Starting phenix.real_space_refine on Sun Dec 29 04:44:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bwp_16293/12_2024/8bwp_16293.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bwp_16293/12_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/cci-nas-00/data/ceres_data/8bwp_16293/12_2024/8bwp_16293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bwp_16293/12_2024/8bwp_16293.map" model { file = "/net/cci-nas-00/data/ceres_data/8bwp_16293/12_2024/8bwp_16293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bwp_16293/12_2024/8bwp_16293.cif" } 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. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.57, per 1000 atoms: 0.69 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.2 seconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB MTX A1401 " Number of C-beta restraints generated: 2266 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 5 sheets defined 73.1% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 27 through 35 removed outlier: 3.742A pdb=" N PHE A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 75 removed outlier: 4.316A pdb=" N GLY A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.769A pdb=" N ALA A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 121 removed outlier: 4.157A pdb=" N LEU A 93 " --> pdb=" O TRP A 89 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 127 through 150 Processing helix chain 'A' and resid 150 through 181 removed outlier: 3.956A pdb=" N LEU A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) 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 182 through 189 Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 204 through 212 removed outlier: 4.337A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 235 through 246 removed outlier: 3.944A pdb=" N ALA A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 282 removed outlier: 3.893A pdb=" N LEU A 250 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 291 through 342 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 347 through 367 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 367 through 391 removed outlier: 3.509A pdb=" N LEU A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 460 Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 500 through 511 Processing helix chain 'A' and resid 513 through 521 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 536 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 567 through 576 removed outlier: 4.392A pdb=" N PHE A 574 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 600 removed outlier: 3.873A pdb=" N LYS A 598 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 697 through 709 removed outlier: 3.505A pdb=" N GLY A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 745 removed outlier: 3.647A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 808 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 809 through 816 removed outlier: 3.697A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 827 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 827 through 835 removed outlier: 4.611A pdb=" N ASP A 833 " --> pdb=" O ILE A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 861 Processing helix chain 'A' and resid 864 through 896 Proline residue: A 870 - end of helix removed outlier: 3.599A pdb=" N ARG A 880 " --> pdb=" O ILE A 876 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.891A pdb=" N PHE A 901 " --> pdb=" O ARG A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 removed outlier: 3.724A pdb=" N TYR A 917 " --> pdb=" O THR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 970 removed outlier: 4.016A pdb=" N CYS A 923 " --> pdb=" O ALA A 919 " (cutoff:3.500A) 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 975 through 987 Processing helix chain 'A' and resid 988 through 1007 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) Processing helix chain 'A' and resid 1007 through 1018 removed outlier: 3.772A pdb=" N TYR A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A1018 " --> pdb=" O ILE A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1089 Processing helix chain 'A' and resid 1109 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 1130 through 1136 Processing helix chain 'A' and resid 1142 through 1153 Processing helix chain 'A' and resid 1155 through 1161 Processing helix chain 'A' and resid 1164 through 1168 Processing helix chain 'A' and resid 1171 through 1175 Processing helix chain 'A' and resid 1178 through 1194 Processing helix chain 'A' and resid 1203 through 1207 Processing helix chain 'A' and resid 1208 through 1223 Processing helix chain 'A' and resid 1234 through 1238 Processing helix chain 'A' and resid 1257 through 1264 Processing helix chain 'A' and resid 1267 through 1275 Processing helix chain 'A' and resid 1276 through 1278 No H-bonds generated for 'chain 'A' and resid 1276 through 1278' Processing helix chain 'A' and resid 1279 through 1294 Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 435 removed outlier: 5.804A pdb=" N GLN A 429 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ALA A 417 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE A 433 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLN A 413 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL A 435 " --> pdb=" O HIS A 411 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N HIS A 411 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE A 415 " --> pdb=" O HIS A 466 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N HIS A 466 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.847A pdb=" N ALA A 476 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA A 442 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU A 606 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL A 444 " --> pdb=" O LEU A 606 " (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=AA3, first strand: chain 'A' and resid 487 through 488 removed outlier: 4.644A pdb=" N GLY A 487 " --> pdb=" O ILE A 528 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1058 through 1065 removed outlier: 5.790A pdb=" N LYS A1059 " --> pdb=" O PHE A1048 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE A1048 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ALA A1063 " --> pdb=" O ASP A1044 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP A1044 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE A1065 " --> pdb=" O ILE A1042 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE A1042 " --> pdb=" O ILE A1065 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL A1046 " --> pdb=" O GLU A1095 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU A1095 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1117 through 1120 removed outlier: 6.451A pdb=" N LEU A1198 " --> pdb=" O LEU A1229 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE A1231 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE A1200 " --> pdb=" O ILE A1231 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS A1070 " --> pdb=" O LYS A1243 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N MET A1245 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY A1072 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU A1247 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL A1074 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) 609 hydrogen bonds defined for protein. 1761 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: 3.55 Time building geometry restraints manager: 2.98 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: 0.00 - 1.88: 12676 1.88 - 3.77: 488 3.77 - 5.65: 75 5.65 - 7.54: 18 7.54 - 9.42: 5 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: 1421 2.75 - 3.29: 10324 3.29 - 3.83: 15536 3.83 - 4.36: 18837 4.36 - 4.90: 31944 Nonbonded interactions: 78062 Sorted by model distance: nonbonded pdb=" NH1 ARG A 303 " pdb=" OE1 GLU A 306 " model vdw 2.213 3.120 nonbonded pdb=" OH TYR A 92 " pdb=" O THR A 209 " model vdw 2.214 3.040 nonbonded pdb=" O SER A1241 " pdb=" OH TYR A1292 " model vdw 2.219 3.040 nonbonded pdb=" O GLU A 521 " pdb=" OG1 THR A 526 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR A 269 " pdb=" OE2 GLU A 306 " model vdw 2.247 3.040 ... (remaining 78057 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: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.460 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.110 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 5 poor density : 207 time to evaluate : 1.232 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: 0.2743 time to fit residues: 76.8740 Evaluate side-chains 140 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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: 1.9990 chunk 50 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 0.0870 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 994 GLN ** A1216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9784 Z= 0.260 Angle : 0.612 7.709 13262 Z= 0.331 Chirality : 0.043 0.173 1538 Planarity : 0.004 0.039 1646 Dihedral : 6.777 82.668 1304 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.82 % Allowed : 8.06 % Favored : 90.12 % 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: 0.38 (0.24), residues: 1187 helix: 0.26 (0.18), residues: 788 sheet: 0.55 (0.76), residues: 52 loop : 0.61 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 711 HIS 0.006 0.001 HIS A1225 PHE 0.033 0.002 PHE A 258 TYR 0.023 0.002 TYR A1292 ARG 0.009 0.001 ARG A1220 *********************** 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 201 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ILE cc_start: 0.8124 (mm) cc_final: 0.7920 (tt) REVERT: A 200 ASN cc_start: 0.8444 (t0) cc_final: 0.8094 (t0) REVERT: A 306 GLU cc_start: 0.8116 (tt0) cc_final: 0.7908 (tt0) REVERT: A 706 ARG cc_start: 0.7908 (tpp-160) cc_final: 0.7570 (mmt180) REVERT: A 744 MET cc_start: 0.7782 (mmm) cc_final: 0.7026 (mtp) REVERT: A 994 GLN cc_start: 0.7960 (mt0) cc_final: 0.7703 (mp10) REVERT: A 1016 TYR cc_start: 0.7548 (m-10) cc_final: 0.6530 (m-10) REVERT: A 1056 LEU cc_start: 0.8779 (mt) cc_final: 0.8533 (tp) REVERT: A 1058 LEU cc_start: 0.9318 (mp) cc_final: 0.9020 (tt) REVERT: A 1117 MET cc_start: 0.8304 (mtm) cc_final: 0.8097 (mtt) REVERT: A 1118 SER cc_start: 0.9148 (t) cc_final: 0.8732 (p) REVERT: A 1131 MET cc_start: 0.7379 (mmm) cc_final: 0.7156 (tpp) REVERT: A 1136 ASP cc_start: 0.7949 (t0) cc_final: 0.7236 (t70) REVERT: A 1196 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7413 (tp40) outliers start: 19 outliers final: 15 residues processed: 194 average time/residue: 0.2180 time to fit residues: 59.7392 Evaluate side-chains 159 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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: 4.9990 chunk 33 optimal weight: 0.2980 chunk 89 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1134 ASN A1206 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9784 Z= 0.232 Angle : 0.567 7.112 13262 Z= 0.303 Chirality : 0.042 0.193 1538 Planarity : 0.004 0.034 1646 Dihedral : 6.458 87.807 1303 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.17 % Allowed : 10.36 % Favored : 86.47 % 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: 0.83 (0.25), residues: 1187 helix: 0.64 (0.18), residues: 787 sheet: 1.55 (0.84), residues: 45 loop : 0.56 (0.36), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 89 HIS 0.004 0.001 HIS A 831 PHE 0.033 0.002 PHE A 258 TYR 0.021 0.002 TYR A 289 ARG 0.005 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 190 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8644 (tp40) cc_final: 0.8313 (tp40) REVERT: A 67 GLU cc_start: 0.8761 (tp30) cc_final: 0.8379 (tp30) REVERT: A 97 ILE cc_start: 0.8105 (mm) cc_final: 0.7885 (tt) REVERT: A 184 MET cc_start: 0.7557 (mpp) cc_final: 0.7207 (ptp) REVERT: A 706 ARG cc_start: 0.7892 (tpp-160) cc_final: 0.7517 (mmt180) REVERT: A 744 MET cc_start: 0.7659 (mmm) cc_final: 0.6903 (mtp) REVERT: A 1016 TYR cc_start: 0.7424 (m-10) cc_final: 0.6567 (m-10) REVERT: A 1027 TYR cc_start: 0.7641 (m-80) cc_final: 0.7415 (m-10) REVERT: A 1056 LEU cc_start: 0.8831 (mt) cc_final: 0.8537 (tp) REVERT: A 1068 GLN cc_start: 0.8439 (mt0) cc_final: 0.8055 (mm-40) REVERT: A 1122 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7518 (tp40) REVERT: A 1136 ASP cc_start: 0.8160 (t0) cc_final: 0.7255 (t0) REVERT: A 1181 GLN cc_start: 0.7949 (mp10) cc_final: 0.7699 (mp10) outliers start: 33 outliers final: 23 residues processed: 181 average time/residue: 0.2283 time to fit residues: 59.2310 Evaluate side-chains 156 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 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 818 ILE Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 902 SER 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 1064 LEU Chi-restraints excluded: chain A residue 1082 SER 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: 0.5980 chunk 56 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 0.0060 chunk 72 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 102 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 95 optimal weight: 0.0000 overall best weight: 0.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9784 Z= 0.173 Angle : 0.542 8.681 13262 Z= 0.288 Chirality : 0.040 0.168 1538 Planarity : 0.004 0.033 1646 Dihedral : 6.247 89.173 1302 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.40 % Allowed : 12.48 % Favored : 85.12 % 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: 1.09 (0.25), residues: 1187 helix: 0.87 (0.19), residues: 792 sheet: 1.26 (0.82), residues: 47 loop : 0.60 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 89 HIS 0.003 0.001 HIS A 934 PHE 0.033 0.001 PHE A 258 TYR 0.024 0.002 TYR A 289 ARG 0.006 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 175 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8626 (tp40) cc_final: 0.8117 (tp-100) REVERT: A 67 GLU cc_start: 0.8771 (tp30) cc_final: 0.8531 (tp30) REVERT: A 184 MET cc_start: 0.7545 (mpp) cc_final: 0.7020 (ptp) REVERT: A 289 TYR cc_start: 0.7682 (m-80) cc_final: 0.7365 (m-80) REVERT: A 306 GLU cc_start: 0.8113 (tt0) cc_final: 0.7888 (tt0) REVERT: A 706 ARG cc_start: 0.7871 (tpp-160) cc_final: 0.7522 (mmt180) REVERT: A 728 TYR cc_start: 0.7925 (t80) cc_final: 0.7708 (t80) REVERT: A 744 MET cc_start: 0.7615 (mmm) cc_final: 0.7023 (mtt) REVERT: A 1016 TYR cc_start: 0.7435 (m-10) cc_final: 0.6665 (m-10) REVERT: A 1056 LEU cc_start: 0.8826 (mt) cc_final: 0.8554 (tp) REVERT: A 1068 GLN cc_start: 0.8436 (mt0) cc_final: 0.8068 (mm-40) REVERT: A 1120 ILE cc_start: 0.8608 (mp) cc_final: 0.8285 (pt) REVERT: A 1122 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7081 (tp40) REVERT: A 1136 ASP cc_start: 0.8138 (t0) cc_final: 0.7510 (t0) REVERT: A 1201 ASP cc_start: 0.8126 (t0) cc_final: 0.7649 (t0) REVERT: A 1202 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6595 (mm-30) outliers start: 25 outliers final: 18 residues processed: 166 average time/residue: 0.2495 time to fit residues: 59.2446 Evaluate side-chains 152 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 308 SER 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 818 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1082 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 79 optimal weight: 0.0770 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1134 ASN ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9784 Z= 0.210 Angle : 0.540 8.690 13262 Z= 0.284 Chirality : 0.041 0.172 1538 Planarity : 0.004 0.035 1646 Dihedral : 6.017 84.389 1302 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.59 % Allowed : 13.24 % Favored : 84.17 % 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: 1.23 (0.25), residues: 1187 helix: 0.96 (0.19), residues: 790 sheet: 1.47 (0.84), residues: 47 loop : 0.69 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1099 HIS 0.004 0.001 HIS A 934 PHE 0.033 0.002 PHE A 258 TYR 0.021 0.001 TYR A 289 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 169 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8629 (tp40) cc_final: 0.8108 (tp-100) REVERT: A 67 GLU cc_start: 0.8748 (tp30) cc_final: 0.8537 (tp30) REVERT: A 184 MET cc_start: 0.7527 (mpp) cc_final: 0.7040 (ptp) REVERT: A 276 MET cc_start: 0.7863 (tpp) cc_final: 0.7550 (mmm) REVERT: A 289 TYR cc_start: 0.7728 (m-80) cc_final: 0.7416 (m-80) REVERT: A 306 GLU cc_start: 0.8097 (tt0) cc_final: 0.7861 (tt0) REVERT: A 706 ARG cc_start: 0.7869 (tpp-160) cc_final: 0.7461 (mmt180) REVERT: A 744 MET cc_start: 0.7624 (mmm) cc_final: 0.7026 (mtt) REVERT: A 1016 TYR cc_start: 0.7434 (m-10) cc_final: 0.6701 (m-10) REVERT: A 1029 LYS cc_start: 0.7970 (tptp) cc_final: 0.7723 (tptp) REVERT: A 1068 GLN cc_start: 0.8388 (mt0) cc_final: 0.7944 (mm-40) REVERT: A 1117 MET cc_start: 0.8272 (mtm) cc_final: 0.7945 (mtt) REVERT: A 1122 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7147 (tp40) REVERT: A 1136 ASP cc_start: 0.8164 (t0) cc_final: 0.7510 (t0) REVERT: A 1201 ASP cc_start: 0.8108 (t0) cc_final: 0.7555 (t0) REVERT: A 1202 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6441 (mm-30) outliers start: 27 outliers final: 24 residues processed: 159 average time/residue: 0.2260 time to fit residues: 50.8846 Evaluate side-chains 158 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 308 SER 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 767 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1082 SER Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.7860 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9784 Z= 0.260 Angle : 0.559 8.419 13262 Z= 0.292 Chirality : 0.042 0.174 1538 Planarity : 0.004 0.036 1646 Dihedral : 5.881 80.389 1302 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.36 % Allowed : 13.24 % Favored : 83.40 % 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: 1.24 (0.25), residues: 1187 helix: 0.94 (0.19), residues: 790 sheet: 1.73 (0.85), residues: 45 loop : 0.73 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1099 HIS 0.004 0.001 HIS A 831 PHE 0.034 0.002 PHE A 258 TYR 0.021 0.002 TYR A 289 ARG 0.007 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 176 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8667 (tp40) cc_final: 0.8137 (tp-100) REVERT: A 184 MET cc_start: 0.7535 (mpp) cc_final: 0.7112 (ptp) REVERT: A 241 MET cc_start: 0.8037 (mmm) cc_final: 0.7785 (mmm) REVERT: A 276 MET cc_start: 0.7907 (tpp) cc_final: 0.7557 (mmm) REVERT: A 289 TYR cc_start: 0.7801 (m-80) cc_final: 0.7439 (m-80) REVERT: A 306 GLU cc_start: 0.8108 (tt0) cc_final: 0.7845 (tt0) REVERT: A 706 ARG cc_start: 0.7848 (tpp-160) cc_final: 0.7452 (mmt180) REVERT: A 744 MET cc_start: 0.7636 (mmm) cc_final: 0.7084 (mtt) REVERT: A 1016 TYR cc_start: 0.7442 (m-10) cc_final: 0.6744 (m-10) REVERT: A 1029 LYS cc_start: 0.7921 (tptp) cc_final: 0.7715 (tptp) REVERT: A 1117 MET cc_start: 0.8245 (mtm) cc_final: 0.7847 (mtt) REVERT: A 1120 ILE cc_start: 0.8562 (mp) cc_final: 0.8254 (pt) REVERT: A 1122 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7682 (tp40) REVERT: A 1136 ASP cc_start: 0.8235 (t0) cc_final: 0.7576 (t0) outliers start: 35 outliers final: 29 residues processed: 166 average time/residue: 0.2204 time to fit residues: 51.3847 Evaluate side-chains 161 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 81 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 129 VAL 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 286 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 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 818 ILE Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1005 ASN 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 1082 SER Chi-restraints excluded: chain A residue 1216 GLN Chi-restraints excluded: chain A residue 1272 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 96 optimal weight: 7.9990 chunk 64 optimal weight: 0.5980 chunk 114 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1134 ASN A1195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9784 Z= 0.221 Angle : 0.544 10.519 13262 Z= 0.283 Chirality : 0.041 0.171 1538 Planarity : 0.004 0.035 1646 Dihedral : 5.736 75.810 1302 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.07 % Allowed : 14.30 % Favored : 82.63 % 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: 1.29 (0.25), residues: 1187 helix: 0.99 (0.19), residues: 790 sheet: 1.92 (0.84), residues: 45 loop : 0.71 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1099 HIS 0.003 0.001 HIS A 934 PHE 0.034 0.002 PHE A 258 TYR 0.021 0.001 TYR A 289 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 165 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8650 (tp40) cc_final: 0.8095 (tp-100) REVERT: A 184 MET cc_start: 0.7532 (mpp) cc_final: 0.7123 (ptp) REVERT: A 289 TYR cc_start: 0.7771 (m-80) cc_final: 0.7438 (m-80) REVERT: A 306 GLU cc_start: 0.8124 (tt0) cc_final: 0.7870 (tt0) REVERT: A 706 ARG cc_start: 0.7850 (tpp-160) cc_final: 0.7437 (mmt180) REVERT: A 744 MET cc_start: 0.7633 (mmm) cc_final: 0.7104 (mtt) REVERT: A 1016 TYR cc_start: 0.7416 (m-10) cc_final: 0.6730 (m-10) REVERT: A 1120 ILE cc_start: 0.8522 (mp) cc_final: 0.8275 (pt) REVERT: A 1122 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7720 (tp40) REVERT: A 1132 ARG cc_start: 0.7360 (mmm-85) cc_final: 0.6954 (mmm-85) REVERT: A 1136 ASP cc_start: 0.8134 (t0) cc_final: 0.7511 (t0) outliers start: 32 outliers final: 30 residues processed: 157 average time/residue: 0.2214 time to fit residues: 49.4791 Evaluate side-chains 158 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 81 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 129 VAL 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 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 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 818 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1082 SER Chi-restraints excluded: chain A residue 1146 LEU Chi-restraints excluded: chain A residue 1216 GLN Chi-restraints excluded: chain A residue 1272 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 100 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 GLN A1225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9784 Z= 0.224 Angle : 0.540 10.632 13262 Z= 0.283 Chirality : 0.041 0.195 1538 Planarity : 0.004 0.036 1646 Dihedral : 5.566 69.621 1302 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.36 % Allowed : 13.92 % Favored : 82.73 % 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: 1.31 (0.25), residues: 1187 helix: 1.03 (0.19), residues: 791 sheet: 1.64 (0.82), residues: 47 loop : 0.69 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1099 HIS 0.005 0.001 HIS A1225 PHE 0.034 0.002 PHE A 258 TYR 0.020 0.001 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 169 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8656 (tp40) cc_final: 0.8119 (tp-100) REVERT: A 184 MET cc_start: 0.7516 (mpp) cc_final: 0.7289 (ptp) REVERT: A 276 MET cc_start: 0.7819 (tpp) cc_final: 0.7568 (mmm) REVERT: A 289 TYR cc_start: 0.7790 (m-10) cc_final: 0.7519 (m-80) REVERT: A 306 GLU cc_start: 0.8086 (tt0) cc_final: 0.7811 (tt0) REVERT: A 706 ARG cc_start: 0.7839 (tpp-160) cc_final: 0.7439 (mmt180) REVERT: A 744 MET cc_start: 0.7649 (mmm) cc_final: 0.7061 (mtt) REVERT: A 1016 TYR cc_start: 0.7390 (m-10) cc_final: 0.6743 (m-80) REVERT: A 1029 LYS cc_start: 0.7897 (tptp) cc_final: 0.7609 (tptp) REVERT: A 1117 MET cc_start: 0.7676 (mtt) cc_final: 0.7468 (mtt) REVERT: A 1120 ILE cc_start: 0.8500 (mp) cc_final: 0.8250 (pt) REVERT: A 1122 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7780 (tp40) REVERT: A 1136 ASP cc_start: 0.8123 (t0) cc_final: 0.7283 (p0) outliers start: 35 outliers final: 32 residues processed: 159 average time/residue: 0.2205 time to fit residues: 50.5895 Evaluate side-chains 161 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 81 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 129 VAL 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 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 818 ILE Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1005 ASN 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 1082 SER Chi-restraints excluded: chain A residue 1146 LEU Chi-restraints excluded: chain A residue 1216 GLN Chi-restraints excluded: chain A residue 1225 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 68 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1195 ASN A1225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9784 Z= 0.210 Angle : 0.547 9.401 13262 Z= 0.285 Chirality : 0.041 0.186 1538 Planarity : 0.004 0.036 1646 Dihedral : 5.506 65.830 1302 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.17 % Allowed : 14.20 % Favored : 82.63 % 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: 1.34 (0.25), residues: 1187 helix: 1.05 (0.19), residues: 791 sheet: 1.64 (0.71), residues: 58 loop : 0.66 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1099 HIS 0.004 0.001 HIS A1225 PHE 0.033 0.002 PHE A 258 TYR 0.033 0.002 TYR A1259 ARG 0.008 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 169 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8653 (tp40) cc_final: 0.8110 (tp-100) REVERT: A 184 MET cc_start: 0.7534 (mpp) cc_final: 0.7297 (ptp) REVERT: A 276 MET cc_start: 0.7825 (tpp) cc_final: 0.7506 (mmm) REVERT: A 289 TYR cc_start: 0.7793 (m-10) cc_final: 0.7544 (m-80) REVERT: A 306 GLU cc_start: 0.8064 (tt0) cc_final: 0.7786 (tt0) REVERT: A 706 ARG cc_start: 0.7878 (tpp-160) cc_final: 0.7480 (mmt180) REVERT: A 744 MET cc_start: 0.7644 (mmm) cc_final: 0.7058 (mtt) REVERT: A 1016 TYR cc_start: 0.7391 (m-10) cc_final: 0.6748 (m-80) REVERT: A 1029 LYS cc_start: 0.7870 (tptp) cc_final: 0.7579 (tptp) REVERT: A 1117 MET cc_start: 0.7769 (mtt) cc_final: 0.7523 (mtt) REVERT: A 1120 ILE cc_start: 0.8476 (mp) cc_final: 0.8232 (pt) REVERT: A 1122 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7831 (tp40) REVERT: A 1136 ASP cc_start: 0.8111 (t0) cc_final: 0.7286 (p0) outliers start: 33 outliers final: 28 residues processed: 159 average time/residue: 0.2153 time to fit residues: 49.1170 Evaluate side-chains 158 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 308 SER 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 767 ILE 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 1002 GLU Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1082 SER Chi-restraints excluded: chain A residue 1146 LEU Chi-restraints excluded: chain A residue 1216 GLN Chi-restraints excluded: chain A residue 1225 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9784 Z= 0.285 Angle : 0.580 7.392 13262 Z= 0.302 Chirality : 0.042 0.175 1538 Planarity : 0.004 0.035 1646 Dihedral : 5.508 63.072 1302 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.07 % Allowed : 14.78 % Favored : 82.15 % 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: 1.28 (0.25), residues: 1187 helix: 1.02 (0.19), residues: 784 sheet: 1.60 (0.71), residues: 58 loop : 0.60 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 947 HIS 0.009 0.001 HIS A1225 PHE 0.034 0.002 PHE A 258 TYR 0.029 0.002 TYR A1259 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 to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8663 (tp40) cc_final: 0.8119 (tp-100) REVERT: A 184 MET cc_start: 0.7550 (mpp) cc_final: 0.7334 (ptp) REVERT: A 276 MET cc_start: 0.7859 (tpp) cc_final: 0.7523 (mmm) REVERT: A 306 GLU cc_start: 0.8087 (tt0) cc_final: 0.7811 (tt0) REVERT: A 706 ARG cc_start: 0.7879 (tpp-160) cc_final: 0.7475 (mmt180) REVERT: A 744 MET cc_start: 0.7666 (mmm) cc_final: 0.7211 (mtt) REVERT: A 1016 TYR cc_start: 0.7398 (m-10) cc_final: 0.6753 (m-80) REVERT: A 1029 LYS cc_start: 0.7921 (tptp) cc_final: 0.7639 (tptp) REVERT: A 1117 MET cc_start: 0.8003 (mtt) cc_final: 0.7722 (mtt) REVERT: A 1122 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7899 (tp40) REVERT: A 1136 ASP cc_start: 0.8088 (t0) cc_final: 0.7374 (p0) outliers start: 32 outliers final: 29 residues processed: 157 average time/residue: 0.2127 time to fit residues: 47.6446 Evaluate side-chains 161 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 308 SER 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 818 ILE Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1082 SER Chi-restraints excluded: chain A residue 1146 LEU Chi-restraints excluded: chain A residue 1216 GLN Chi-restraints excluded: chain A residue 1225 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.221030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.177189 restraints weight = 11843.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.174483 restraints weight = 10079.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.176161 restraints weight = 9575.595| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9784 Z= 0.228 Angle : 0.563 7.785 13262 Z= 0.292 Chirality : 0.041 0.174 1538 Planarity : 0.004 0.036 1646 Dihedral : 5.418 59.747 1302 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.88 % Allowed : 15.45 % Favored : 81.67 % 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: 1.36 (0.25), residues: 1187 helix: 1.08 (0.19), residues: 784 sheet: 1.55 (0.70), residues: 58 loop : 0.67 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1099 HIS 0.005 0.001 HIS A1225 PHE 0.035 0.002 PHE A 258 TYR 0.031 0.002 TYR A 289 ARG 0.008 0.000 ARG A1030 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2143.78 seconds wall clock time: 40 minutes 20.48 seconds (2420.48 seconds total)