Starting phenix.real_space_refine on Sat Apr 6 22:40:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7p_10111/04_2024/6s7p_10111_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7p_10111/04_2024/6s7p_10111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7p_10111/04_2024/6s7p_10111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7p_10111/04_2024/6s7p_10111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7p_10111/04_2024/6s7p_10111_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7p_10111/04_2024/6s7p_10111_updated.pdb" } resolution = 3.2 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= 0.004 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 1 5.21 5 S 30 5.16 5 C 5864 2.51 5 N 1493 2.21 5 O 1634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 159": "NH1" <-> "NH2" Residue "A ARG 590": "NH1" <-> "NH2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A ARG 957": "NH1" <-> "NH2" Residue "A ARG 969": "NH1" <-> "NH2" Residue "A ARG 1013": "NH1" <-> "NH2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "A ARG 1232": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9028 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1139, 9028 Unusual residues: {' MG': 1, 'ATP': 2, 'CLR': 8} Classifications: {'peptide': 1128, 'undetermined': 11} Link IDs: {'PTRANS': 28, 'TRANS': 1099, None: 11} Not linked: pdbres="LYS A1251 " pdbres="ATP A1301 " Not linked: pdbres="ATP A1301 " pdbres="ATP A1302 " Not linked: pdbres="ATP A1302 " pdbres=" MG A1303 " Not linked: pdbres=" MG A1303 " pdbres="CLR A1304 " Not linked: pdbres="CLR A1304 " pdbres="CLR A1305 " ... (remaining 6 not shown) Chain breaks: 2 Time building chain proxies: 5.63, per 1000 atoms: 0.62 Number of scatterers: 9028 At special positions: 0 Unit cell: (100.8, 115.92, 116.76, 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 30 16.00 P 6 15.00 Mg 1 11.99 O 1634 8.00 N 1493 7.00 C 5864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.8 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 4 sheets defined 63.1% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 51 through 68 Processing helix chain 'A' and resid 70 through 80 removed outlier: 4.263A pdb=" N MET A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 159 removed outlier: 3.874A pdb=" N VAL A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TRP A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.720A pdb=" N ILE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 187 Processing helix chain 'A' and resid 190 through 212 Processing helix chain 'A' and resid 214 through 261 removed outlier: 3.687A pdb=" N LEU A 218 " --> pdb=" O TRP A 214 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix removed outlier: 3.616A pdb=" N ALA A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 272 through 324 removed outlier: 4.007A pdb=" N HIS A 282 " --> pdb=" O ARG A 278 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A 321 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 322 " --> pdb=" O TYR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 372 removed outlier: 3.832A pdb=" N VAL A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Proline residue: A 352 - end of helix removed outlier: 4.126A pdb=" N TYR A 365 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N VAL A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 442 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 465 through 471 Processing helix chain 'A' and resid 486 through 494 removed outlier: 4.025A pdb=" N ARG A 494 " --> pdb=" O ILE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'A' and resid 512 through 517 Processing helix chain 'A' and resid 521 through 523 No H-bonds generated for 'chain 'A' and resid 521 through 523' Processing helix chain 'A' and resid 528 through 530 No H-bonds generated for 'chain 'A' and resid 528 through 530' Processing helix chain 'A' and resid 538 through 549 removed outlier: 4.370A pdb=" N ARG A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 578 Processing helix chain 'A' and resid 614 through 618 Processing helix chain 'A' and resid 623 through 628 Processing helix chain 'A' and resid 697 through 700 No H-bonds generated for 'chain 'A' and resid 697 through 700' Processing helix chain 'A' and resid 708 through 738 removed outlier: 4.603A pdb=" N LEU A 724 " --> pdb=" O ALA A 720 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLN A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) Proline residue: A 726 - end of helix removed outlier: 4.756A pdb=" N SER A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL A 730 " --> pdb=" O PRO A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 795 removed outlier: 3.693A pdb=" N ILE A 753 " --> pdb=" O GLN A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 804 Processing helix chain 'A' and resid 810 through 828 removed outlier: 3.582A pdb=" N LEU A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 818 " --> pdb=" O SER A 814 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 852 removed outlier: 3.595A pdb=" N ILE A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 860 removed outlier: 3.838A pdb=" N LEU A 858 " --> pdb=" O TRP A 854 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU A 859 " --> pdb=" O GLN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 901 removed outlier: 3.855A pdb=" N GLY A 880 " --> pdb=" O LYS A 876 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 890 " --> pdb=" O LYS A 886 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 891 " --> pdb=" O LYS A 887 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 895 " --> pdb=" O ALA A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 909 Processing helix chain 'A' and resid 912 through 965 removed outlier: 5.297A pdb=" N GLY A 925 " --> pdb=" O GLU A 921 " (cutoff:3.500A) Proline residue: A 926 - end of helix removed outlier: 4.027A pdb=" N SER A 951 " --> pdb=" O PHE A 947 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR A 952 " --> pdb=" O MET A 948 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA A 953 " --> pdb=" O TYR A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 1012 removed outlier: 4.152A pdb=" N PHE A 982 " --> pdb=" O SER A 978 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY A 988 " --> pdb=" O ALA A 984 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N HIS A 989 " --> pdb=" O VAL A 985 " (cutoff:3.500A) Proline residue: A 995 - end of helix removed outlier: 4.291A pdb=" N ALA A 998 " --> pdb=" O ALA A 994 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS A 999 " --> pdb=" O PRO A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1083 removed outlier: 3.951A pdb=" N VAL A1079 " --> pdb=" O LYS A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1110 Processing helix chain 'A' and resid 1126 through 1133 removed outlier: 4.489A pdb=" N GLY A1133 " --> pdb=" O ASN A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1151 Processing helix chain 'A' and resid 1154 through 1159 Processing helix chain 'A' and resid 1170 through 1172 No H-bonds generated for 'chain 'A' and resid 1170 through 1172' Processing helix chain 'A' and resid 1177 through 1191 removed outlier: 4.601A pdb=" N ARG A1191 " --> pdb=" O ARG A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1220 removed outlier: 3.546A pdb=" N GLU A1215 " --> pdb=" O LYS A1211 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A1216 " --> pdb=" O VAL A1212 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 395 through 397 removed outlier: 3.570A pdb=" N THR A 452 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 424 through 427 removed outlier: 6.256A pdb=" N THR A 584 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU A 427 " --> pdb=" O THR A 584 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL A 586 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1056 through 1059 removed outlier: 3.599A pdb=" N LEU A1057 " --> pdb=" O PHE A1036 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A1092 " --> pdb=" O ASN A1037 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1241 through 1244 removed outlier: 6.987A pdb=" N CYS A1226 " --> pdb=" O LEU A1065 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N LEU A1067 " --> pdb=" O CYS A1226 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL A1228 " --> pdb=" O LEU A1067 " (cutoff:3.500A) 501 hydrogen bonds defined for protein. 1494 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: 2.83 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2410 1.33 - 1.45: 1648 1.45 - 1.57: 5097 1.57 - 1.69: 10 1.69 - 1.81: 51 Bond restraints: 9216 Sorted by residual: bond pdb=" C4 ATP A1302 " pdb=" C5 ATP A1302 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.95e+01 bond pdb=" C4 ATP A1301 " pdb=" C5 ATP A1301 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.93e+01 bond pdb=" C5 ATP A1302 " pdb=" C6 ATP A1302 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.97e+01 bond pdb=" C5 ATP A1301 " pdb=" C6 ATP A1301 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.80e+01 bond pdb=" C4 ATP A1301 " pdb=" N9 ATP A1301 " ideal model delta sigma weight residual 1.374 1.318 0.056 1.00e-02 1.00e+04 3.12e+01 ... (remaining 9211 not shown) Histogram of bond angle deviations from ideal: 98.71 - 106.17: 209 106.17 - 113.62: 5295 113.62 - 121.07: 4750 121.07 - 128.52: 2213 128.52 - 135.97: 50 Bond angle restraints: 12517 Sorted by residual: angle pdb=" PB ATP A1301 " pdb=" O3B ATP A1301 " pdb=" PG ATP A1301 " ideal model delta sigma weight residual 139.87 121.76 18.11 1.00e+00 1.00e+00 3.28e+02 angle pdb=" PB ATP A1302 " pdb=" O3B ATP A1302 " pdb=" PG ATP A1302 " ideal model delta sigma weight residual 139.87 122.92 16.95 1.00e+00 1.00e+00 2.87e+02 angle pdb=" PA ATP A1302 " pdb=" O3A ATP A1302 " pdb=" PB ATP A1302 " ideal model delta sigma weight residual 136.83 123.18 13.65 1.00e+00 1.00e+00 1.86e+02 angle pdb=" PA ATP A1301 " pdb=" O3A ATP A1301 " pdb=" PB ATP A1301 " ideal model delta sigma weight residual 136.83 124.45 12.38 1.00e+00 1.00e+00 1.53e+02 angle pdb=" C5 ATP A1302 " pdb=" C4 ATP A1302 " pdb=" N3 ATP A1302 " ideal model delta sigma weight residual 126.80 118.08 8.72 1.00e+00 1.00e+00 7.60e+01 ... (remaining 12512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 5508 15.93 - 31.86: 294 31.86 - 47.79: 60 47.79 - 63.71: 22 63.71 - 79.64: 7 Dihedral angle restraints: 5891 sinusoidal: 2658 harmonic: 3233 Sorted by residual: dihedral pdb=" CA GLN A 520 " pdb=" C GLN A 520 " pdb=" N LYS A 521 " pdb=" CA LYS A 521 " ideal model delta harmonic sigma weight residual -180.00 -153.70 -26.30 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA PRO A1161 " pdb=" C PRO A1161 " pdb=" N HIS A1162 " pdb=" CA HIS A1162 " ideal model delta harmonic sigma weight residual 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA VAL A 609 " pdb=" C VAL A 609 " pdb=" N GLU A 610 " pdb=" CA GLU A 610 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1255 0.093 - 0.187: 162 0.187 - 0.280: 18 0.280 - 0.373: 11 0.373 - 0.466: 6 Chirality restraints: 1452 Sorted by residual: chirality pdb=" C14 CLR A1306 " pdb=" C13 CLR A1306 " pdb=" C15 CLR A1306 " pdb=" C8 CLR A1306 " both_signs ideal model delta sigma weight residual False -2.32 -2.78 0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" C14 CLR A1304 " pdb=" C13 CLR A1304 " pdb=" C15 CLR A1304 " pdb=" C8 CLR A1304 " both_signs ideal model delta sigma weight residual False -2.32 -2.76 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" C14 CLR A1309 " pdb=" C13 CLR A1309 " pdb=" C15 CLR A1309 " pdb=" C8 CLR A1309 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 1449 not shown) Planarity restraints: 1534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 71 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO A 72 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 994 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO A 995 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 995 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 995 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1163 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C LYS A1163 " 0.037 2.00e-02 2.50e+03 pdb=" O LYS A1163 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR A1164 " -0.013 2.00e-02 2.50e+03 ... (remaining 1531 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 69 2.65 - 3.21: 8032 3.21 - 3.77: 13381 3.77 - 4.34: 18798 4.34 - 4.90: 31186 Nonbonded interactions: 71466 Sorted by model distance: nonbonded pdb=" O2G ATP A1302 " pdb="MG MG A1303 " model vdw 2.085 2.170 nonbonded pdb=" OE1 GLN A1117 " pdb="MG MG A1303 " model vdw 2.087 2.170 nonbonded pdb=" O2B ATP A1302 " pdb="MG MG A1303 " model vdw 2.088 2.170 nonbonded pdb=" NZ LYS A1075 " pdb=" O1G ATP A1302 " model vdw 2.347 2.520 nonbonded pdb=" OG SER A 483 " pdb=" OE1 GLU A 898 " model vdw 2.350 2.440 ... (remaining 71461 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: 1.090 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: 6.250 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 28.730 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.009 0.074 9216 Z= 0.601 Angle : 1.132 18.107 12517 Z= 0.664 Chirality : 0.075 0.466 1452 Planarity : 0.007 0.071 1534 Dihedral : 11.278 79.642 3817 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.33 % Allowed : 2.07 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.20), residues: 1122 helix: -1.69 (0.15), residues: 745 sheet: -1.23 (0.59), residues: 65 loop : -2.54 (0.29), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A1107 HIS 0.010 0.002 HIS A1154 PHE 0.036 0.004 PHE A 603 TYR 0.033 0.004 TYR A 118 ARG 0.018 0.002 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 81 MET cc_start: 0.3927 (ptt) cc_final: 0.3483 (mmp) REVERT: A 326 LYS cc_start: 0.7949 (mttt) cc_final: 0.7276 (mmmt) REVERT: A 1102 LYS cc_start: 0.7957 (mmtm) cc_final: 0.7739 (mttt) outliers start: 3 outliers final: 2 residues processed: 151 average time/residue: 0.2764 time to fit residues: 54.9836 Evaluate side-chains 88 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 775 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 GLN A 550 ASN A1037 ASN A1154 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9216 Z= 0.175 Angle : 0.506 8.755 12517 Z= 0.268 Chirality : 0.040 0.149 1452 Planarity : 0.003 0.037 1534 Dihedral : 8.974 84.460 1800 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.63 % Allowed : 5.98 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.24), residues: 1122 helix: 0.18 (0.18), residues: 745 sheet: -0.83 (0.59), residues: 70 loop : -1.99 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 317 HIS 0.005 0.001 HIS A 67 PHE 0.017 0.002 PHE A1085 TYR 0.011 0.001 TYR A 279 ARG 0.003 0.000 ARG A1013 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 0.991 Fit side-chains REVERT: A 71 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8246 (tt) REVERT: A 1071 SER cc_start: 0.8926 (t) cc_final: 0.8626 (m) outliers start: 15 outliers final: 8 residues processed: 121 average time/residue: 0.2147 time to fit residues: 36.9218 Evaluate side-chains 92 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1240 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9216 Z= 0.261 Angle : 0.557 8.005 12517 Z= 0.290 Chirality : 0.042 0.144 1452 Planarity : 0.003 0.043 1534 Dihedral : 8.720 85.652 1799 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.83 % Allowed : 7.62 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1122 helix: 0.58 (0.18), residues: 753 sheet: -0.98 (0.55), residues: 75 loop : -1.82 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 317 HIS 0.003 0.001 HIS A 67 PHE 0.017 0.002 PHE A 396 TYR 0.011 0.002 TYR A 132 ARG 0.003 0.000 ARG A1084 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 86 time to evaluate : 1.002 Fit side-chains REVERT: A 113 MET cc_start: 0.7415 (mmm) cc_final: 0.7202 (mtt) REVERT: A 949 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.6658 (t80) REVERT: A 1071 SER cc_start: 0.8955 (t) cc_final: 0.8646 (m) outliers start: 26 outliers final: 14 residues processed: 107 average time/residue: 0.1939 time to fit residues: 30.2113 Evaluate side-chains 93 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1240 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 0.0570 chunk 109 optimal weight: 0.6980 chunk 97 optimal weight: 0.0570 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A1037 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9216 Z= 0.162 Angle : 0.471 7.391 12517 Z= 0.248 Chirality : 0.039 0.140 1452 Planarity : 0.003 0.042 1534 Dihedral : 8.137 80.546 1799 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.96 % Allowed : 9.03 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1122 helix: 1.11 (0.19), residues: 751 sheet: -0.79 (0.56), residues: 75 loop : -1.62 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 317 HIS 0.004 0.001 HIS A 67 PHE 0.015 0.001 PHE A 316 TYR 0.014 0.001 TYR A 961 ARG 0.002 0.000 ARG A1013 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 1.003 Fit side-chains REVERT: A 196 PHE cc_start: 0.8013 (m-80) cc_final: 0.7804 (m-80) REVERT: A 949 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.6821 (t80) REVERT: A 1071 SER cc_start: 0.8864 (t) cc_final: 0.8626 (m) outliers start: 18 outliers final: 13 residues processed: 104 average time/residue: 0.1966 time to fit residues: 29.7977 Evaluate side-chains 93 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1240 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9216 Z= 0.255 Angle : 0.528 6.197 12517 Z= 0.276 Chirality : 0.041 0.151 1452 Planarity : 0.003 0.045 1534 Dihedral : 8.265 83.317 1798 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.26 % Allowed : 8.38 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.30 (0.25), residues: 1122 helix: 1.03 (0.19), residues: 752 sheet: -0.79 (0.56), residues: 75 loop : -1.61 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 317 HIS 0.002 0.001 HIS A 806 PHE 0.017 0.002 PHE A 316 TYR 0.020 0.002 TYR A 118 ARG 0.002 0.000 ARG A 969 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 90 time to evaluate : 1.054 Fit side-chains REVERT: A 470 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6763 (mt-10) REVERT: A 949 TYR cc_start: 0.7630 (OUTLIER) cc_final: 0.6740 (t80) REVERT: A 1071 SER cc_start: 0.8893 (t) cc_final: 0.8644 (m) outliers start: 30 outliers final: 18 residues processed: 111 average time/residue: 0.1874 time to fit residues: 30.7450 Evaluate side-chains 102 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 898 GLU Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1240 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 109 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9216 Z= 0.154 Angle : 0.466 6.037 12517 Z= 0.246 Chirality : 0.038 0.142 1452 Planarity : 0.003 0.044 1534 Dihedral : 7.934 78.280 1798 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.50 % Allowed : 9.79 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1122 helix: 1.44 (0.19), residues: 744 sheet: -0.61 (0.58), residues: 75 loop : -1.42 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 317 HIS 0.004 0.001 HIS A 67 PHE 0.017 0.001 PHE A 78 TYR 0.015 0.001 TYR A 961 ARG 0.002 0.000 ARG A 969 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 1.038 Fit side-chains REVERT: A 75 MET cc_start: 0.7518 (mmt) cc_final: 0.6669 (mmm) REVERT: A 618 MET cc_start: 0.6452 (tpt) cc_final: 0.6226 (tpt) REVERT: A 949 TYR cc_start: 0.7469 (OUTLIER) cc_final: 0.7019 (t80) outliers start: 23 outliers final: 19 residues processed: 113 average time/residue: 0.1901 time to fit residues: 31.5165 Evaluate side-chains 107 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 898 GLU Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1240 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9216 Z= 0.279 Angle : 0.549 6.238 12517 Z= 0.288 Chirality : 0.042 0.154 1452 Planarity : 0.003 0.048 1534 Dihedral : 8.144 83.836 1798 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.72 % Allowed : 10.45 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1122 helix: 1.16 (0.19), residues: 744 sheet: -0.59 (0.56), residues: 75 loop : -1.54 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 317 HIS 0.003 0.001 HIS A 67 PHE 0.023 0.002 PHE A 316 TYR 0.031 0.002 TYR A 118 ARG 0.002 0.000 ARG A 969 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 456 ASP cc_start: 0.7821 (t0) cc_final: 0.7588 (t0) REVERT: A 470 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6756 (mt-10) REVERT: A 618 MET cc_start: 0.6603 (tpt) cc_final: 0.6376 (tpt) REVERT: A 949 TYR cc_start: 0.7723 (OUTLIER) cc_final: 0.6777 (t80) outliers start: 25 outliers final: 20 residues processed: 110 average time/residue: 0.1971 time to fit residues: 31.3380 Evaluate side-chains 108 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 801 SER Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 898 GLU Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1240 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 104 optimal weight: 0.0870 chunk 95 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 349 GLN A 929 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9216 Z= 0.154 Angle : 0.473 6.028 12517 Z= 0.250 Chirality : 0.039 0.141 1452 Planarity : 0.003 0.045 1534 Dihedral : 7.518 78.516 1798 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.72 % Allowed : 10.88 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1122 helix: 1.48 (0.19), residues: 743 sheet: -0.51 (0.56), residues: 75 loop : -1.46 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 317 HIS 0.003 0.001 HIS A 67 PHE 0.015 0.001 PHE A 316 TYR 0.009 0.001 TYR A 852 ARG 0.001 0.000 ARG A 969 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 1.000 Fit side-chains REVERT: A 196 PHE cc_start: 0.7947 (m-80) cc_final: 0.7733 (m-80) REVERT: A 470 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6855 (mt-10) REVERT: A 618 MET cc_start: 0.6521 (tpt) cc_final: 0.6304 (tpt) REVERT: A 949 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.6801 (t80) outliers start: 25 outliers final: 19 residues processed: 107 average time/residue: 0.2031 time to fit residues: 31.4631 Evaluate side-chains 107 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 801 SER Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 898 GLU Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1240 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9216 Z= 0.169 Angle : 0.485 7.343 12517 Z= 0.254 Chirality : 0.039 0.144 1452 Planarity : 0.003 0.046 1534 Dihedral : 7.448 78.369 1798 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.39 % Allowed : 11.32 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1122 helix: 1.53 (0.19), residues: 743 sheet: -0.40 (0.56), residues: 75 loop : -1.39 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 317 HIS 0.003 0.001 HIS A 67 PHE 0.015 0.001 PHE A 316 TYR 0.034 0.001 TYR A 118 ARG 0.003 0.000 ARG A 595 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 1.033 Fit side-chains REVERT: A 618 MET cc_start: 0.6641 (tpt) cc_final: 0.6379 (tpt) REVERT: A 949 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.7022 (t80) outliers start: 22 outliers final: 20 residues processed: 104 average time/residue: 0.1968 time to fit residues: 30.2706 Evaluate side-chains 108 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 801 SER Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 898 GLU Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1240 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9216 Z= 0.171 Angle : 0.483 6.220 12517 Z= 0.254 Chirality : 0.039 0.144 1452 Planarity : 0.003 0.046 1534 Dihedral : 7.371 77.550 1798 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.18 % Allowed : 11.53 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1122 helix: 1.56 (0.19), residues: 743 sheet: -0.32 (0.56), residues: 75 loop : -1.32 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 317 HIS 0.004 0.001 HIS A 67 PHE 0.015 0.001 PHE A 316 TYR 0.010 0.001 TYR A 852 ARG 0.002 0.000 ARG A 969 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 1.034 Fit side-chains REVERT: A 470 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6856 (mt-10) REVERT: A 618 MET cc_start: 0.6588 (tpt) cc_final: 0.6339 (tpt) REVERT: A 949 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.6883 (t80) REVERT: A 1199 ASP cc_start: 0.8391 (t0) cc_final: 0.7986 (t0) outliers start: 20 outliers final: 18 residues processed: 103 average time/residue: 0.1904 time to fit residues: 28.8885 Evaluate side-chains 107 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 801 SER Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 898 GLU Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1240 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.146593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.127596 restraints weight = 11088.365| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.31 r_work: 0.3290 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9216 Z= 0.164 Angle : 0.474 6.112 12517 Z= 0.249 Chirality : 0.039 0.143 1452 Planarity : 0.003 0.046 1534 Dihedral : 7.278 76.951 1798 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.61 % Allowed : 11.10 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1122 helix: 1.60 (0.19), residues: 743 sheet: -0.27 (0.56), residues: 75 loop : -1.26 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 317 HIS 0.003 0.001 HIS A 67 PHE 0.013 0.001 PHE A 316 TYR 0.034 0.001 TYR A 118 ARG 0.002 0.000 ARG A 969 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2118.43 seconds wall clock time: 39 minutes 15.14 seconds (2355.14 seconds total)