Starting phenix.real_space_refine on Thu Jul 2 18:29:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oe4_70386/07_2026/9oe4_70386.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oe4_70386/07_2026/9oe4_70386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oe4_70386/07_2026/9oe4_70386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oe4_70386/07_2026/9oe4_70386.map" model { file = "/net/cci-nas-00/data/ceres_data/9oe4_70386/07_2026/9oe4_70386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oe4_70386/07_2026/9oe4_70386.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 49 5.16 5 C 5932 2.51 5 N 1561 2.21 5 O 1723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9273 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1179, 9138 Classifications: {'peptide': 1179} Link IDs: {'PTRANS': 27, 'TRANS': 1151} Chain breaks: 2 Chain: "A" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 135 Unusual residues: {' MG': 2, 'AGS': 2, 'CHD': 1, 'R0Z': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 1.90, per 1000 atoms: 0.20 Number of scatterers: 9273 At special positions: 0 Unit cell: (72.21, 115.37, 150.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 49 16.00 P 6 15.00 Mg 2 11.99 O 1723 8.00 N 1561 7.00 C 5932 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: 0.89 Conformation dependent library (CDL) restraints added in 306.4 milliseconds 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 68.2% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 49 through 96 removed outlier: 3.668A pdb=" N MET A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU A 70 " --> pdb=" O ASN A 66 " (cutoff:3.500A) Proline residue: A 71 - end of helix removed outlier: 4.056A pdb=" N VAL A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 162 removed outlier: 3.575A pdb=" N LYS A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 172 through 191 removed outlier: 4.394A pdb=" N ASP A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 216 removed outlier: 3.826A pdb=" N GLY A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 265 removed outlier: 4.177A pdb=" N VAL A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 3.657A pdb=" N ALA A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 272 Processing helix chain 'A' and resid 274 through 327 removed outlier: 3.638A pdb=" N ILE A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 323 " --> pdb=" O PHE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 353 Processing helix chain 'A' and resid 353 through 376 removed outlier: 3.724A pdb=" N LYS A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 445 removed outlier: 3.565A pdb=" N THR A 441 " --> pdb=" O GLY A 437 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 513 through 520 removed outlier: 4.602A pdb=" N PHE A 517 " --> pdb=" O ASN A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 551 Processing helix chain 'A' and resid 570 through 579 removed outlier: 4.012A pdb=" N ALA A 576 " --> pdb=" O THR A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 598 removed outlier: 4.092A pdb=" N ILE A 597 " --> pdb=" O ARG A 593 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 593 through 598' Processing helix chain 'A' and resid 616 through 622 Processing helix chain 'A' and resid 626 through 638 removed outlier: 3.851A pdb=" N GLN A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 702 Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 706 through 736 removed outlier: 3.650A pdb=" N ALA A 717 " --> pdb=" O GLY A 713 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Proline residue: A 725 - end of helix removed outlier: 3.505A pdb=" N ALA A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 735 " --> pdb=" O PHE A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 740 Processing helix chain 'A' and resid 742 through 797 Processing helix chain 'A' and resid 798 through 804 removed outlier: 3.772A pdb=" N TYR A 802 " --> pdb=" O ASP A 798 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 808 through 816 Processing helix chain 'A' and resid 822 through 826 Processing helix chain 'A' and resid 827 through 851 removed outlier: 4.204A pdb=" N THR A 843 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 901 removed outlier: 3.847A pdb=" N THR A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 858 " --> pdb=" O GLN A 854 " (cutoff:3.500A) Proline residue: A 864 - end of helix removed outlier: 4.397A pdb=" N ALA A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP A 884 " --> pdb=" O HIS A 880 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS A 885 " --> pdb=" O ALA A 881 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLN A 890 " --> pdb=" O LYS A 886 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ALA A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE A 894 " --> pdb=" O GLN A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 910 through 921 Processing helix chain 'A' and resid 922 through 964 removed outlier: 3.508A pdb=" N HIS A 934 " --> pdb=" O LYS A 930 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE A 947 " --> pdb=" O SER A 943 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TYR A 948 " --> pdb=" O GLN A 944 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE A 949 " --> pdb=" O ALA A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 992 Processing helix chain 'A' and resid 995 through 1012 removed outlier: 3.673A pdb=" N SER A1002 " --> pdb=" O LYS A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1082 Processing helix chain 'A' and resid 1103 through 1110 Processing helix chain 'A' and resid 1124 through 1131 Processing helix chain 'A' and resid 1140 through 1150 Processing helix chain 'A' and resid 1152 through 1158 Processing helix chain 'A' and resid 1161 through 1165 Processing helix chain 'A' and resid 1177 through 1190 removed outlier: 4.307A pdb=" N ARG A1190 " --> pdb=" O ARG A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1220 removed outlier: 3.500A pdb=" N GLN A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP A1214 " --> pdb=" O LYS A1210 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A1215 " --> pdb=" O ILE A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1259 Processing helix chain 'A' and resid 1264 through 1269 Processing sheet with id=AA1, first strand: chain 'A' and resid 420 through 422 Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 5.948A pdb=" N GLY A 476 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASP A 560 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL A 478 " --> pdb=" O ASP A 560 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A 557 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL A 590 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 559 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE A 428 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR A 427 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ALA A 604 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA A 429 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N PHE A 606 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 431 " --> pdb=" O PHE A 606 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU A 613 " --> pdb=" O GLY A 605 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN A 607 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE A 611 " --> pdb=" O GLN A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1051 through 1057 removed outlier: 6.557A pdb=" N GLN A1052 " --> pdb=" O TYR A1039 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR A1039 " --> pdb=" O GLN A1052 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU A1054 " --> pdb=" O HIS A1037 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1111 through 1114 removed outlier: 6.539A pdb=" N GLY A1112 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASP A1198 " --> pdb=" O GLY A1112 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A1114 " --> pdb=" O ASP A1198 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ALA A1242 " --> pdb=" O THR A1063 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ALA A1065 " --> pdb=" O ALA A1242 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL A1244 " --> pdb=" O ALA A1065 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL A1067 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU A1251 " --> pdb=" O VAL A1243 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1689 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: 1.83 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 3068 1.37 - 1.52: 3104 1.52 - 1.66: 3179 1.66 - 1.81: 69 1.81 - 1.95: 18 Bond restraints: 9438 Sorted by residual: bond pdb=" C37 R0Z A1305 " pdb=" C38 R0Z A1305 " ideal model delta sigma weight residual 1.502 1.367 0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" C17 R0Z A1305 " pdb=" C18 R0Z A1305 " ideal model delta sigma weight residual 1.491 1.387 0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C21 R0Z A1305 " pdb=" N20 R0Z A1305 " ideal model delta sigma weight residual 1.403 1.310 0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C31 R0Z A1305 " pdb=" C32 R0Z A1305 " ideal model delta sigma weight residual 1.505 1.414 0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" O3B AGS A1303 " pdb=" PB AGS A1303 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.02e+01 ... (remaining 9433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 12534 2.20 - 4.40: 180 4.40 - 6.60: 43 6.60 - 8.81: 15 8.81 - 11.01: 8 Bond angle restraints: 12780 Sorted by residual: angle pdb=" C28 R0Z A1305 " pdb=" N29 R0Z A1305 " pdb=" C30 R0Z A1305 " ideal model delta sigma weight residual 115.78 104.77 11.01 3.00e+00 1.11e-01 1.35e+01 angle pdb=" O3A AGS A1304 " pdb=" PB AGS A1304 " pdb=" O3B AGS A1304 " ideal model delta sigma weight residual 100.38 110.91 -10.53 3.00e+00 1.11e-01 1.23e+01 angle pdb=" O3A AGS A1303 " pdb=" PB AGS A1303 " pdb=" O3B AGS A1303 " ideal model delta sigma weight residual 100.38 110.20 -9.82 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C LEU A 700 " pdb=" N LYS A 701 " pdb=" CA LYS A 701 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 angle pdb=" C ALA A 512 " pdb=" N ASN A 513 " pdb=" CA ASN A 513 " ideal model delta sigma weight residual 122.08 126.72 -4.64 1.47e+00 4.63e-01 9.96e+00 ... (remaining 12775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 5446 35.35 - 70.69: 255 70.69 - 106.04: 24 106.04 - 141.38: 7 141.38 - 176.73: 2 Dihedral angle restraints: 5734 sinusoidal: 2349 harmonic: 3385 Sorted by residual: dihedral pdb=" O3A AGS A1304 " pdb=" O3B AGS A1304 " pdb=" PB AGS A1304 " pdb=" PG AGS A1304 " ideal model delta sinusoidal sigma weight residual -107.39 69.34 -176.73 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS A1303 " pdb=" O3A AGS A1303 " pdb=" PA AGS A1303 " pdb=" PB AGS A1303 " ideal model delta sinusoidal sigma weight residual 82.37 -79.10 161.47 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CA ARG A 552 " pdb=" C ARG A 552 " pdb=" N ASN A 553 " pdb=" CA ASN A 553 " ideal model delta harmonic sigma weight residual 180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 5731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1163 0.051 - 0.103: 271 0.103 - 0.154: 40 0.154 - 0.206: 2 0.206 - 0.257: 3 Chirality restraints: 1479 Sorted by residual: chirality pdb=" C3' AGS A1304 " pdb=" C2' AGS A1304 " pdb=" C4' AGS A1304 " pdb=" O3' AGS A1304 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL A 477 " pdb=" CA VAL A 477 " pdb=" CG1 VAL A 477 " pdb=" CG2 VAL A 477 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C3' AGS A1303 " pdb=" C2' AGS A1303 " pdb=" C4' AGS A1303 " pdb=" O3' AGS A1303 " both_signs ideal model delta sigma weight residual False -2.37 -2.61 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1476 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 R0Z A1305 " 0.030 2.00e-02 2.50e+03 2.89e-02 1.04e+01 pdb=" C18 R0Z A1305 " -0.025 2.00e-02 2.50e+03 pdb=" C21 R0Z A1305 " 0.033 2.00e-02 2.50e+03 pdb=" N20 R0Z A1305 " -0.039 2.00e-02 2.50e+03 pdb=" O19 R0Z A1305 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 309 " -0.013 2.00e-02 2.50e+03 2.52e-02 6.36e+00 pdb=" C PHE A 309 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE A 309 " -0.016 2.00e-02 2.50e+03 pdb=" N MET A 310 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 300 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C VAL A 300 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL A 300 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN A 301 " 0.014 2.00e-02 2.50e+03 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 85 2.62 - 3.19: 8143 3.19 - 3.76: 14622 3.76 - 4.33: 20077 4.33 - 4.90: 32847 Nonbonded interactions: 75774 Sorted by model distance: nonbonded pdb="MG MG A1301 " pdb=" O3G AGS A1304 " model vdw 2.054 2.170 nonbonded pdb=" OE1 GLN A1116 " pdb="MG MG A1301 " model vdw 2.190 2.170 nonbonded pdb=" O MET A 794 " pdb=" OH TYR A 802 " model vdw 2.273 3.040 nonbonded pdb=" O ASP A1205 " pdb=" OG SER A1208 " model vdw 2.290 3.040 nonbonded pdb=" O ILE A 626 " pdb=" OG SER A 629 " model vdw 2.306 3.040 ... (remaining 75769 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.740 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:8.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 9438 Z= 0.248 Angle : 0.766 11.007 12780 Z= 0.374 Chirality : 0.044 0.257 1479 Planarity : 0.005 0.047 1604 Dihedral : 19.749 176.731 3560 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 3.98 % Allowed : 17.98 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.23), residues: 1173 helix: -0.41 (0.18), residues: 758 sheet: 0.06 (0.63), residues: 68 loop : -2.00 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 552 TYR 0.012 0.001 TYR A 515 PHE 0.018 0.002 PHE A 969 TRP 0.008 0.001 TRP A1106 HIS 0.003 0.001 HIS A 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.25 ( 9438) covalent geometry : angle 0.76613 / 0.37 (12780) hydrogen bonds : bond 0.19557 / 12.80 ( 573) hydrogen bonds : angle 6.76142 / 4.82 ( 1689) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 56 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8611 (mtt) REVERT: A 532 ARG cc_start: 0.8638 (mmm160) cc_final: 0.8406 (mmp-170) REVERT: A 635 MET cc_start: 0.8939 (mpm) cc_final: 0.8242 (ptp) REVERT: A 786 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9005 (mp) REVERT: A 882 LEU cc_start: 0.9217 (pt) cc_final: 0.8996 (mm) REVERT: A 984 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7785 (ttt) REVERT: A 1093 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7619 (mmm) REVERT: A 1139 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7173 (p0) outliers start: 39 outliers final: 15 residues processed: 88 average time/residue: 0.4694 time to fit residues: 44.8508 Evaluate side-chains 71 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1194 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.0050 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.090048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.064334 restraints weight = 23423.235| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.89 r_work: 0.3027 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9438 Z= 0.196 Angle : 0.587 7.219 12780 Z= 0.302 Chirality : 0.043 0.263 1479 Planarity : 0.004 0.041 1604 Dihedral : 12.340 163.302 1463 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.58 % Favored : 96.33 % Rotamer: Outliers : 4.29 % Allowed : 18.28 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.25), residues: 1173 helix: 0.80 (0.19), residues: 763 sheet: -0.22 (0.59), residues: 73 loop : -1.81 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 910 TYR 0.015 0.002 TYR A 282 PHE 0.017 0.002 PHE A 969 TRP 0.008 0.001 TRP A 960 HIS 0.003 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 ( 9438) covalent geometry : angle 0.58697 / 0.30 (12780) hydrogen bonds : bond 0.05292 / 3.42 ( 573) hydrogen bonds : angle 4.30140 / 3.06 ( 1689) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 54 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 57 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8609 (mtt) REVERT: A 317 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8472 (mm) REVERT: A 506 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: A 532 ARG cc_start: 0.8576 (mmm160) cc_final: 0.8339 (mmp-170) REVERT: A 635 MET cc_start: 0.8931 (mpm) cc_final: 0.8543 (mtp) REVERT: A 786 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9046 (mp) REVERT: A 882 LEU cc_start: 0.9154 (pt) cc_final: 0.8950 (mm) REVERT: A 984 MET cc_start: 0.8220 (mpt) cc_final: 0.7706 (ptm) REVERT: A 1055 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7666 (tmmm) REVERT: A 1093 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7566 (mtt) REVERT: A 1115 SER cc_start: 0.8566 (m) cc_final: 0.8240 (t) REVERT: A 1139 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7429 (p0) outliers start: 42 outliers final: 20 residues processed: 91 average time/residue: 0.4238 time to fit residues: 42.3796 Evaluate side-chains 78 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 51 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 723 MET Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1055 LYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1194 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 HIS A 368 HIS A 822 GLN A1134 ASN ** A1236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.091001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.065252 restraints weight = 23221.878| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.92 r_work: 0.3054 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9438 Z= 0.128 Angle : 0.536 8.413 12780 Z= 0.268 Chirality : 0.040 0.194 1479 Planarity : 0.003 0.040 1604 Dihedral : 10.543 141.775 1453 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.42 % Rotamer: Outliers : 4.19 % Allowed : 19.10 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.25), residues: 1173 helix: 1.34 (0.19), residues: 763 sheet: -0.02 (0.59), residues: 75 loop : -1.63 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 598 TYR 0.014 0.001 TYR A 252 PHE 0.014 0.001 PHE A 969 TRP 0.008 0.001 TRP A 960 HIS 0.002 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 9438) covalent geometry : angle 0.53581 / 0.27 (12780) hydrogen bonds : bond 0.04529 / 2.94 ( 573) hydrogen bonds : angle 3.94630 / 2.81 ( 1689) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 54 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 57 MET cc_start: 0.8879 (ttp) cc_final: 0.8600 (mtt) REVERT: A 110 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9077 (pp) REVERT: A 317 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8477 (mm) REVERT: A 506 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8465 (mp0) REVERT: A 635 MET cc_start: 0.8927 (mpm) cc_final: 0.8552 (mtp) REVERT: A 984 MET cc_start: 0.8236 (mpt) cc_final: 0.7622 (ttm) REVERT: A 1115 SER cc_start: 0.8554 (m) cc_final: 0.8209 (t) REVERT: A 1139 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7311 (p0) outliers start: 41 outliers final: 14 residues processed: 93 average time/residue: 0.4171 time to fit residues: 42.3131 Evaluate side-chains 67 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 723 MET Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1194 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 31 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.088430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.061982 restraints weight = 23724.412| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.85 r_work: 0.2966 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9438 Z= 0.218 Angle : 0.579 7.161 12780 Z= 0.294 Chirality : 0.042 0.187 1479 Planarity : 0.003 0.040 1604 Dihedral : 10.071 137.943 1442 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.18 % Favored : 95.74 % Rotamer: Outliers : 4.29 % Allowed : 19.92 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.25), residues: 1173 helix: 1.40 (0.19), residues: 765 sheet: 0.40 (0.62), residues: 63 loop : -1.65 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 910 TYR 0.019 0.002 TYR A1266 PHE 0.017 0.002 PHE A 969 TRP 0.007 0.001 TRP A 960 HIS 0.003 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 ( 9438) covalent geometry : angle 0.57869 / 0.29 (12780) hydrogen bonds : bond 0.04887 / 3.16 ( 573) hydrogen bonds : angle 4.01105 / 2.85 ( 1689) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 50 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 57 MET cc_start: 0.8914 (ttp) cc_final: 0.8650 (mtt) REVERT: A 197 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8186 (mpp) REVERT: A 317 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8436 (mm) REVERT: A 506 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8417 (mp0) REVERT: A 532 ARG cc_start: 0.8380 (mmp-170) cc_final: 0.8053 (mmp80) REVERT: A 635 MET cc_start: 0.8902 (mpm) cc_final: 0.8585 (mtp) REVERT: A 984 MET cc_start: 0.8131 (mpt) cc_final: 0.7612 (ttm) REVERT: A 1093 MET cc_start: 0.8515 (mmm) cc_final: 0.8038 (mmm) REVERT: A 1115 SER cc_start: 0.8614 (m) cc_final: 0.8305 (t) REVERT: A 1139 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7421 (p0) outliers start: 42 outliers final: 21 residues processed: 89 average time/residue: 0.3715 time to fit residues: 36.4418 Evaluate side-chains 72 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 47 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 723 MET Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1194 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 87 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.090328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.064270 restraints weight = 23340.559| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.83 r_work: 0.3009 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9438 Z= 0.128 Angle : 0.538 10.166 12780 Z= 0.266 Chirality : 0.039 0.164 1479 Planarity : 0.003 0.039 1604 Dihedral : 9.852 137.498 1441 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.42 % Rotamer: Outliers : 3.88 % Allowed : 21.04 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.25), residues: 1173 helix: 1.57 (0.19), residues: 769 sheet: 0.36 (0.59), residues: 73 loop : -1.56 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1181 TYR 0.016 0.001 TYR A1266 PHE 0.013 0.001 PHE A 969 TRP 0.009 0.001 TRP A 960 HIS 0.002 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 9438) covalent geometry : angle 0.53767 / 0.27 (12780) hydrogen bonds : bond 0.04323 / 2.81 ( 573) hydrogen bonds : angle 3.79065 / 2.70 ( 1689) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 55 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8881 (ttp) cc_final: 0.8622 (mtt) REVERT: A 110 ILE cc_start: 0.9430 (OUTLIER) cc_final: 0.9146 (pp) REVERT: A 506 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8430 (mp0) REVERT: A 519 MET cc_start: 0.8623 (mmm) cc_final: 0.8386 (mmt) REVERT: A 532 ARG cc_start: 0.8396 (mmp-170) cc_final: 0.8083 (mmp80) REVERT: A 543 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.6927 (ttp-110) REVERT: A 635 MET cc_start: 0.8911 (mpm) cc_final: 0.8632 (mtp) REVERT: A 984 MET cc_start: 0.8091 (mpt) cc_final: 0.7585 (ttm) REVERT: A 1115 SER cc_start: 0.8680 (m) cc_final: 0.8357 (t) REVERT: A 1139 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7342 (p0) outliers start: 38 outliers final: 21 residues processed: 89 average time/residue: 0.3976 time to fit residues: 38.6999 Evaluate side-chains 75 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 50 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1194 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 ASN ** A1236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.089599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.063648 restraints weight = 23548.317| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.81 r_work: 0.2988 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9438 Z= 0.165 Angle : 0.562 11.363 12780 Z= 0.278 Chirality : 0.041 0.162 1479 Planarity : 0.003 0.039 1604 Dihedral : 9.827 137.700 1441 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.42 % Rotamer: Outliers : 4.29 % Allowed : 21.04 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.25), residues: 1173 helix: 1.58 (0.19), residues: 769 sheet: 0.41 (0.59), residues: 73 loop : -1.51 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 910 TYR 0.015 0.001 TYR A1266 PHE 0.015 0.001 PHE A 969 TRP 0.007 0.001 TRP A 960 HIS 0.002 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 9438) covalent geometry : angle 0.56207 / 0.28 (12780) hydrogen bonds : bond 0.04478 / 2.90 ( 573) hydrogen bonds : angle 3.82733 / 2.72 ( 1689) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 50 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8854 (ttp) cc_final: 0.8576 (mtt) REVERT: A 317 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8476 (mm) REVERT: A 506 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8421 (mp0) REVERT: A 532 ARG cc_start: 0.8413 (mmp-170) cc_final: 0.8125 (mmp80) REVERT: A 635 MET cc_start: 0.8947 (mpm) cc_final: 0.8656 (mtp) REVERT: A 984 MET cc_start: 0.8065 (mpt) cc_final: 0.7506 (ttm) REVERT: A 1055 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7601 (tmmm) REVERT: A 1115 SER cc_start: 0.8712 (m) cc_final: 0.8378 (t) REVERT: A 1139 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7410 (p0) REVERT: A 1268 LEU cc_start: 0.9141 (mm) cc_final: 0.8866 (mm) outliers start: 42 outliers final: 22 residues processed: 88 average time/residue: 0.4333 time to fit residues: 41.4014 Evaluate side-chains 75 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 49 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1055 LYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1194 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 ASN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.090752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.064791 restraints weight = 23313.512| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.82 r_work: 0.3012 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9438 Z= 0.123 Angle : 0.551 12.133 12780 Z= 0.269 Chirality : 0.039 0.148 1479 Planarity : 0.003 0.038 1604 Dihedral : 9.707 138.127 1441 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.15 % Favored : 96.76 % Rotamer: Outliers : 3.37 % Allowed : 22.27 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.25), residues: 1173 helix: 1.68 (0.19), residues: 769 sheet: 0.59 (0.60), residues: 73 loop : -1.56 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1181 TYR 0.014 0.001 TYR A1266 PHE 0.012 0.001 PHE A 969 TRP 0.009 0.001 TRP A 960 HIS 0.002 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 9438) covalent geometry : angle 0.55050 / 0.27 (12780) hydrogen bonds : bond 0.04186 / 2.72 ( 573) hydrogen bonds : angle 3.71583 / 2.64 ( 1689) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 55 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 57 MET cc_start: 0.8853 (ttp) cc_final: 0.8611 (mtt) REVERT: A 317 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8469 (mm) REVERT: A 506 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8430 (mp0) REVERT: A 532 ARG cc_start: 0.8443 (mmp-170) cc_final: 0.8168 (mmp80) REVERT: A 635 MET cc_start: 0.8908 (mpm) cc_final: 0.8637 (mtp) REVERT: A 984 MET cc_start: 0.8079 (mpt) cc_final: 0.7481 (ttm) REVERT: A 1093 MET cc_start: 0.8509 (mmm) cc_final: 0.8006 (mmm) REVERT: A 1115 SER cc_start: 0.8727 (m) cc_final: 0.8390 (t) outliers start: 33 outliers final: 23 residues processed: 85 average time/residue: 0.3881 time to fit residues: 36.0884 Evaluate side-chains 73 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 48 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1194 VAL Chi-restraints excluded: chain A residue 1266 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 77 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 51 optimal weight: 0.0670 chunk 41 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 ASN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.090563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.064402 restraints weight = 23260.367| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.86 r_work: 0.3022 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9438 Z= 0.122 Angle : 0.570 12.787 12780 Z= 0.276 Chirality : 0.040 0.185 1479 Planarity : 0.003 0.038 1604 Dihedral : 9.642 138.436 1439 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.50 % Rotamer: Outliers : 3.88 % Allowed : 22.27 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.25), residues: 1173 helix: 1.75 (0.19), residues: 768 sheet: 0.59 (0.59), residues: 74 loop : -1.56 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1181 TYR 0.014 0.001 TYR A1266 PHE 0.012 0.001 PHE A 969 TRP 0.009 0.001 TRP A 960 HIS 0.002 0.001 HIS A1153 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9438) covalent geometry : angle 0.57012 / 0.28 (12780) hydrogen bonds : bond 0.04117 / 2.68 ( 573) hydrogen bonds : angle 3.71722 / 2.65 ( 1689) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 50 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 57 MET cc_start: 0.8836 (ttp) cc_final: 0.8596 (mtt) REVERT: A 317 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8482 (mm) REVERT: A 506 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8421 (mp0) REVERT: A 532 ARG cc_start: 0.8436 (mmp-170) cc_final: 0.8170 (mmp80) REVERT: A 635 MET cc_start: 0.8887 (mpm) cc_final: 0.8637 (mtp) REVERT: A 984 MET cc_start: 0.8105 (mpt) cc_final: 0.7531 (ttm) REVERT: A 1115 SER cc_start: 0.8720 (m) cc_final: 0.8390 (t) REVERT: A 1139 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7337 (p0) outliers start: 38 outliers final: 24 residues processed: 85 average time/residue: 0.3927 time to fit residues: 36.3343 Evaluate side-chains 73 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 46 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1194 VAL Chi-restraints excluded: chain A residue 1266 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 69 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 GLN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.090845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.064832 restraints weight = 23304.350| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.84 r_work: 0.3030 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9438 Z= 0.121 Angle : 0.578 13.313 12780 Z= 0.278 Chirality : 0.040 0.173 1479 Planarity : 0.003 0.037 1604 Dihedral : 9.617 138.801 1439 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.50 % Rotamer: Outliers : 3.68 % Allowed : 22.88 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.25), residues: 1173 helix: 1.82 (0.19), residues: 768 sheet: 0.61 (0.59), residues: 74 loop : -1.53 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1181 TYR 0.013 0.001 TYR A 252 PHE 0.012 0.001 PHE A 969 TRP 0.008 0.001 TRP A 960 HIS 0.002 0.000 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 9438) covalent geometry : angle 0.57805 / 0.28 (12780) hydrogen bonds : bond 0.04078 / 2.66 ( 573) hydrogen bonds : angle 3.68083 / 2.62 ( 1689) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 51 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 57 MET cc_start: 0.8820 (ttp) cc_final: 0.8586 (mtt) REVERT: A 317 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8469 (mm) REVERT: A 506 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8416 (mp0) REVERT: A 635 MET cc_start: 0.8891 (mpm) cc_final: 0.8627 (mtp) REVERT: A 984 MET cc_start: 0.8089 (mpt) cc_final: 0.7486 (ttm) REVERT: A 1093 MET cc_start: 0.8486 (mmm) cc_final: 0.8040 (mmm) REVERT: A 1115 SER cc_start: 0.8706 (m) cc_final: 0.8351 (t) REVERT: A 1139 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7320 (p0) REVERT: A 1172 THR cc_start: 0.7146 (OUTLIER) cc_final: 0.6925 (p) outliers start: 36 outliers final: 26 residues processed: 83 average time/residue: 0.4402 time to fit residues: 39.5121 Evaluate side-chains 77 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 47 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1194 VAL Chi-restraints excluded: chain A residue 1266 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1178 GLN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.090538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.064547 restraints weight = 23517.935| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.85 r_work: 0.3000 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9438 Z= 0.148 Angle : 0.611 12.806 12780 Z= 0.295 Chirality : 0.041 0.247 1479 Planarity : 0.003 0.037 1604 Dihedral : 9.607 139.257 1437 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.42 % Rotamer: Outliers : 3.06 % Allowed : 23.70 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.25), residues: 1173 helix: 1.80 (0.19), residues: 768 sheet: 0.55 (0.58), residues: 74 loop : -1.54 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1181 TYR 0.016 0.001 TYR A1266 PHE 0.019 0.001 PHE A1155 TRP 0.007 0.001 TRP A 960 HIS 0.002 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 9438) covalent geometry : angle 0.61120 / 0.29 (12780) hydrogen bonds : bond 0.04226 / 2.76 ( 573) hydrogen bonds : angle 3.71712 / 2.65 ( 1689) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 49 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 57 MET cc_start: 0.8833 (ttp) cc_final: 0.8603 (mtt) REVERT: A 317 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8473 (mm) REVERT: A 506 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: A 532 ARG cc_start: 0.8273 (mmp-170) cc_final: 0.7992 (mmp80) REVERT: A 635 MET cc_start: 0.8897 (mpm) cc_final: 0.8633 (mtp) REVERT: A 984 MET cc_start: 0.8096 (mpt) cc_final: 0.7525 (ttm) REVERT: A 1093 MET cc_start: 0.8511 (mmm) cc_final: 0.8075 (mmm) REVERT: A 1115 SER cc_start: 0.8728 (m) cc_final: 0.8385 (t) REVERT: A 1139 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7366 (p0) REVERT: A 1172 THR cc_start: 0.7218 (OUTLIER) cc_final: 0.6986 (p) outliers start: 30 outliers final: 25 residues processed: 75 average time/residue: 0.3576 time to fit residues: 29.3320 Evaluate side-chains 77 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 48 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1194 VAL Chi-restraints excluded: chain A residue 1266 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 103 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 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 = 0.3702 r_free = 0.3702 target = 0.090665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.064558 restraints weight = 23236.052| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.86 r_work: 0.3020 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9438 Z= 0.132 Angle : 0.609 13.084 12780 Z= 0.292 Chirality : 0.040 0.233 1479 Planarity : 0.003 0.037 1604 Dihedral : 9.572 139.792 1435 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.59 % Rotamer: Outliers : 3.47 % Allowed : 23.29 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.25), residues: 1173 helix: 1.85 (0.19), residues: 767 sheet: 0.57 (0.59), residues: 74 loop : -1.48 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1181 TYR 0.014 0.001 TYR A1266 PHE 0.017 0.001 PHE A1155 TRP 0.008 0.001 TRP A 960 HIS 0.002 0.000 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 9438) covalent geometry : angle 0.60873 / 0.29 (12780) hydrogen bonds : bond 0.04167 / 2.72 ( 573) hydrogen bonds : angle 3.69680 / 2.64 ( 1689) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2280.32 seconds wall clock time: 39 minutes 50.22 seconds (2390.22 seconds total)