Starting phenix.real_space_refine on Wed Feb 14 15:31:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwp_16293/02_2024/8bwp_16293_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwp_16293/02_2024/8bwp_16293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwp_16293/02_2024/8bwp_16293.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwp_16293/02_2024/8bwp_16293.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwp_16293/02_2024/8bwp_16293_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwp_16293/02_2024/8bwp_16293_updated.pdb" } resolution = 3.6 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= -0.000 sd= 0.070 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 6221 2.51 5 N 1610 2.21 5 O 1704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9578 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9545 Classifications: {'peptide': 1195} Link IDs: {'PTRANS': 37, 'TRANS': 1157} Chain breaks: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'MTX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.37, per 1000 atoms: 0.56 Number of scatterers: 9578 At special positions: 0 Unit cell: (77.376, 107.328, 144.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1704 8.00 N 1610 7.00 C 6221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.97 Conformation dependent library (CDL) restraints added in 1.7 seconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB MTX A1401 " Number of C-beta restraints generated: 2266 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 5 sheets defined 65.7% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 12 through 14 No H-bonds generated for 'chain 'A' and resid 12 through 14' Processing helix chain 'A' and resid 18 through 21 No H-bonds generated for 'chain 'A' and resid 18 through 21' Processing helix chain 'A' and resid 25 through 36 Proline residue: A 29 - end of helix removed outlier: 3.968A pdb=" N HIS A 35 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 53 through 74 removed outlier: 4.316A pdb=" N GLY A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 86 removed outlier: 3.702A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 122 removed outlier: 3.518A pdb=" N GLY A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.578A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A 122 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 149 Processing helix chain 'A' and resid 151 through 180 removed outlier: 3.835A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 191 through 199 Processing helix chain 'A' and resid 202 through 232 removed outlier: 4.311A pdb=" N VAL A 208 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR A 209 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE A 211 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 212 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N HIS A 213 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA A 217 " --> pdb=" O PHE A 214 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLY A 218 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Proline residue: A 219 - end of helix removed outlier: 3.852A pdb=" N VAL A 225 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 281 removed outlier: 3.711A pdb=" N MET A 241 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 242 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A 246 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 4.093A pdb=" N PHE A 258 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 261 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A 269 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 292 through 341 removed outlier: 4.369A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 366 removed outlier: 3.690A pdb=" N ALA A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 390 Processing helix chain 'A' and resid 451 through 459 removed outlier: 4.150A pdb=" N LEU A 454 " --> pdb=" O LYS A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 514 through 520 Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 537 through 551 removed outlier: 3.534A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 575 removed outlier: 4.392A pdb=" N PHE A 574 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 removed outlier: 3.873A pdb=" N LYS A 598 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 698 through 708 removed outlier: 3.505A pdb=" N GLY A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 744 removed outlier: 3.809A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 807 removed outlier: 3.708A pdb=" N GLY A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 803 " --> pdb=" O ASN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 815 Processing helix chain 'A' and resid 818 through 826 removed outlier: 3.636A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 825 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 834 removed outlier: 4.611A pdb=" N ASP A 833 " --> pdb=" O ILE A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 860 Processing helix chain 'A' and resid 862 through 895 removed outlier: 3.647A pdb=" N ALA A 865 " --> pdb=" O PRO A 862 " (cutoff:3.500A) Proline residue: A 867 - end of helix Proline residue: A 870 - end of helix removed outlier: 3.689A pdb=" N ILE A 876 " --> pdb=" O ILE A 873 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 879 " --> pdb=" O ILE A 876 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 882 " --> pdb=" O ARG A 879 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU A 884 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ARG A 887 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 890 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 893 " --> pdb=" O LYS A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 916 removed outlier: 6.413A pdb=" N TRP A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR A 913 " --> pdb=" O GLN A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 969 removed outlier: 3.534A pdb=" N PHE A 927 " --> pdb=" O CYS A 923 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU A 936 " --> pdb=" O ASP A 932 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 945 " --> pdb=" O PHE A 941 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 1017 removed outlier: 4.546A pdb=" N THR A 988 " --> pdb=" O SER A 984 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 989 " --> pdb=" O TYR A 985 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N MET A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP A 995 " --> pdb=" O GLY A 991 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1088 removed outlier: 3.777A pdb=" N LEU A1084 " --> pdb=" O LYS A1081 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A1087 " --> pdb=" O LEU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1116 removed outlier: 3.689A pdb=" N LYS A1115 " --> pdb=" O HIS A1111 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A1116 " --> pdb=" O ASP A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1136 Processing helix chain 'A' and resid 1143 through 1152 Processing helix chain 'A' and resid 1156 through 1160 Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1172 through 1174 No H-bonds generated for 'chain 'A' and resid 1172 through 1174' Processing helix chain 'A' and resid 1179 through 1193 Processing helix chain 'A' and resid 1203 through 1206 Processing helix chain 'A' and resid 1209 through 1222 Processing helix chain 'A' and resid 1235 through 1237 No H-bonds generated for 'chain 'A' and resid 1235 through 1237' Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'A' and resid 1268 through 1276 Processing helix chain 'A' and resid 1279 through 1293 removed outlier: 3.510A pdb=" N LEU A1284 " --> pdb=" O ALA A1281 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 433 through 435 Processing sheet with id= B, first strand: chain 'A' and resid 441 through 444 removed outlier: 6.578A pdb=" N GLN A 602 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL A 444 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A 604 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LYS A 607 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N MET A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.062A pdb=" N ILE A 555 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL A 478 " --> pdb=" O ILE A 555 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU A 557 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 586 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 558 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE A 588 " --> pdb=" O LEU A 558 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 1063 through 1065 Processing sheet with id= E, first strand: chain 'A' and resid 1251 through 1256 removed outlier: 6.487A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A1228 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE A1073 " --> pdb=" O VAL A1228 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR A1230 " --> pdb=" O ILE A1073 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N GLY A1075 " --> pdb=" O THR A1230 " (cutoff:3.500A) 535 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3024 1.34 - 1.46: 1607 1.46 - 1.58: 5082 1.58 - 1.69: 1 1.69 - 1.81: 70 Bond restraints: 9784 Sorted by residual: bond pdb=" C2 MTX A1401 " pdb=" NA2 MTX A1401 " ideal model delta sigma weight residual 1.341 1.407 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" CG LEU A 27 " pdb=" CD1 LEU A 27 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.97e+00 bond pdb=" CB GLN A 931 " pdb=" CG GLN A 931 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.12e+00 bond pdb=" C8A MTX A1401 " pdb=" N8 MTX A1401 " ideal model delta sigma weight residual 1.348 1.393 -0.045 2.00e-02 2.50e+03 5.09e+00 bond pdb=" CB ARG A 946 " pdb=" CG ARG A 946 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.09e+00 ... (remaining 9779 not shown) Histogram of bond angle deviations from ideal: 97.41 - 104.75: 136 104.75 - 112.08: 4817 112.08 - 119.42: 3602 119.42 - 126.76: 4577 126.76 - 134.10: 130 Bond angle restraints: 13262 Sorted by residual: angle pdb=" C THR A 943 " pdb=" N THR A 944 " pdb=" CA THR A 944 " ideal model delta sigma weight residual 120.29 115.76 4.53 1.42e+00 4.96e-01 1.02e+01 angle pdb=" CB ARG A 951 " pdb=" CG ARG A 951 " pdb=" CD ARG A 951 " ideal model delta sigma weight residual 111.30 118.25 -6.95 2.30e+00 1.89e-01 9.12e+00 angle pdb=" CA GLN A 849 " pdb=" CB GLN A 849 " pdb=" CG GLN A 849 " ideal model delta sigma weight residual 114.10 120.10 -6.00 2.00e+00 2.50e-01 9.00e+00 angle pdb=" C HIS A 153 " pdb=" N LEU A 154 " pdb=" CA LEU A 154 " ideal model delta sigma weight residual 120.29 116.07 4.22 1.42e+00 4.96e-01 8.84e+00 angle pdb=" CA ARG A 951 " pdb=" CB ARG A 951 " pdb=" CG ARG A 951 " ideal model delta sigma weight residual 114.10 119.50 -5.40 2.00e+00 2.50e-01 7.30e+00 ... (remaining 13257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 5411 16.96 - 33.92: 329 33.92 - 50.87: 71 50.87 - 67.83: 17 67.83 - 84.79: 7 Dihedral angle restraints: 5835 sinusoidal: 2341 harmonic: 3494 Sorted by residual: dihedral pdb=" CA LEU A1091 " pdb=" C LEU A1091 " pdb=" N SER A1092 " pdb=" CA SER A1092 " ideal model delta harmonic sigma weight residual 180.00 154.13 25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA CYS A1226 " pdb=" C CYS A1226 " pdb=" N THR A1227 " pdb=" CA THR A1227 " ideal model delta harmonic sigma weight residual 180.00 155.45 24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA LYS A1021 " pdb=" C LYS A1021 " pdb=" N GLU A1022 " pdb=" CA GLU A1022 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 5832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1187 0.068 - 0.136: 309 0.136 - 0.204: 38 0.204 - 0.272: 3 0.272 - 0.340: 1 Chirality restraints: 1538 Sorted by residual: chirality pdb=" CA MTX A1401 " pdb=" N MTX A1401 " pdb=" CB MTX A1401 " pdb=" CT MTX A1401 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA PHE A 258 " pdb=" N PHE A 258 " pdb=" C PHE A 258 " pdb=" CB PHE A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA PHE A 24 " pdb=" N PHE A 24 " pdb=" C PHE A 24 " pdb=" CB PHE A 24 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1535 not shown) Planarity restraints: 1646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 26 " -0.020 2.00e-02 2.50e+03 1.55e-02 5.98e+00 pdb=" CG TRP A 26 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 26 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 26 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 26 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 26 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 26 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 26 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 26 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 26 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 939 " -0.024 2.00e-02 2.50e+03 1.84e-02 5.91e+00 pdb=" CG PHE A 939 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 939 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 939 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 939 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 939 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 939 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1292 " 0.009 2.00e-02 2.50e+03 1.64e-02 5.40e+00 pdb=" CG TYR A1292 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR A1292 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A1292 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A1292 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR A1292 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A1292 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR A1292 " 0.027 2.00e-02 2.50e+03 ... (remaining 1643 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1441 2.75 - 3.29: 10403 3.29 - 3.83: 15557 3.83 - 4.36: 18986 4.36 - 4.90: 31971 Nonbonded interactions: 78358 Sorted by model distance: nonbonded pdb=" NH1 ARG A 303 " pdb=" OE1 GLU A 306 " model vdw 2.213 2.520 nonbonded pdb=" OH TYR A 92 " pdb=" O THR A 209 " model vdw 2.214 2.440 nonbonded pdb=" O SER A1241 " pdb=" OH TYR A1292 " model vdw 2.219 2.440 nonbonded pdb=" O GLU A 521 " pdb=" OG1 THR A 526 " model vdw 2.227 2.440 nonbonded pdb=" OG1 THR A 269 " pdb=" OE2 GLU A 306 " model vdw 2.247 2.440 ... (remaining 78353 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.120 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: 12.280 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 29.080 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 0.011 0.081 9784 Z= 0.704 Angle : 0.899 9.422 13262 Z= 0.492 Chirality : 0.060 0.340 1538 Planarity : 0.008 0.078 1646 Dihedral : 12.537 84.791 3569 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.48 % Allowed : 1.82 % Favored : 97.70 % Cbeta Deviations : 0.09 % 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: -1.51 (0.22), residues: 1187 helix: -1.44 (0.15), residues: 769 sheet: 0.56 (0.78), residues: 50 loop : 0.32 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 26 HIS 0.014 0.002 HIS A 172 PHE 0.042 0.004 PHE A 939 TYR 0.028 0.005 TYR A 881 ARG 0.023 0.003 ARG A 897 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 207 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8467 (t0) cc_final: 0.8211 (t0) REVERT: A 67 GLU cc_start: 0.8510 (tp30) cc_final: 0.8278 (tp30) REVERT: A 200 ASN cc_start: 0.8411 (t0) cc_final: 0.7787 (t0) REVERT: A 206 ASP cc_start: 0.7918 (t70) cc_final: 0.7708 (t70) REVERT: A 276 MET cc_start: 0.8329 (tpp) cc_final: 0.8109 (tpp) REVERT: A 316 LEU cc_start: 0.8398 (tp) cc_final: 0.7992 (tt) REVERT: A 728 TYR cc_start: 0.8546 (t80) cc_final: 0.8310 (t80) REVERT: A 953 ASP cc_start: 0.8492 (m-30) cc_final: 0.7945 (m-30) REVERT: A 985 TYR cc_start: 0.8166 (m-80) cc_final: 0.7717 (m-80) REVERT: A 998 ARG cc_start: 0.7298 (ttm-80) cc_final: 0.7020 (mmt-90) REVERT: A 1045 ASN cc_start: 0.9065 (t0) cc_final: 0.8806 (t0) REVERT: A 1104 LEU cc_start: 0.9073 (tp) cc_final: 0.8539 (tp) REVERT: A 1122 GLN cc_start: 0.7517 (tt0) cc_final: 0.6847 (tm-30) REVERT: A 1136 ASP cc_start: 0.7587 (t0) cc_final: 0.6875 (t0) REVERT: A 1196 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7621 (mp10) REVERT: A 1212 ASP cc_start: 0.8769 (t0) cc_final: 0.8278 (m-30) REVERT: A 1253 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8766 (mmtm) outliers start: 5 outliers final: 3 residues processed: 211 average time/residue: 0.2699 time to fit residues: 75.5457 Evaluate side-chains 140 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9784 Z= 0.253 Angle : 0.599 8.062 13262 Z= 0.325 Chirality : 0.043 0.154 1538 Planarity : 0.005 0.032 1646 Dihedral : 6.835 82.641 1304 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.82 % Allowed : 8.25 % Favored : 89.92 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1187 helix: -0.41 (0.17), residues: 778 sheet: 0.49 (0.76), residues: 50 loop : 0.56 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 912 HIS 0.004 0.001 HIS A 172 PHE 0.022 0.002 PHE A 258 TYR 0.026 0.002 TYR A1292 ARG 0.005 0.001 ARG A 897 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 173 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ILE cc_start: 0.8118 (mm) cc_final: 0.7906 (tt) REVERT: A 200 ASN cc_start: 0.8323 (t0) cc_final: 0.7896 (t0) REVERT: A 706 ARG cc_start: 0.7889 (tpp-160) cc_final: 0.7424 (mmt180) REVERT: A 744 MET cc_start: 0.7786 (mmm) cc_final: 0.7278 (mtt) REVERT: A 953 ASP cc_start: 0.8363 (m-30) cc_final: 0.7786 (m-30) REVERT: A 985 TYR cc_start: 0.8044 (m-80) cc_final: 0.7664 (m-80) REVERT: A 994 GLN cc_start: 0.7869 (mt0) cc_final: 0.7568 (mp10) REVERT: A 1016 TYR cc_start: 0.7525 (m-10) cc_final: 0.6546 (m-10) REVERT: A 1056 LEU cc_start: 0.8779 (mt) cc_final: 0.8545 (tp) REVERT: A 1118 SER cc_start: 0.9150 (t) cc_final: 0.8737 (p) REVERT: A 1131 MET cc_start: 0.7422 (mmm) cc_final: 0.7142 (tpp) REVERT: A 1136 ASP cc_start: 0.7621 (t0) cc_final: 0.7027 (t0) REVERT: A 1196 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7392 (tp40) REVERT: A 1225 HIS cc_start: 0.8035 (p-80) cc_final: 0.7802 (p-80) outliers start: 19 outliers final: 15 residues processed: 184 average time/residue: 0.2350 time to fit residues: 62.0187 Evaluate side-chains 153 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 107 optimal weight: 0.0020 chunk 36 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9784 Z= 0.320 Angle : 0.589 7.235 13262 Z= 0.313 Chirality : 0.043 0.144 1538 Planarity : 0.004 0.032 1646 Dihedral : 6.562 85.615 1303 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.26 % Allowed : 10.65 % Favored : 86.08 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1187 helix: -0.27 (0.18), residues: 779 sheet: 0.71 (0.78), residues: 47 loop : 0.50 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 947 HIS 0.005 0.001 HIS A 172 PHE 0.020 0.002 PHE A 258 TYR 0.019 0.002 TYR A 728 ARG 0.004 0.000 ARG A1030 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ASN cc_start: 0.8318 (t0) cc_final: 0.8068 (t0) REVERT: A 316 LEU cc_start: 0.7950 (tp) cc_final: 0.7440 (tt) REVERT: A 744 MET cc_start: 0.7749 (mmm) cc_final: 0.6955 (mtt) REVERT: A 953 ASP cc_start: 0.8360 (m-30) cc_final: 0.7874 (m-30) REVERT: A 985 TYR cc_start: 0.8062 (m-80) cc_final: 0.7716 (m-80) REVERT: A 1016 TYR cc_start: 0.7464 (m-10) cc_final: 0.6603 (m-10) REVERT: A 1056 LEU cc_start: 0.8840 (mt) cc_final: 0.8556 (tp) REVERT: A 1122 GLN cc_start: 0.7507 (tt0) cc_final: 0.6990 (tp40) REVERT: A 1131 MET cc_start: 0.7499 (mmm) cc_final: 0.7241 (tpp) REVERT: A 1136 ASP cc_start: 0.7770 (t0) cc_final: 0.7014 (p0) REVERT: A 1169 GLU cc_start: 0.7682 (pp20) cc_final: 0.7467 (pp20) REVERT: A 1196 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7578 (mm-40) outliers start: 34 outliers final: 25 residues processed: 169 average time/residue: 0.2320 time to fit residues: 55.7128 Evaluate side-chains 158 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.4980 chunk 81 optimal weight: 0.6980 chunk 56 optimal weight: 0.0170 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 HIS A1134 ASN ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1196 GLN A1225 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9784 Z= 0.198 Angle : 0.520 7.449 13262 Z= 0.277 Chirality : 0.040 0.147 1538 Planarity : 0.004 0.032 1646 Dihedral : 6.444 89.762 1302 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.17 % Allowed : 12.57 % Favored : 84.26 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), residues: 1187 helix: -0.03 (0.18), residues: 777 sheet: 0.96 (0.79), residues: 45 loop : 0.43 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1099 HIS 0.004 0.001 HIS A 934 PHE 0.022 0.002 PHE A 258 TYR 0.018 0.002 TYR A 917 ARG 0.004 0.000 ARG A1030 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 144 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8708 (tp40) cc_final: 0.8345 (tp40) REVERT: A 200 ASN cc_start: 0.8225 (t0) cc_final: 0.7987 (t0) REVERT: A 289 TYR cc_start: 0.8412 (m-80) cc_final: 0.8132 (m-80) REVERT: A 706 ARG cc_start: 0.7900 (tpp-160) cc_final: 0.7353 (mmt180) REVERT: A 728 TYR cc_start: 0.8004 (t80) cc_final: 0.7784 (t80) REVERT: A 744 MET cc_start: 0.7634 (mmm) cc_final: 0.6860 (mtt) REVERT: A 1016 TYR cc_start: 0.7419 (m-10) cc_final: 0.6624 (m-10) REVERT: A 1056 LEU cc_start: 0.8840 (mt) cc_final: 0.8544 (tp) REVERT: A 1058 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9117 (mp) REVERT: A 1068 GLN cc_start: 0.8548 (mt0) cc_final: 0.8276 (mm-40) REVERT: A 1122 GLN cc_start: 0.7634 (tt0) cc_final: 0.7084 (tp40) REVERT: A 1136 ASP cc_start: 0.7868 (t0) cc_final: 0.7025 (p0) outliers start: 33 outliers final: 26 residues processed: 166 average time/residue: 0.2148 time to fit residues: 50.5107 Evaluate side-chains 159 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 132 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1118 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.5980 chunk 1 optimal weight: 0.0040 chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 9.9990 chunk 98 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9784 Z= 0.192 Angle : 0.512 7.298 13262 Z= 0.273 Chirality : 0.040 0.168 1538 Planarity : 0.004 0.028 1646 Dihedral : 6.142 86.934 1302 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.45 % Allowed : 13.44 % Favored : 83.11 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1187 helix: 0.17 (0.19), residues: 774 sheet: 0.77 (0.76), residues: 45 loop : 0.41 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1099 HIS 0.003 0.001 HIS A 934 PHE 0.020 0.001 PHE A 258 TYR 0.020 0.001 TYR A 917 ARG 0.006 0.000 ARG A1030 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8713 (tp40) cc_final: 0.8354 (tp40) REVERT: A 200 ASN cc_start: 0.8220 (t0) cc_final: 0.8002 (t0) REVERT: A 289 TYR cc_start: 0.8326 (m-80) cc_final: 0.8080 (m-80) REVERT: A 367 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8037 (tp) REVERT: A 607 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8612 (mmtt) REVERT: A 706 ARG cc_start: 0.7887 (tpp-160) cc_final: 0.7349 (mmt180) REVERT: A 728 TYR cc_start: 0.8003 (t80) cc_final: 0.7772 (t80) REVERT: A 744 MET cc_start: 0.7615 (mmm) cc_final: 0.6925 (mtt) REVERT: A 953 ASP cc_start: 0.8119 (m-30) cc_final: 0.7198 (m-30) REVERT: A 1016 TYR cc_start: 0.7383 (m-10) cc_final: 0.6649 (m-10) REVERT: A 1056 LEU cc_start: 0.8858 (mt) cc_final: 0.8559 (tp) REVERT: A 1058 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9078 (mp) REVERT: A 1068 GLN cc_start: 0.8565 (mt0) cc_final: 0.8323 (mm-40) REVERT: A 1120 ILE cc_start: 0.8570 (mp) cc_final: 0.8352 (pt) REVERT: A 1122 GLN cc_start: 0.7563 (tt0) cc_final: 0.7155 (tp40) REVERT: A 1136 ASP cc_start: 0.7962 (t0) cc_final: 0.7073 (p0) REVERT: A 1218 LYS cc_start: 0.9238 (mmtt) cc_final: 0.8955 (mmmt) outliers start: 36 outliers final: 27 residues processed: 164 average time/residue: 0.2208 time to fit residues: 50.8779 Evaluate side-chains 162 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1118 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 95 optimal weight: 0.0470 chunk 53 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9784 Z= 0.196 Angle : 0.507 7.382 13262 Z= 0.268 Chirality : 0.040 0.164 1538 Planarity : 0.004 0.027 1646 Dihedral : 5.858 80.541 1302 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.65 % Allowed : 13.15 % Favored : 83.21 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.24), residues: 1187 helix: 0.22 (0.19), residues: 776 sheet: 0.66 (0.75), residues: 47 loop : 0.42 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1099 HIS 0.003 0.001 HIS A 934 PHE 0.018 0.001 PHE A 258 TYR 0.020 0.001 TYR A 917 ARG 0.006 0.000 ARG A1030 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 142 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8711 (tp40) cc_final: 0.8336 (tp40) REVERT: A 200 ASN cc_start: 0.8167 (t0) cc_final: 0.7847 (t0) REVERT: A 289 TYR cc_start: 0.8306 (m-80) cc_final: 0.8055 (m-80) REVERT: A 367 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8080 (tp) REVERT: A 706 ARG cc_start: 0.7867 (tpp-160) cc_final: 0.7294 (mmt180) REVERT: A 744 MET cc_start: 0.7562 (mmm) cc_final: 0.6894 (mtt) REVERT: A 953 ASP cc_start: 0.8171 (m-30) cc_final: 0.7264 (m-30) REVERT: A 1016 TYR cc_start: 0.7371 (m-10) cc_final: 0.6729 (m-10) REVERT: A 1074 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8288 (m) REVERT: A 1120 ILE cc_start: 0.8552 (mp) cc_final: 0.8304 (pt) REVERT: A 1122 GLN cc_start: 0.7567 (tt0) cc_final: 0.6839 (tp40) REVERT: A 1132 ARG cc_start: 0.7201 (mmm-85) cc_final: 0.6901 (mmm-85) REVERT: A 1136 ASP cc_start: 0.7924 (t0) cc_final: 0.6946 (p0) REVERT: A 1201 ASP cc_start: 0.7974 (t0) cc_final: 0.7671 (t0) REVERT: A 1202 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6529 (mm-30) REVERT: A 1218 LYS cc_start: 0.9228 (mmtt) cc_final: 0.8949 (mmmt) outliers start: 38 outliers final: 27 residues processed: 163 average time/residue: 0.2207 time to fit residues: 50.7404 Evaluate side-chains 161 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1135 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 64 optimal weight: 0.1980 chunk 114 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 20.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9784 Z= 0.223 Angle : 0.535 7.304 13262 Z= 0.280 Chirality : 0.041 0.256 1538 Planarity : 0.004 0.028 1646 Dihedral : 5.719 76.034 1302 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.55 % Allowed : 14.40 % Favored : 82.05 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.24), residues: 1187 helix: 0.26 (0.19), residues: 772 sheet: 0.44 (0.66), residues: 58 loop : 0.52 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1147 HIS 0.003 0.001 HIS A 798 PHE 0.017 0.002 PHE A 258 TYR 0.033 0.002 TYR A1259 ARG 0.007 0.000 ARG A1030 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 136 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8715 (tp40) cc_final: 0.8337 (tp40) REVERT: A 200 ASN cc_start: 0.8126 (t0) cc_final: 0.7788 (t0) REVERT: A 367 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8041 (tp) REVERT: A 409 MET cc_start: 0.5781 (ppp) cc_final: 0.5364 (ppp) REVERT: A 744 MET cc_start: 0.7544 (mmm) cc_final: 0.6895 (mtt) REVERT: A 953 ASP cc_start: 0.8167 (m-30) cc_final: 0.7865 (m-30) REVERT: A 1016 TYR cc_start: 0.7374 (m-10) cc_final: 0.6761 (m-10) REVERT: A 1074 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8291 (m) REVERT: A 1120 ILE cc_start: 0.8562 (mp) cc_final: 0.8340 (pt) REVERT: A 1122 GLN cc_start: 0.7540 (tt0) cc_final: 0.6821 (tp40) REVERT: A 1132 ARG cc_start: 0.7213 (mmm-85) cc_final: 0.6923 (mmm-85) REVERT: A 1136 ASP cc_start: 0.7961 (t0) cc_final: 0.7034 (p0) REVERT: A 1166 MET cc_start: 0.7692 (mmm) cc_final: 0.7450 (mmp) REVERT: A 1201 ASP cc_start: 0.7948 (t0) cc_final: 0.7688 (t0) REVERT: A 1202 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6514 (mm-30) REVERT: A 1218 LYS cc_start: 0.9250 (mmtt) cc_final: 0.8974 (mmmt) outliers start: 37 outliers final: 30 residues processed: 159 average time/residue: 0.2074 time to fit residues: 47.0406 Evaluate side-chains 163 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 131 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1134 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9784 Z= 0.221 Angle : 0.549 9.831 13262 Z= 0.288 Chirality : 0.041 0.163 1538 Planarity : 0.004 0.031 1646 Dihedral : 5.583 71.614 1302 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.36 % Allowed : 15.45 % Favored : 81.19 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.24), residues: 1187 helix: 0.27 (0.19), residues: 773 sheet: 0.44 (0.66), residues: 58 loop : 0.55 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1099 HIS 0.003 0.001 HIS A 798 PHE 0.016 0.001 PHE A 336 TYR 0.022 0.002 TYR A 289 ARG 0.007 0.000 ARG A1030 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 135 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8714 (tp40) cc_final: 0.8332 (tp40) REVERT: A 200 ASN cc_start: 0.8076 (t0) cc_final: 0.7742 (t0) REVERT: A 289 TYR cc_start: 0.8472 (m-80) cc_final: 0.8008 (m-80) REVERT: A 367 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8058 (tp) REVERT: A 409 MET cc_start: 0.5781 (ppp) cc_final: 0.5379 (ppp) REVERT: A 744 MET cc_start: 0.7535 (mmm) cc_final: 0.6919 (mtt) REVERT: A 1016 TYR cc_start: 0.7368 (m-10) cc_final: 0.6730 (m-10) REVERT: A 1074 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8301 (m) REVERT: A 1120 ILE cc_start: 0.8560 (mp) cc_final: 0.8334 (pt) REVERT: A 1122 GLN cc_start: 0.7509 (tt0) cc_final: 0.6832 (tp40) REVERT: A 1132 ARG cc_start: 0.7204 (mmm-85) cc_final: 0.6858 (mmm-85) REVERT: A 1136 ASP cc_start: 0.7970 (t0) cc_final: 0.7046 (p0) REVERT: A 1166 MET cc_start: 0.7552 (mmm) cc_final: 0.7301 (mmm) REVERT: A 1201 ASP cc_start: 0.7918 (t0) cc_final: 0.7708 (t0) REVERT: A 1218 LYS cc_start: 0.9246 (mmtt) cc_final: 0.8968 (mmmt) outliers start: 35 outliers final: 28 residues processed: 156 average time/residue: 0.2289 time to fit residues: 51.3390 Evaluate side-chains 163 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1134 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 68 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9784 Z= 0.211 Angle : 0.536 7.889 13262 Z= 0.280 Chirality : 0.041 0.178 1538 Planarity : 0.004 0.102 1646 Dihedral : 5.433 65.953 1302 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.26 % Allowed : 15.64 % Favored : 81.09 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1187 helix: 0.34 (0.19), residues: 771 sheet: 0.39 (0.67), residues: 58 loop : 0.58 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1099 HIS 0.003 0.001 HIS A 934 PHE 0.022 0.001 PHE A 258 TYR 0.021 0.001 TYR A 289 ARG 0.007 0.000 ARG A1030 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8712 (tp40) cc_final: 0.8331 (tp40) REVERT: A 200 ASN cc_start: 0.8083 (t0) cc_final: 0.7762 (t0) REVERT: A 289 TYR cc_start: 0.8471 (m-80) cc_final: 0.8004 (m-80) REVERT: A 367 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8116 (tp) REVERT: A 409 MET cc_start: 0.5739 (ppp) cc_final: 0.5349 (ppp) REVERT: A 744 MET cc_start: 0.7516 (mmm) cc_final: 0.6918 (mtt) REVERT: A 1016 TYR cc_start: 0.7331 (m-10) cc_final: 0.6698 (m-10) REVERT: A 1074 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8320 (m) REVERT: A 1120 ILE cc_start: 0.8514 (mp) cc_final: 0.8299 (pt) REVERT: A 1122 GLN cc_start: 0.7550 (tt0) cc_final: 0.6867 (tp40) REVERT: A 1132 ARG cc_start: 0.7289 (mmm-85) cc_final: 0.6899 (mmm-85) REVERT: A 1136 ASP cc_start: 0.7992 (t0) cc_final: 0.7061 (p0) REVERT: A 1201 ASP cc_start: 0.7882 (t0) cc_final: 0.7651 (t0) REVERT: A 1218 LYS cc_start: 0.9233 (mmtt) cc_final: 0.8962 (mmmt) outliers start: 34 outliers final: 27 residues processed: 161 average time/residue: 0.2327 time to fit residues: 54.1006 Evaluate side-chains 158 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 1027 TYR Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1118 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 94 optimal weight: 0.0670 chunk 9 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9784 Z= 0.198 Angle : 0.545 8.594 13262 Z= 0.279 Chirality : 0.040 0.167 1538 Planarity : 0.004 0.075 1646 Dihedral : 5.245 59.211 1302 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.07 % Allowed : 16.31 % Favored : 80.61 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1187 helix: 0.37 (0.19), residues: 777 sheet: 0.34 (0.66), residues: 58 loop : 0.48 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1099 HIS 0.003 0.001 HIS A 934 PHE 0.025 0.001 PHE A 258 TYR 0.022 0.001 TYR A 289 ARG 0.008 0.000 ARG A1030 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8708 (tp40) cc_final: 0.8322 (tp40) REVERT: A 200 ASN cc_start: 0.8046 (t0) cc_final: 0.7792 (t0) REVERT: A 289 TYR cc_start: 0.8458 (m-80) cc_final: 0.7979 (m-80) REVERT: A 367 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8147 (tp) REVERT: A 409 MET cc_start: 0.5785 (ppp) cc_final: 0.5508 (pmm) REVERT: A 706 ARG cc_start: 0.7849 (tpp-160) cc_final: 0.7299 (mmt180) REVERT: A 728 TYR cc_start: 0.7879 (t80) cc_final: 0.7679 (t80) REVERT: A 744 MET cc_start: 0.7497 (mmm) cc_final: 0.6934 (mtt) REVERT: A 1016 TYR cc_start: 0.7336 (m-10) cc_final: 0.6711 (m-10) REVERT: A 1074 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8312 (m) REVERT: A 1122 GLN cc_start: 0.7544 (tt0) cc_final: 0.6897 (tp40) REVERT: A 1132 ARG cc_start: 0.7250 (mmm-85) cc_final: 0.6764 (mmm-85) REVERT: A 1136 ASP cc_start: 0.8038 (t0) cc_final: 0.7078 (p0) REVERT: A 1202 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6573 (mm-30) REVERT: A 1218 LYS cc_start: 0.9251 (mmtt) cc_final: 0.8984 (mmmt) outliers start: 32 outliers final: 27 residues processed: 155 average time/residue: 0.2216 time to fit residues: 48.2174 Evaluate side-chains 162 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 1027 TYR Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1134 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.221253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.179975 restraints weight = 11824.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.178776 restraints weight = 12199.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.180149 restraints weight = 11613.200| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.205 9784 Z= 0.343 Angle : 0.886 59.200 13262 Z= 0.517 Chirality : 0.050 1.109 1538 Planarity : 0.005 0.090 1646 Dihedral : 5.339 59.173 1302 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.60 % Favored : 98.32 % Rotamer: Outliers : 2.88 % Allowed : 16.51 % Favored : 80.61 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1187 helix: 0.36 (0.19), residues: 777 sheet: 0.34 (0.66), residues: 58 loop : 0.46 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1099 HIS 0.003 0.001 HIS A 934 PHE 0.024 0.001 PHE A 258 TYR 0.021 0.001 TYR A 289 ARG 0.015 0.000 ARG A 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2164.72 seconds wall clock time: 40 minutes 15.49 seconds (2415.49 seconds total)