 (p) REVERT: A 155 ASN cc_start: 0.8109 (m110) cc_final: 0.7894 (m110) REVERT: A 166 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6758 (mt-10) REVERT: A 191 LYS cc_start: 0.7863 (ttmm) cc_final: 0.7552 (mtpp) REVERT: A 1009 LYS cc_start: 0.7706 (mttt) cc_final: 0.7462 (mtmm) REVERT: A 1027 GLU cc_start: 0.6901 (tm-30) cc_final: 0.6628 (tm-30) REVERT: A 1148 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7344 (mtm) REVERT: B 170 LYS cc_start: 0.7998 (ttmm) cc_final: 0.7753 (ttmm) REVERT: B 239 VAL cc_start: 0.8443 (p) cc_final: 0.8180 (t) REVERT: B 275 LYS cc_start: 0.7802 (pttp) cc_final: 0.7462 (pttp) REVERT: B 1254 GLU cc_start: 0.5321 (OUTLIER) cc_final: 0.4564 (mp0) REVERT: B 1271 PHE cc_start: 0.7919 (t80) cc_final: 0.7574 (t80) REVERT: B 1281 MET cc_start: 0.8294 (tpp) cc_final: 0.7968 (tpp) REVERT: B 1309 SER cc_start: 0.8313 (m) cc_final: 0.8072 (m) REVERT: B 1358 ASP cc_start: 0.6472 (t70) cc_final: 0.6232 (t70) REVERT: B 1360 ARG cc_start: 0.7477 (mtp-110) cc_final: 0.7231 (mtp180) REVERT: C 30 ASN cc_start: 0.7710 (m110) cc_final: 0.7351 (m-40) REVERT: C 63 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6669 (pp) REVERT: C 73 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7417 (mp10) REVERT: C 215 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7842 (ttt180) REVERT: C 637 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8034 (m) REVERT: C 664 GLU cc_start: 0.7332 (tp30) cc_final: 0.7067 (tp30) REVERT: D 62 PHE cc_start: 0.5934 (m-10) cc_final: 0.5690 (m-10) REVERT: D 120 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7597 (tm130) REVERT: D 163 GLN cc_start: 0.8062 (pt0) cc_final: 0.7526 (pt0) REVERT: D 166 ASN cc_start: 0.7770 (m110) cc_final: 0.7387 (m110) REVERT: D 190 ASP cc_start: 0.7308 (t0) cc_final: 0.7053 (t0) REVERT: D 264 GLU cc_start: 0.6782 (mp0) cc_final: 0.6355 (mp0) REVERT: D 313 MET cc_start: 0.8110 (tpt) cc_final: 0.7886 (mmt) REVERT: D 317 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8426 (OUTLIER) REVERT: D 324 SER cc_start: 0.8533 (t) cc_final: 0.8032 (p) REVERT: D 364 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6688 (mp0) REVERT: D 365 GLU cc_start: 0.6810 (tm-30) cc_final: 0.6305 (tm-30) REVERT: D 424 LYS cc_start: 0.8038 (ttmm) cc_final: 0.7770 (ttmm) REVERT: D 590 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.7060 (mmm) REVERT: D 610 GLN cc_start: 0.7059 (mm110) cc_final: 0.6790 (mm110) REVERT: D 657 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7392 (mp10) REVERT: D 787 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6708 (mm-30) REVERT: D 918 GLN cc_start: 0.6775 (tp-100) cc_final: 0.6388 (tp-100) REVERT: D 941 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6880 (mt-10) REVERT: D 972 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7886 (mtpp) REVERT: D 982 ILE cc_start: 0.8282 (mm) cc_final: 0.7971 (mp) REVERT: D 1022 ARG cc_start: 0.7780 (tpp-160) cc_final: 0.7504 (tpm170) REVERT: D 1025 ASP cc_start: 0.7932 (t70) cc_final: 0.7291 (m-30) REVERT: D 1075 PHE cc_start: 0.7176 (OUTLIER) cc_final: 0.6856 (m-80) REVERT: D 1130 LYS cc_start: 0.7915 (mmtm) cc_final: 0.7640 (mtpp) outliers start: 72 outliers final: 20 residues processed: 526 average time/residue: 1.3886 time to fit residues: 808.2404 Evaluate side-chains 511 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 481 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 1254 GLU Chi-restraints excluded: chain B residue 1410 LYS Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 701 LYS Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 429 HIS Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 590 MET Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 1075 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 191 optimal weight: 7.9990 chunk 202 optimal weight: 20.0000 chunk 100 optimal weight: 0.6980 chunk 181 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 193 GLN A1075 ASN B 171 GLN B 266 ASN B1272 ASN B1290 ASN B1375 ASN B1385 ASN C 321 ASN D 111 HIS ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 HIS D 634 ASN D 845 GLN D1010 ASN D1087 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18121 Z= 0.258 Angle : 0.573 10.042 24639 Z= 0.297 Chirality : 0.040 0.167 2873 Planarity : 0.003 0.034 2905 Dihedral : 17.151 177.626 2876 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.03 % Allowed : 18.68 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.11 (0.19), residues: 2032 helix: 2.41 (0.14), residues: 1272 sheet: 1.39 (0.41), residues: 170 loop : -0.95 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 49 HIS 0.021 0.002 HIS D 429 PHE 0.025 0.002 PHE C 170 TYR 0.022 0.002 TYR B 326 ARG 0.012 0.001 ARG B1400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 502 time to evaluate : 1.781 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.6738 (pt0) cc_final: 0.6519 (pt0) REVERT: A 20 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7556 (mt) REVERT: A 53 SER cc_start: 0.8480 (t) cc_final: 0.7940 (p) REVERT: A 90 ASN cc_start: 0.6838 (t0) cc_final: 0.6534 (t0) REVERT: A 100 GLN cc_start: 0.7076 (tp-100) cc_final: 0.6384 (tp40) REVERT: A 155 ASN cc_start: 0.8160 (m110) cc_final: 0.7955 (m110) REVERT: A 166 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6748 (mt-10) REVERT: A 1009 LYS cc_start: 0.7714 (mttt) cc_final: 0.7487 (mtmm) REVERT: A 1027 GLU cc_start: 0.6846 (tm-30) cc_final: 0.6564 (tm-30) REVERT: A 1042 ASN cc_start: 0.8261 (m-40) cc_final: 0.8010 (m-40) REVERT: A 1113 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7101 (mm-30) REVERT: A 1148 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7313 (mtm) REVERT: B 170 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7761 (ttmm) REVERT: B 1254 GLU cc_start: 0.5332 (OUTLIER) cc_final: 0.4615 (mp0) REVERT: B 1271 PHE cc_start: 0.7953 (t80) cc_final: 0.7332 (t80) REVERT: B 1275 SER cc_start: 0.8104 (OUTLIER) cc_final: 0.7599 (m) REVERT: B 1281 MET cc_start: 0.8332 (tpp) cc_final: 0.7991 (tpp) REVERT: B 1309 SER cc_start: 0.8332 (m) cc_final: 0.8075 (m) REVERT: B 1360 ARG cc_start: 0.7509 (mtp-110) cc_final: 0.7300 (mtp180) REVERT: C 30 ASN cc_start: 0.7769 (m-40) cc_final: 0.7426 (m-40) REVERT: C 73 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.7387 (mp-120) REVERT: C 87 SER cc_start: 0.7776 (m) cc_final: 0.7526 (p) REVERT: C 637 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8122 (m) REVERT: C 664 GLU cc_start: 0.7330 (tp30) cc_final: 0.7043 (tp30) REVERT: D 62 PHE cc_start: 0.6000 (m-10) cc_final: 0.5743 (m-10) REVERT: D 120 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7571 (tm130) REVERT: D 163 GLN cc_start: 0.7973 (pt0) cc_final: 0.7623 (pt0) REVERT: D 166 ASN cc_start: 0.7836 (m110) cc_final: 0.7451 (m110) REVERT: D 190 ASP cc_start: 0.7326 (t0) cc_final: 0.7123 (t0) REVERT: D 195 LEU cc_start: 0.7595 (mt) cc_final: 0.7374 (mt) REVERT: D 202 VAL cc_start: 0.8842 (t) cc_final: 0.8581 (t) REVERT: D 264 GLU cc_start: 0.6841 (mp0) cc_final: 0.6466 (mp0) REVERT: D 281 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.6814 (ttm110) REVERT: D 313 MET cc_start: 0.8243 (tpt) cc_final: 0.7973 (mmt) REVERT: D 324 SER cc_start: 0.8545 (t) cc_final: 0.8121 (p) REVERT: D 331 VAL cc_start: 0.8118 (t) cc_final: 0.7650 (p) REVERT: D 362 LEU cc_start: 0.8248 (tm) cc_final: 0.8046 (tp) REVERT: D 364 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6718 (mt-10) REVERT: D 365 GLU cc_start: 0.6748 (tm-30) cc_final: 0.6239 (tm-30) REVERT: D 424 LYS cc_start: 0.8016 (ttmm) cc_final: 0.7737 (ttmm) REVERT: D 637 ILE cc_start: 0.8286 (pt) cc_final: 0.7941 (mt) REVERT: D 750 ARG cc_start: 0.7470 (mtt180) cc_final: 0.7215 (mtt180) REVERT: D 769 ASP cc_start: 0.6515 (p0) cc_final: 0.6284 (p0) REVERT: D 787 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6730 (mm-30) REVERT: D 918 GLN cc_start: 0.7059 (tp-100) cc_final: 0.6708 (tp-100) REVERT: D 941 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6900 (mt-10) REVERT: D 972 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7909 (mtpp) REVERT: D 982 ILE cc_start: 0.8328 (mm) cc_final: 0.7971 (mp) REVERT: D 1022 ARG cc_start: 0.7802 (tpp-160) cc_final: 0.7471 (tpm170) REVERT: D 1025 ASP cc_start: 0.7979 (t70) cc_final: 0.7297 (m-30) REVERT: D 1075 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.6941 (m-80) REVERT: D 1089 PHE cc_start: 0.7629 (t80) cc_final: 0.7414 (t80) REVERT: D 1130 LYS cc_start: 0.7935 (mmtm) cc_final: 0.7634 (mtpp) outliers start: 76 outliers final: 32 residues processed: 533 average time/residue: 1.4118 time to fit residues: 832.1002 Evaluate side-chains 516 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 476 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1115 ASP Chi-restraints excluded: chain A residue 1133 ARG Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 1254 GLU Chi-restraints excluded: chain B residue 1275 SER Chi-restraints excluded: chain B residue 1390 LEU Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 281 ARG Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 321 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 1075 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 2 optimal weight: 0.2980 chunk 151 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 173 optimal weight: 0.0030 chunk 140 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 overall best weight: 2.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 193 GLN A1075 ASN B 171 GLN B 265 ASN B1290 ASN B1375 ASN B1385 ASN D 111 HIS ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 555 ASN D 845 GLN D1010 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18121 Z= 0.289 Angle : 0.591 8.928 24639 Z= 0.307 Chirality : 0.042 0.274 2873 Planarity : 0.004 0.035 2905 Dihedral : 17.188 174.496 2876 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.88 % Allowed : 19.11 % Favored : 76.01 % 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: 1.95 (0.19), residues: 2032 helix: 2.25 (0.14), residues: 1275 sheet: 1.33 (0.41), residues: 169 loop : -0.95 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 49 HIS 0.009 0.001 HIS D 111 PHE 0.025 0.002 PHE C 170 TYR 0.025 0.002 TYR B 326 ARG 0.009 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 496 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.6764 (pt0) cc_final: 0.6453 (pt0) REVERT: A 20 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7696 (mt) REVERT: A 53 SER cc_start: 0.8494 (t) cc_final: 0.8067 (p) REVERT: A 90 ASN cc_start: 0.6850 (t0) cc_final: 0.6552 (t0) REVERT: A 100 GLN cc_start: 0.7165 (tp-100) cc_final: 0.6314 (tp40) REVERT: A 159 SER cc_start: 0.8277 (OUTLIER) cc_final: 0.8063 (p) REVERT: A 166 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6835 (mt-10) REVERT: A 177 ARG cc_start: 0.7558 (ttm-80) cc_final: 0.7305 (tpm170) REVERT: A 187 LYS cc_start: 0.8031 (ttmm) cc_final: 0.7768 (ttmm) REVERT: A 989 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.6406 (ttm) REVERT: A 1009 LYS cc_start: 0.7753 (mttt) cc_final: 0.7529 (mtmm) REVERT: A 1027 GLU cc_start: 0.6797 (tm-30) cc_final: 0.6523 (tm-30) REVERT: A 1042 ASN cc_start: 0.8419 (m-40) cc_final: 0.8183 (m-40) REVERT: B 170 LYS cc_start: 0.8038 (ttmm) cc_final: 0.7678 (ttpp) REVERT: B 179 SER cc_start: 0.8127 (p) cc_final: 0.7922 (m) REVERT: B 284 LYS cc_start: 0.7859 (ttmt) cc_final: 0.7615 (ttmm) REVERT: B 1254 GLU cc_start: 0.5381 (OUTLIER) cc_final: 0.4681 (mp0) REVERT: B 1281 MET cc_start: 0.8333 (tpp) cc_final: 0.8005 (tpp) REVERT: B 1287 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7484 (mtp) REVERT: C 30 ASN cc_start: 0.7841 (m-40) cc_final: 0.7550 (m-40) REVERT: C 87 SER cc_start: 0.7881 (m) cc_final: 0.7643 (p) REVERT: C 637 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8166 (m) REVERT: C 664 GLU cc_start: 0.7300 (tp30) cc_final: 0.7020 (tp30) REVERT: D 62 PHE cc_start: 0.6018 (m-10) cc_final: 0.5715 (m-10) REVERT: D 120 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7581 (tm130) REVERT: D 165 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6398 (mp0) REVERT: D 166 ASN cc_start: 0.7874 (m110) cc_final: 0.7489 (m110) REVERT: D 190 ASP cc_start: 0.7510 (t0) cc_final: 0.7302 (t0) REVERT: D 226 CYS cc_start: 0.7662 (m) cc_final: 0.7435 (m) REVERT: D 264 GLU cc_start: 0.6822 (mp0) cc_final: 0.6453 (mp0) REVERT: D 281 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.6897 (ttm110) REVERT: D 324 SER cc_start: 0.8542 (t) cc_final: 0.8151 (p) REVERT: D 364 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6751 (mt-10) REVERT: D 365 GLU cc_start: 0.6772 (tm-30) cc_final: 0.6202 (tm-30) REVERT: D 380 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7289 (mt0) REVERT: D 424 LYS cc_start: 0.8096 (ttmm) cc_final: 0.7860 (tppp) REVERT: D 602 VAL cc_start: 0.7914 (m) cc_final: 0.7690 (p) REVERT: D 637 ILE cc_start: 0.8267 (pt) cc_final: 0.8066 (mt) REVERT: D 648 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6696 (tt0) REVERT: D 657 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7355 (mp10) REVERT: D 750 ARG cc_start: 0.7579 (mtt180) cc_final: 0.7109 (mtt180) REVERT: D 787 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6726 (mm-30) REVERT: D 918 GLN cc_start: 0.7109 (tp-100) cc_final: 0.6838 (tp-100) REVERT: D 941 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6929 (mt-10) REVERT: D 972 LYS cc_start: 0.8252 (mtpt) cc_final: 0.7991 (mtpp) REVERT: D 982 ILE cc_start: 0.8351 (mm) cc_final: 0.7995 (mp) REVERT: D 1022 ARG cc_start: 0.7845 (tpp-160) cc_final: 0.7551 (tpm170) REVERT: D 1025 ASP cc_start: 0.7989 (t70) cc_final: 0.7321 (m-30) REVERT: D 1069 ASP cc_start: 0.6599 (m-30) cc_final: 0.6139 (m-30) REVERT: D 1075 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6832 (m-80) REVERT: D 1126 GLN cc_start: 0.7495 (mt0) cc_final: 0.7245 (tt0) REVERT: D 1130 LYS cc_start: 0.7967 (mmtm) cc_final: 0.7758 (mtpp) outliers start: 92 outliers final: 45 residues processed: 533 average time/residue: 1.4343 time to fit residues: 850.8110 Evaluate side-chains 535 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 479 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1115 ASP Chi-restraints excluded: chain A residue 1133 ARG Chi-restraints excluded: chain A residue 1157 ARG Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 1254 GLU Chi-restraints excluded: chain B residue 1287 MET Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 281 ARG Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1075 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 203 optimal weight: 20.0000 chunk 168 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 129 GLN A 132 GLN A 155 ASN A 193 GLN A1075 ASN B1290 ASN B1375 ASN B1385 ASN C 73 GLN D 111 HIS D 163 GLN ** D 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 ASN D 429 HIS D 845 GLN D1010 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18121 Z= 0.208 Angle : 0.566 11.304 24639 Z= 0.290 Chirality : 0.039 0.156 2873 Planarity : 0.003 0.035 2905 Dihedral : 17.093 175.698 2873 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.09 % Allowed : 21.60 % Favored : 74.31 % 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: 2.05 (0.19), residues: 2032 helix: 2.35 (0.14), residues: 1278 sheet: 1.34 (0.41), residues: 170 loop : -0.96 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 49 HIS 0.011 0.001 HIS D 111 PHE 0.020 0.002 PHE B1264 TYR 0.022 0.001 TYR D 117 ARG 0.007 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 486 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.6753 (pt0) cc_final: 0.6468 (pt0) REVERT: A 20 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7702 (mt) REVERT: A 53 SER cc_start: 0.8502 (t) cc_final: 0.8081 (p) REVERT: A 90 ASN cc_start: 0.6824 (t0) cc_final: 0.6511 (t0) REVERT: A 100 GLN cc_start: 0.7150 (tp-100) cc_final: 0.6270 (tp40) REVERT: A 108 VAL cc_start: 0.7981 (t) cc_final: 0.7726 (p) REVERT: A 166 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6744 (mt-10) REVERT: A 989 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.6339 (ttm) REVERT: A 1009 LYS cc_start: 0.7729 (mttt) cc_final: 0.7496 (mtmm) REVERT: A 1027 GLU cc_start: 0.6795 (tm-30) cc_final: 0.6530 (tm-30) REVERT: A 1042 ASN cc_start: 0.8369 (m-40) cc_final: 0.8126 (m-40) REVERT: A 1115 ASP cc_start: 0.7870 (p0) cc_final: 0.7662 (p0) REVERT: B 170 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7804 (ttmm) REVERT: B 1254 GLU cc_start: 0.5332 (OUTLIER) cc_final: 0.4639 (mp0) REVERT: B 1271 PHE cc_start: 0.7946 (t80) cc_final: 0.7639 (t80) REVERT: B 1281 MET cc_start: 0.8260 (tpp) cc_final: 0.7940 (tpp) REVERT: C 30 ASN cc_start: 0.7821 (m-40) cc_final: 0.7520 (m-40) REVERT: C 48 SER cc_start: 0.8352 (OUTLIER) cc_final: 0.8067 (m) REVERT: C 87 SER cc_start: 0.7857 (m) cc_final: 0.7646 (p) REVERT: C 167 LEU cc_start: 0.6965 (mt) cc_final: 0.6706 (mm) REVERT: C 212 ASN cc_start: 0.6476 (m-40) cc_final: 0.6090 (m110) REVERT: C 637 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.8101 (m) REVERT: C 664 GLU cc_start: 0.7299 (tp30) cc_final: 0.7023 (tp30) REVERT: D 62 PHE cc_start: 0.6154 (m-10) cc_final: 0.5824 (m-10) REVERT: D 120 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7478 (tm130) REVERT: D 163 GLN cc_start: 0.8031 (pt0) cc_final: 0.7627 (pt0) REVERT: D 165 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6402 (mp0) REVERT: D 166 ASN cc_start: 0.7866 (m110) cc_final: 0.7486 (m110) REVERT: D 190 ASP cc_start: 0.7499 (t0) cc_final: 0.7257 (t0) REVERT: D 226 CYS cc_start: 0.7607 (m) cc_final: 0.7388 (m) REVERT: D 264 GLU cc_start: 0.6815 (mp0) cc_final: 0.6442 (mp0) REVERT: D 324 SER cc_start: 0.8557 (t) cc_final: 0.8147 (p) REVERT: D 331 VAL cc_start: 0.8104 (t) cc_final: 0.7545 (p) REVERT: D 364 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6747 (mt-10) REVERT: D 365 GLU cc_start: 0.6758 (tm-30) cc_final: 0.6323 (tm-30) REVERT: D 424 LYS cc_start: 0.8029 (ttmm) cc_final: 0.7801 (tppp) REVERT: D 547 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8296 (mt) REVERT: D 602 VAL cc_start: 0.7852 (m) cc_final: 0.7650 (p) REVERT: D 643 ASP cc_start: 0.7264 (m-30) cc_final: 0.7059 (m-30) REVERT: D 648 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6778 (tt0) REVERT: D 918 GLN cc_start: 0.7084 (tp-100) cc_final: 0.6849 (tp-100) REVERT: D 941 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6869 (mt-10) REVERT: D 972 LYS cc_start: 0.8258 (mtpt) cc_final: 0.8000 (mtpp) REVERT: D 982 ILE cc_start: 0.8318 (mm) cc_final: 0.7967 (mp) REVERT: D 1004 MET cc_start: 0.7584 (mtm) cc_final: 0.7244 (mtt) REVERT: D 1022 ARG cc_start: 0.7841 (tpp-160) cc_final: 0.7151 (mmp-170) REVERT: D 1025 ASP cc_start: 0.7945 (t70) cc_final: 0.7295 (m-30) REVERT: D 1069 ASP cc_start: 0.6633 (m-30) cc_final: 0.6166 (m-30) REVERT: D 1075 PHE cc_start: 0.7079 (OUTLIER) cc_final: 0.6826 (m-80) REVERT: D 1130 LYS cc_start: 0.7983 (mmtm) cc_final: 0.7782 (mtpp) outliers start: 77 outliers final: 42 residues processed: 520 average time/residue: 1.3495 time to fit residues: 778.7790 Evaluate side-chains 533 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 483 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 1254 GLU Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 321 ASN Chi-restraints excluded: chain D residue 371 ASN Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1075 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 202 optimal weight: 20.0000 chunk 126 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 85 ASN A 193 GLN A1075 ASN B 171 GLN B1290 ASN B1375 ASN B1385 ASN C 738 ASN D 111 HIS ** D 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN D 262 ASN D 371 ASN ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 555 ASN D 794 GLN D 845 GLN D1046 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 18121 Z= 0.387 Angle : 0.662 16.456 24639 Z= 0.337 Chirality : 0.043 0.148 2873 Planarity : 0.004 0.048 2905 Dihedral : 17.171 171.389 2873 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.56 % Allowed : 21.92 % Favored : 73.51 % 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: 1.66 (0.19), residues: 2032 helix: 2.08 (0.14), residues: 1280 sheet: 1.15 (0.40), residues: 170 loop : -1.19 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 49 HIS 0.013 0.001 HIS D 111 PHE 0.024 0.002 PHE B1388 TYR 0.029 0.002 TYR B 326 ARG 0.008 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 502 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6459 (pt0) REVERT: A 20 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7778 (mt) REVERT: A 53 SER cc_start: 0.8499 (t) cc_final: 0.8133 (p) REVERT: A 90 ASN cc_start: 0.6819 (t0) cc_final: 0.6488 (t0) REVERT: A 100 GLN cc_start: 0.7187 (tp-100) cc_final: 0.6174 (tp40) REVERT: A 166 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6844 (mt-10) REVERT: A 209 LYS cc_start: 0.7830 (mtpt) cc_final: 0.7619 (mttt) REVERT: A 1009 LYS cc_start: 0.7780 (mttt) cc_final: 0.7550 (mtmm) REVERT: A 1027 GLU cc_start: 0.6770 (tm-30) cc_final: 0.6496 (tm-30) REVERT: A 1042 ASN cc_start: 0.8598 (m-40) cc_final: 0.8380 (m-40) REVERT: B 170 LYS cc_start: 0.8056 (ttmm) cc_final: 0.7812 (ttmm) REVERT: B 301 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8118 (mp) REVERT: B 1254 GLU cc_start: 0.5264 (OUTLIER) cc_final: 0.4503 (mp0) REVERT: B 1281 MET cc_start: 0.8352 (tpp) cc_final: 0.8044 (tpp) REVERT: C 30 ASN cc_start: 0.7903 (m-40) cc_final: 0.7623 (m-40) REVERT: C 87 SER cc_start: 0.7922 (m) cc_final: 0.7654 (p) REVERT: C 637 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8168 (m) REVERT: C 664 GLU cc_start: 0.7377 (tp30) cc_final: 0.7086 (tp30) REVERT: C 708 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8256 (mt) REVERT: D 62 PHE cc_start: 0.6111 (m-10) cc_final: 0.5759 (m-10) REVERT: D 86 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7901 (mtmm) REVERT: D 118 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8451 (mp) REVERT: D 120 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7565 (tm130) REVERT: D 163 GLN cc_start: 0.8110 (pt0) cc_final: 0.7776 (pt0) REVERT: D 165 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6465 (mp0) REVERT: D 166 ASN cc_start: 0.7922 (m110) cc_final: 0.7536 (m110) REVERT: D 190 ASP cc_start: 0.7585 (t0) cc_final: 0.7372 (t0) REVERT: D 226 CYS cc_start: 0.7637 (m) cc_final: 0.7424 (m) REVERT: D 264 GLU cc_start: 0.6918 (mp0) cc_final: 0.6497 (mp0) REVERT: D 324 SER cc_start: 0.8654 (t) cc_final: 0.8246 (p) REVERT: D 364 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6732 (mt-10) REVERT: D 365 GLU cc_start: 0.6823 (tm-30) cc_final: 0.6330 (tm-30) REVERT: D 404 VAL cc_start: 0.8627 (t) cc_final: 0.8401 (m) REVERT: D 424 LYS cc_start: 0.8063 (ttmm) cc_final: 0.7827 (tppp) REVERT: D 547 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8310 (mt) REVERT: D 568 LEU cc_start: 0.8536 (tp) cc_final: 0.8329 (tp) REVERT: D 643 ASP cc_start: 0.7319 (m-30) cc_final: 0.7093 (m-30) REVERT: D 648 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6903 (tt0) REVERT: D 872 LYS cc_start: 0.7805 (tttm) cc_final: 0.7446 (ttpp) REVERT: D 918 GLN cc_start: 0.7151 (tp-100) cc_final: 0.6949 (tp-100) REVERT: D 972 LYS cc_start: 0.8269 (mtpt) cc_final: 0.8000 (mtpp) REVERT: D 982 ILE cc_start: 0.8347 (mm) cc_final: 0.8068 (mp) REVERT: D 990 ASP cc_start: 0.7611 (t0) cc_final: 0.7398 (t70) REVERT: D 1022 ARG cc_start: 0.7839 (tpp-160) cc_final: 0.7306 (mmp-170) REVERT: D 1069 ASP cc_start: 0.6803 (m-30) cc_final: 0.6365 (m-30) REVERT: D 1075 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6789 (m-80) REVERT: D 1130 LYS cc_start: 0.7991 (mmtm) cc_final: 0.7766 (mtpp) outliers start: 86 outliers final: 52 residues processed: 545 average time/residue: 1.3764 time to fit residues: 830.5262 Evaluate side-chains 555 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 493 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1133 ARG Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 1254 GLU Chi-restraints excluded: chain B residue 1309 SER Chi-restraints excluded: chain B residue 1330 LEU Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 321 ASN Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1075 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 132 GLN A 137 ASN A1075 ASN B1375 ASN B1385 ASN C 660 ASN D 111 HIS ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 HIS D1010 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18121 Z= 0.179 Angle : 0.574 11.399 24639 Z= 0.295 Chirality : 0.039 0.250 2873 Planarity : 0.003 0.038 2905 Dihedral : 17.103 175.098 2873 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.93 % Allowed : 23.46 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.19), residues: 2032 helix: 2.31 (0.14), residues: 1278 sheet: 1.23 (0.41), residues: 170 loop : -1.01 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 49 HIS 0.013 0.001 HIS D 111 PHE 0.026 0.001 PHE D 919 TYR 0.021 0.001 TYR B 326 ARG 0.006 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 492 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.6727 (pt0) cc_final: 0.6466 (pt0) REVERT: A 20 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7719 (mt) REVERT: A 53 SER cc_start: 0.8498 (t) cc_final: 0.8116 (p) REVERT: A 90 ASN cc_start: 0.6725 (t0) cc_final: 0.6418 (t0) REVERT: A 100 GLN cc_start: 0.7106 (tp-100) cc_final: 0.6222 (tp40) REVERT: A 108 VAL cc_start: 0.7945 (t) cc_final: 0.7693 (p) REVERT: A 166 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6789 (mt-10) REVERT: A 997 GLU cc_start: 0.6966 (tt0) cc_final: 0.6734 (tt0) REVERT: A 1009 LYS cc_start: 0.7740 (mttt) cc_final: 0.7506 (mtmm) REVERT: A 1027 GLU cc_start: 0.6777 (tm-30) cc_final: 0.6529 (tm-30) REVERT: A 1042 ASN cc_start: 0.8351 (m-40) cc_final: 0.8097 (m-40) REVERT: A 1113 GLU cc_start: 0.7617 (tp30) cc_final: 0.7010 (mm-30) REVERT: A 1115 ASP cc_start: 0.7896 (p0) cc_final: 0.7684 (p0) REVERT: B 138 GLN cc_start: 0.7134 (mm110) cc_final: 0.6791 (mm110) REVERT: B 170 LYS cc_start: 0.8027 (ttmm) cc_final: 0.7815 (ttmm) REVERT: B 301 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7751 (mp) REVERT: B 1254 GLU cc_start: 0.5306 (OUTLIER) cc_final: 0.4514 (mp0) REVERT: B 1271 PHE cc_start: 0.7917 (t80) cc_final: 0.7647 (t80) REVERT: B 1281 MET cc_start: 0.8268 (tpp) cc_final: 0.7960 (tpp) REVERT: C 30 ASN cc_start: 0.7694 (m-40) cc_final: 0.7342 (m-40) REVERT: C 87 SER cc_start: 0.7730 (m) cc_final: 0.7494 (p) REVERT: C 167 LEU cc_start: 0.7030 (mt) cc_final: 0.6741 (mm) REVERT: C 637 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8076 (m) REVERT: C 664 GLU cc_start: 0.7350 (tp30) cc_final: 0.7109 (tp30) REVERT: C 708 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8189 (mt) REVERT: D 62 PHE cc_start: 0.6037 (m-10) cc_final: 0.5717 (m-10) REVERT: D 86 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7860 (mtmm) REVERT: D 115 TYR cc_start: 0.8254 (m-80) cc_final: 0.7897 (m-80) REVERT: D 120 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7470 (tm130) REVERT: D 163 GLN cc_start: 0.8031 (pt0) cc_final: 0.7656 (pt0) REVERT: D 165 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6412 (mp0) REVERT: D 166 ASN cc_start: 0.7887 (m110) cc_final: 0.7489 (m110) REVERT: D 190 ASP cc_start: 0.7484 (t0) cc_final: 0.7250 (t0) REVERT: D 226 CYS cc_start: 0.7615 (m) cc_final: 0.7412 (m) REVERT: D 264 GLU cc_start: 0.6802 (mp0) cc_final: 0.6430 (mp0) REVERT: D 281 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.6482 (ttm110) REVERT: D 324 SER cc_start: 0.8608 (t) cc_final: 0.8193 (p) REVERT: D 331 VAL cc_start: 0.8043 (t) cc_final: 0.7605 (p) REVERT: D 364 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6622 (mt-10) REVERT: D 365 GLU cc_start: 0.6777 (tm-30) cc_final: 0.6338 (tm-30) REVERT: D 425 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7934 (mm) REVERT: D 648 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6648 (tt0) REVERT: D 750 ARG cc_start: 0.7585 (mtt180) cc_final: 0.7105 (mtt180) REVERT: D 751 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7408 (ptp) REVERT: D 918 GLN cc_start: 0.7121 (tp-100) cc_final: 0.6920 (tp-100) REVERT: D 972 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7915 (mtpp) REVERT: D 982 ILE cc_start: 0.8333 (mm) cc_final: 0.7979 (mp) REVERT: D 990 ASP cc_start: 0.7563 (t0) cc_final: 0.7273 (t0) REVERT: D 1004 MET cc_start: 0.7558 (mtm) cc_final: 0.7291 (mtt) REVERT: D 1020 TYR cc_start: 0.7862 (m-80) cc_final: 0.7321 (m-80) REVERT: D 1022 ARG cc_start: 0.7799 (tpp-160) cc_final: 0.7222 (mmp-170) REVERT: D 1025 ASP cc_start: 0.7907 (t70) cc_final: 0.7338 (m-30) REVERT: D 1029 MET cc_start: 0.7520 (pp-130) cc_final: 0.7318 (ppp) REVERT: D 1069 ASP cc_start: 0.6786 (m-30) cc_final: 0.6333 (m-30) REVERT: D 1073 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6996 (tt) REVERT: D 1075 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.6762 (m-80) REVERT: D 1126 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7499 (mm-40) REVERT: D 1130 LYS cc_start: 0.7966 (mmtm) cc_final: 0.7728 (mtpp) outliers start: 74 outliers final: 39 residues processed: 528 average time/residue: 1.4074 time to fit residues: 822.7776 Evaluate side-chains 536 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 486 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1133 ARG Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 1254 GLU Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 281 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain D residue 386 CYS Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1073 LEU Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1077 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 7.9990 chunk 176 optimal weight: 0.8980 chunk 188 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 193 GLN A1075 ASN B 171 GLN B1375 ASN B1385 ASN D 72 GLN D 111 HIS ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 555 ASN D 845 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18121 Z= 0.182 Angle : 0.575 11.897 24639 Z= 0.294 Chirality : 0.039 0.244 2873 Planarity : 0.003 0.038 2905 Dihedral : 17.030 173.913 2873 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.18 % Allowed : 24.42 % Favored : 72.40 % 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: 2.00 (0.19), residues: 2032 helix: 2.31 (0.14), residues: 1286 sheet: 1.37 (0.41), residues: 169 loop : -1.04 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 49 HIS 0.016 0.001 HIS D 111 PHE 0.018 0.001 PHE B1388 TYR 0.020 0.001 TYR B 326 ARG 0.007 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 490 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.6710 (pt0) cc_final: 0.6466 (pt0) REVERT: A 20 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7724 (mt) REVERT: A 53 SER cc_start: 0.8486 (t) cc_final: 0.8104 (p) REVERT: A 90 ASN cc_start: 0.6744 (t0) cc_final: 0.6508 (t0) REVERT: A 100 GLN cc_start: 0.7112 (tp-100) cc_final: 0.6231 (tp40) REVERT: A 108 VAL cc_start: 0.7901 (t) cc_final: 0.7651 (p) REVERT: A 112 THR cc_start: 0.7096 (p) cc_final: 0.6779 (p) REVERT: A 166 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6730 (mt-10) REVERT: A 997 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6715 (tt0) REVERT: A 1009 LYS cc_start: 0.7726 (mttt) cc_final: 0.7474 (mtmm) REVERT: A 1027 GLU cc_start: 0.6766 (tm-30) cc_final: 0.6514 (tm-30) REVERT: A 1042 ASN cc_start: 0.8206 (m-40) cc_final: 0.7960 (m-40) REVERT: B 170 LYS cc_start: 0.8024 (ttmm) cc_final: 0.7812 (ttmm) REVERT: B 292 ASP cc_start: 0.7023 (t70) cc_final: 0.6678 (t70) REVERT: B 301 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7777 (mp) REVERT: B 1254 GLU cc_start: 0.5319 (OUTLIER) cc_final: 0.4610 (mp0) REVERT: B 1271 PHE cc_start: 0.7919 (t80) cc_final: 0.7605 (t80) REVERT: B 1281 MET cc_start: 0.8272 (tpp) cc_final: 0.7957 (tpp) REVERT: C 30 ASN cc_start: 0.7658 (m-40) cc_final: 0.7309 (m-40) REVERT: C 48 SER cc_start: 0.8272 (OUTLIER) cc_final: 0.7990 (m) REVERT: C 87 SER cc_start: 0.7768 (m) cc_final: 0.7528 (p) REVERT: C 637 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8054 (m) REVERT: C 664 GLU cc_start: 0.7318 (tp30) cc_final: 0.7094 (tp30) REVERT: C 708 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8159 (mt) REVERT: D 62 PHE cc_start: 0.6034 (m-10) cc_final: 0.5710 (m-10) REVERT: D 86 LYS cc_start: 0.8232 (mtmm) cc_final: 0.7903 (mtmp) REVERT: D 115 TYR cc_start: 0.8271 (m-80) cc_final: 0.7870 (m-80) REVERT: D 120 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7485 (tm130) REVERT: D 163 GLN cc_start: 0.8059 (pt0) cc_final: 0.7722 (pt0) REVERT: D 165 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6407 (mp0) REVERT: D 166 ASN cc_start: 0.7883 (m110) cc_final: 0.7498 (m110) REVERT: D 190 ASP cc_start: 0.7518 (t0) cc_final: 0.7275 (t0) REVERT: D 226 CYS cc_start: 0.7614 (m) cc_final: 0.7408 (m) REVERT: D 264 GLU cc_start: 0.6837 (mp0) cc_final: 0.6484 (mp0) REVERT: D 324 SER cc_start: 0.8596 (t) cc_final: 0.8176 (p) REVERT: D 331 VAL cc_start: 0.8035 (t) cc_final: 0.7628 (p) REVERT: D 364 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6602 (mt-10) REVERT: D 365 GLU cc_start: 0.6769 (tm-30) cc_final: 0.6241 (tm-30) REVERT: D 424 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7690 (tppp) REVERT: D 648 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6778 (tt0) REVERT: D 751 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7398 (ptp) REVERT: D 918 GLN cc_start: 0.7113 (tp-100) cc_final: 0.6908 (tp-100) REVERT: D 972 LYS cc_start: 0.8240 (mtpt) cc_final: 0.7989 (mtpp) REVERT: D 982 ILE cc_start: 0.8295 (mm) cc_final: 0.7859 (mp) REVERT: D 1020 TYR cc_start: 0.7917 (m-80) cc_final: 0.7368 (m-80) REVERT: D 1022 ARG cc_start: 0.7783 (tpp-160) cc_final: 0.7211 (mmp-170) REVERT: D 1025 ASP cc_start: 0.7923 (t70) cc_final: 0.7353 (m-30) REVERT: D 1069 ASP cc_start: 0.6774 (m-30) cc_final: 0.6331 (m-30) REVERT: D 1073 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6965 (tt) REVERT: D 1075 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.6773 (m-80) REVERT: D 1126 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7445 (mm-40) REVERT: D 1130 LYS cc_start: 0.7970 (mmtm) cc_final: 0.7747 (mtpp) outliers start: 60 outliers final: 38 residues processed: 522 average time/residue: 1.3858 time to fit residues: 800.3549 Evaluate side-chains 532 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 484 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1133 ARG Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 1254 GLU Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 281 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 321 ASN Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1073 LEU Chi-restraints excluded: chain D residue 1075 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 85 ASN ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN A1075 ASN B 171 GLN B1375 ASN B1385 ASN D 111 HIS ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 845 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18121 Z= 0.270 Angle : 0.621 12.123 24639 Z= 0.315 Chirality : 0.041 0.282 2873 Planarity : 0.003 0.038 2905 Dihedral : 17.034 173.044 2873 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.18 % Allowed : 24.68 % Favored : 72.13 % 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: 1.81 (0.19), residues: 2032 helix: 2.21 (0.14), residues: 1279 sheet: 1.17 (0.39), residues: 177 loop : -1.18 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 49 HIS 0.018 0.001 HIS D 111 PHE 0.020 0.002 PHE B1388 TYR 0.025 0.002 TYR B 326 ARG 0.008 0.001 ARG D 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 497 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.6758 (pt0) cc_final: 0.6378 (pt0) REVERT: A 20 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7751 (mt) REVERT: A 53 SER cc_start: 0.8484 (t) cc_final: 0.8118 (p) REVERT: A 90 ASN cc_start: 0.6846 (t0) cc_final: 0.6597 (t0) REVERT: A 100 GLN cc_start: 0.7146 (tp-100) cc_final: 0.6189 (tp40) REVERT: A 108 VAL cc_start: 0.7964 (t) cc_final: 0.7708 (p) REVERT: A 166 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6756 (mt-10) REVERT: A 997 GLU cc_start: 0.7008 (tt0) cc_final: 0.6741 (tt0) REVERT: A 1009 LYS cc_start: 0.7744 (mttt) cc_final: 0.7511 (mtmm) REVERT: A 1027 GLU cc_start: 0.6773 (tm-30) cc_final: 0.6522 (tm-30) REVERT: A 1042 ASN cc_start: 0.8349 (m-40) cc_final: 0.8087 (m-40) REVERT: A 1108 MET cc_start: 0.8280 (ptp) cc_final: 0.8008 (ptp) REVERT: A 1115 ASP cc_start: 0.7862 (p0) cc_final: 0.7624 (p0) REVERT: B 170 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7814 (ttmm) REVERT: B 301 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7865 (mp) REVERT: B 1254 GLU cc_start: 0.5232 (OUTLIER) cc_final: 0.4537 (mp0) REVERT: B 1281 MET cc_start: 0.8259 (tpp) cc_final: 0.7938 (tpp) REVERT: B 1295 LEU cc_start: 0.8166 (mm) cc_final: 0.7939 (mp) REVERT: C 30 ASN cc_start: 0.7738 (m-40) cc_final: 0.7417 (m-40) REVERT: C 48 SER cc_start: 0.8274 (OUTLIER) cc_final: 0.8005 (m) REVERT: C 87 SER cc_start: 0.7895 (m) cc_final: 0.7647 (p) REVERT: C 637 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8119 (m) REVERT: C 664 GLU cc_start: 0.7356 (tp30) cc_final: 0.7117 (tp30) REVERT: C 708 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8209 (mt) REVERT: D 62 PHE cc_start: 0.6047 (m-10) cc_final: 0.5752 (m-10) REVERT: D 86 LYS cc_start: 0.8254 (mtmm) cc_final: 0.7929 (mtmm) REVERT: D 115 TYR cc_start: 0.8278 (m-80) cc_final: 0.7853 (m-80) REVERT: D 120 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7528 (tm130) REVERT: D 165 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6429 (mp0) REVERT: D 166 ASN cc_start: 0.7905 (m110) cc_final: 0.7522 (m110) REVERT: D 190 ASP cc_start: 0.7563 (t0) cc_final: 0.7333 (t0) REVERT: D 226 CYS cc_start: 0.7647 (m) cc_final: 0.7425 (m) REVERT: D 264 GLU cc_start: 0.6898 (mp0) cc_final: 0.6562 (mp0) REVERT: D 324 SER cc_start: 0.8611 (t) cc_final: 0.8199 (p) REVERT: D 364 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6659 (mt-10) REVERT: D 365 GLU cc_start: 0.6775 (tm-30) cc_final: 0.6397 (tm-30) REVERT: D 648 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6807 (tt0) REVERT: D 812 ASP cc_start: 0.7194 (m-30) cc_final: 0.6931 (m-30) REVERT: D 872 LYS cc_start: 0.7813 (tttm) cc_final: 0.7442 (ttpp) REVERT: D 919 PHE cc_start: 0.8104 (t80) cc_final: 0.7858 (t80) REVERT: D 972 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7988 (mtpp) REVERT: D 982 ILE cc_start: 0.8313 (mm) cc_final: 0.7897 (mp) REVERT: D 1022 ARG cc_start: 0.7848 (tpp-160) cc_final: 0.7397 (mmp-170) REVERT: D 1025 ASP cc_start: 0.7973 (t70) cc_final: 0.7394 (t70) REVERT: D 1069 ASP cc_start: 0.6840 (m-30) cc_final: 0.6389 (m-30) REVERT: D 1073 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.7010 (tp) REVERT: D 1075 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.6779 (m-80) REVERT: D 1126 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7442 (mm-40) REVERT: D 1130 LYS cc_start: 0.7985 (mmtm) cc_final: 0.7764 (mtpp) outliers start: 60 outliers final: 37 residues processed: 529 average time/residue: 1.3988 time to fit residues: 818.5511 Evaluate side-chains 546 residues out of total 1887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 501 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1133 ARG Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 1254 GLU Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 281 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 321 ASN Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 988 SER Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1073 LEU Chi-restraints excluded: chain D residue 1075 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 166 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN A1075 ASN B 171 GLN B1375 ASN B1385 ASN ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN C 738 ASN D 111 HIS ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 845 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.152886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.120988 restraints weight = 23680.314| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.67 r_work: 0.3280 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.136 18121 Z= 0.311 Angle : 0.806 59.025 24639 Z= 0.457 Chirality : 0.041 0.303 2873 Planarity : 0.003 0.038 2905 Dihedral : 17.036 173.036 2873 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.08 % Allowed : 25.37 % Favored : 71.55 % Cbeta Deviations : 0.05 % 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: 1.81 (0.19), residues: 2032 helix: 2.20 (0.14), residues: 1279 sheet: 1.17 (0.39), residues: 177 loop : -1.18 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 49 HIS 0.015 0.001 HIS D 111 PHE 0.020 0.002 PHE B1388 TYR 0.024 0.002 TYR B 326 ARG 0.008 0.000 ARG D 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10475.89 seconds wall clock time: 183 minutes 45.02 seconds (11025.02 seconds total)