Starting phenix.real_space_refine on Tue Nov 19 12:46:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx7_40826/11_2024/8sx7_40826_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx7_40826/11_2024/8sx7_40826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx7_40826/11_2024/8sx7_40826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx7_40826/11_2024/8sx7_40826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx7_40826/11_2024/8sx7_40826_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx7_40826/11_2024/8sx7_40826_trim.cif" } resolution = 2.7 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= 0.002 sd= 0.066 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: 5 Type Number sf(0) Gaussians S 38 5.16 5 C 6177 2.51 5 N 1602 2.21 5 O 1701 1.98 5 H 9719 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19237 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 19203 Classifications: {'peptide': 1188} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 1151} Chain breaks: 3 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {'ZWY': 1} Classifications: {'undetermined': 1, 'water': 3} Link IDs: {None: 3} Time building chain proxies: 9.15, per 1000 atoms: 0.48 Number of scatterers: 19237 At special positions: 0 Unit cell: (84.335, 94.355, 144.455, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 O 1701 8.00 N 1602 7.00 C 6177 6.00 H 9719 1.00 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: 5.19 Conformation dependent library (CDL) restraints added in 1.5 seconds 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2246 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 4 sheets defined 71.5% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 17 through 24 Processing helix chain 'A' and resid 27 through 37 Processing helix chain 'A' and resid 52 through 74 removed outlier: 3.807A pdb=" N GLU A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 95 removed outlier: 3.623A pdb=" N ALA A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 122 Proline residue: A 110 - end of helix removed outlier: 3.652A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 179 removed outlier: 3.532A pdb=" N LEU A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 190 through 201 removed outlier: 3.637A pdb=" N LEU A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.968A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 236 through 290 removed outlier: 4.096A pdb=" N GLY A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 4.128A pdb=" N ALA A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 326 Processing helix chain 'A' and resid 326 through 342 Processing helix chain 'A' and resid 347 through 367 Processing helix chain 'A' and resid 367 through 391 Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 500 through 511 Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 522 through 526 Processing helix chain 'A' and resid 536 through 552 removed outlier: 3.592A pdb=" N ALA A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 577 Processing helix chain 'A' and resid 697 through 709 removed outlier: 3.640A pdb=" N TYR A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 709 " --> pdb=" O PHE A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 745 removed outlier: 3.596A pdb=" N ILE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 745 " --> pdb=" O GLN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 808 removed outlier: 3.741A pdb=" N PHE A 787 " --> pdb=" O SER A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 815 removed outlier: 3.931A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 834 removed outlier: 3.784A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 825 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE A 829 " --> pdb=" O PHE A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 861 removed outlier: 3.766A pdb=" N LEU A 838 " --> pdb=" O ASP A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 910 Proline residue: A 870 - end of helix removed outlier: 4.180A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) Proline residue: A 899 - end of helix Processing helix chain 'A' and resid 910 through 917 Processing helix chain 'A' and resid 919 through 970 Processing helix chain 'A' and resid 971 through 974 Processing helix chain 'A' and resid 975 through 1015 removed outlier: 4.064A pdb=" N MET A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A1015 " --> pdb=" O GLU A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1019 removed outlier: 4.116A pdb=" N LEU A1019 " --> pdb=" O TYR A1016 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1016 through 1019' Processing helix chain 'A' and resid 1080 through 1089 removed outlier: 3.535A pdb=" N ILE A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1108 No H-bonds generated for 'chain 'A' and resid 1106 through 1108' Processing helix chain 'A' and resid 1109 through 1116 removed outlier: 3.737A pdb=" N LEU A1113 " --> pdb=" O GLY A1109 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A1116 " --> pdb=" O ASP A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1153 Processing helix chain 'A' and resid 1155 through 1162 Processing helix chain 'A' and resid 1164 through 1168 Processing helix chain 'A' and resid 1178 through 1193 Processing helix chain 'A' and resid 1208 through 1223 removed outlier: 4.309A pdb=" N LEU A1214 " --> pdb=" O ARG A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1238 Processing helix chain 'A' and resid 1257 through 1264 removed outlier: 3.549A pdb=" N ASN A1264 " --> pdb=" O VAL A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1277 removed outlier: 3.631A pdb=" N LEU A1276 " --> pdb=" O MET A1272 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A1277 " --> pdb=" O VAL A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1297 Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 435 removed outlier: 6.431A pdb=" N GLN A 429 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N THR A 416 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU A 431 " --> pdb=" O ASP A 414 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A 415 " --> pdb=" O GLN A 466 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLN A 466 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.845A pdb=" N TYR A 556 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL A 590 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 558 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE A 603 " --> pdb=" O LYS A 614 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS A 614 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 605 " --> pdb=" O VAL A 612 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1058 through 1065 removed outlier: 6.625A pdb=" N LYS A1059 " --> pdb=" O ASN A1047 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASN A1047 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU A1061 " --> pdb=" O ASN A1045 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N PHE A1043 " --> pdb=" O TRP A1099 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N TRP A1099 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN A1045 " --> pdb=" O LYS A1097 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS A1097 " --> pdb=" O ASN A1045 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1117 through 1120 removed outlier: 6.386A pdb=" N SER A1118 " --> pdb=" O ILE A1199 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ASP A1201 " --> pdb=" O SER A1118 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE A1120 " --> pdb=" O ASP A1201 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A1198 " --> pdb=" O LEU A1229 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE A1231 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE A1200 " --> pdb=" O ILE A1231 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LYS A1070 " --> pdb=" O LYS A1243 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N MET A1245 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY A1072 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU A1247 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL A1074 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A1254 " --> pdb=" O VAL A1246 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1875 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: 7.82 Time building geometry restraints manager: 6.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9705 1.03 - 1.23: 24 1.23 - 1.42: 4023 1.42 - 1.62: 5629 1.62 - 1.81: 60 Bond restraints: 19441 Sorted by residual: bond pdb=" C18 ZWY A1401 " pdb=" O20 ZWY A1401 " ideal model delta sigma weight residual 1.452 1.324 0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C08 ZWY A1401 " pdb=" C09 ZWY A1401 " ideal model delta sigma weight residual 1.541 1.438 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C12 ZWY A1401 " pdb=" C13 ZWY A1401 " ideal model delta sigma weight residual 1.496 1.411 0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C01 ZWY A1401 " pdb=" C02 ZWY A1401 " ideal model delta sigma weight residual 1.547 1.462 0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C03 ZWY A1401 " pdb=" C04 ZWY A1401 " ideal model delta sigma weight residual 1.535 1.457 0.078 2.00e-02 2.50e+03 1.53e+01 ... (remaining 19436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 33760 1.50 - 3.00: 1336 3.00 - 4.49: 82 4.49 - 5.99: 13 5.99 - 7.49: 6 Bond angle restraints: 35197 Sorted by residual: angle pdb=" CA TRP A 947 " pdb=" CB TRP A 947 " pdb=" CG TRP A 947 " ideal model delta sigma weight residual 113.60 119.34 -5.74 1.90e+00 2.77e-01 9.12e+00 angle pdb=" C14 ZWY A1401 " pdb=" C19 ZWY A1401 " pdb=" C18 ZWY A1401 " ideal model delta sigma weight residual 111.99 119.48 -7.49 3.00e+00 1.11e-01 6.23e+00 angle pdb=" C LEU A 582 " pdb=" N HIS A 583 " pdb=" CA HIS A 583 " ideal model delta sigma weight residual 120.54 123.90 -3.36 1.35e+00 5.49e-01 6.19e+00 angle pdb=" C04 ZWY A1401 " pdb=" C05 ZWY A1401 " pdb=" C15 ZWY A1401 " ideal model delta sigma weight residual 112.74 120.14 -7.40 3.00e+00 1.11e-01 6.08e+00 angle pdb=" CB LYS A 375 " pdb=" CG LYS A 375 " pdb=" CD LYS A 375 " ideal model delta sigma weight residual 111.30 116.96 -5.66 2.30e+00 1.89e-01 6.06e+00 ... (remaining 35192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 8360 17.48 - 34.96: 421 34.96 - 52.44: 162 52.44 - 69.92: 136 69.92 - 87.40: 20 Dihedral angle restraints: 9099 sinusoidal: 4953 harmonic: 4146 Sorted by residual: dihedral pdb=" CA ASP A 43 " pdb=" C ASP A 43 " pdb=" N MET A 44 " pdb=" CA MET A 44 " ideal model delta harmonic sigma weight residual 180.00 -153.76 -26.24 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA LYS A 585 " pdb=" C LYS A 585 " pdb=" N ILE A 586 " pdb=" CA ILE A 586 " ideal model delta harmonic sigma weight residual 180.00 154.73 25.27 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ALA A1232 " pdb=" C ALA A1232 " pdb=" N HIS A1233 " pdb=" CA HIS A1233 " ideal model delta harmonic sigma weight residual 180.00 156.50 23.50 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 9096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 1501 0.140 - 0.280: 19 0.280 - 0.420: 0 0.420 - 0.561: 0 0.561 - 0.701: 4 Chirality restraints: 1524 Sorted by residual: chirality pdb=" C05 ZWY A1401 " pdb=" C04 ZWY A1401 " pdb=" C06 ZWY A1401 " pdb=" C15 ZWY A1401 " both_signs ideal model delta sigma weight residual False -2.46 -1.76 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" C06 ZWY A1401 " pdb=" C05 ZWY A1401 " pdb=" C07 ZWY A1401 " pdb=" C12 ZWY A1401 " both_signs ideal model delta sigma weight residual False 2.71 2.08 0.62 2.00e-01 2.50e+01 9.75e+00 chirality pdb=" C18 ZWY A1401 " pdb=" C17 ZWY A1401 " pdb=" C19 ZWY A1401 " pdb=" O20 ZWY A1401 " both_signs ideal model delta sigma weight residual False -2.54 -1.92 -0.62 2.00e-01 2.50e+01 9.71e+00 ... (remaining 1521 not shown) Planarity restraints: 2787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 587 " 0.270 9.50e-02 1.11e+02 9.99e-02 5.08e+01 pdb=" NE ARG A 587 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG A 587 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 587 " 0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG A 587 " -0.085 2.00e-02 2.50e+03 pdb="HH11 ARG A 587 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 587 " -0.040 2.00e-02 2.50e+03 pdb="HH21 ARG A 587 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG A 587 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 52 " -0.184 9.50e-02 1.11e+02 6.76e-02 2.23e+01 pdb=" NE ARG A 52 " -0.002 2.00e-02 2.50e+03 pdb=" CZ ARG A 52 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 52 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 52 " 0.054 2.00e-02 2.50e+03 pdb="HH11 ARG A 52 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 52 " 0.028 2.00e-02 2.50e+03 pdb="HH21 ARG A 52 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 52 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 167 " -0.141 9.50e-02 1.11e+02 5.13e-02 1.15e+01 pdb=" NE ARG A 167 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 167 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 167 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 167 " 0.042 2.00e-02 2.50e+03 pdb="HH11 ARG A 167 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 167 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 167 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 167 " -0.041 2.00e-02 2.50e+03 ... (remaining 2784 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 434 2.11 - 2.73: 33830 2.73 - 3.35: 57112 3.35 - 3.98: 70667 3.98 - 4.60: 113395 Nonbonded interactions: 275438 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 177 " pdb=" OE1 GLU A 394 " model vdw 1.483 2.450 nonbonded pdb=" O LEU A 367 " pdb=" HG SER A 371 " model vdw 1.535 2.450 nonbonded pdb=" O PHE A 333 " pdb=" HG1 THR A 337 " model vdw 1.551 2.450 nonbonded pdb=" O ALA A 296 " pdb=" HG1 THR A 300 " model vdw 1.571 2.450 nonbonded pdb=" OD1 ASP A 842 " pdb=" H1 HOH A1501 " model vdw 1.590 2.450 ... (remaining 275433 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.880 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: 0.340 Extract box with map and model: 0.670 Check model and map are aligned: 0.140 Set scattering table: 0.150 Process input model: 43.040 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.060 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:14.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 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 0.128 9722 Z= 0.360 Angle : 0.699 7.488 13184 Z= 0.393 Chirality : 0.059 0.701 1524 Planarity : 0.006 0.088 1639 Dihedral : 12.399 87.396 3596 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.39 % Allowed : 2.81 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.48 (0.21), residues: 1180 helix: -1.18 (0.16), residues: 764 sheet: 0.39 (0.63), residues: 51 loop : -0.26 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 734 HIS 0.020 0.002 HIS A 153 PHE 0.022 0.002 PHE A 156 TYR 0.025 0.003 TYR A 123 ARG 0.016 0.002 ARG A 887 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 211 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 ARG cc_start: 0.6690 (mtt-85) cc_final: 0.6363 (mmp80) REVERT: A 1045 ASN cc_start: 0.7853 (t0) cc_final: 0.7286 (t0) outliers start: 4 outliers final: 3 residues processed: 215 average time/residue: 2.1534 time to fit residues: 507.4221 Evaluate side-chains 110 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 1248 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 725 GLN A 742 GLN A1111 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9722 Z= 0.302 Angle : 0.682 7.707 13184 Z= 0.367 Chirality : 0.043 0.150 1524 Planarity : 0.005 0.075 1639 Dihedral : 6.043 89.934 1352 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.81 % Allowed : 9.97 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.15 (0.23), residues: 1180 helix: 0.14 (0.17), residues: 778 sheet: 0.41 (0.64), residues: 55 loop : 0.35 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 483 HIS 0.011 0.002 HIS A 153 PHE 0.019 0.002 PHE A 941 TYR 0.017 0.002 TYR A 764 ARG 0.011 0.001 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.6899 (m-30) cc_final: 0.6674 (m-30) REVERT: A 121 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6526 (tm-30) REVERT: A 347 THR cc_start: 0.7281 (OUTLIER) cc_final: 0.7052 (p) REVERT: A 834 ASP cc_start: 0.7236 (t0) cc_final: 0.6954 (t70) REVERT: A 921 GLN cc_start: 0.4865 (pm20) cc_final: 0.4473 (pt0) REVERT: A 1045 ASN cc_start: 0.8046 (t0) cc_final: 0.7484 (t0) REVERT: A 1116 LYS cc_start: 0.7753 (mmpt) cc_final: 0.7225 (mppt) REVERT: A 1131 MET cc_start: 0.7087 (tpp) cc_final: 0.6802 (tpt) REVERT: A 1166 MET cc_start: 0.5470 (OUTLIER) cc_final: 0.5200 (ptt) outliers start: 29 outliers final: 8 residues processed: 124 average time/residue: 2.0833 time to fit residues: 285.2680 Evaluate side-chains 84 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1204 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS A 193 GLN A 344 ASN A 725 GLN A 999 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.6622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9722 Z= 0.291 Angle : 0.612 7.204 13184 Z= 0.330 Chirality : 0.041 0.150 1524 Planarity : 0.005 0.051 1639 Dihedral : 5.329 70.296 1349 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.00 % Allowed : 11.52 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.95 (0.24), residues: 1180 helix: 0.85 (0.18), residues: 778 sheet: -0.08 (0.58), residues: 62 loop : 0.60 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 89 HIS 0.012 0.002 HIS A 153 PHE 0.030 0.002 PHE A 352 TYR 0.017 0.002 TYR A 881 ARG 0.009 0.001 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 801 MET cc_start: 0.8380 (ttp) cc_final: 0.8149 (ttm) REVERT: A 868 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7841 (tt) REVERT: A 1045 ASN cc_start: 0.8227 (t0) cc_final: 0.7719 (t0) REVERT: A 1133 LYS cc_start: 0.5577 (mmtt) cc_final: 0.5204 (tmtm) REVERT: A 1166 MET cc_start: 0.5257 (OUTLIER) cc_final: 0.4853 (ppp) outliers start: 31 outliers final: 10 residues processed: 101 average time/residue: 2.0252 time to fit residues: 226.3730 Evaluate side-chains 76 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1097 LYS Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.7562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 9722 Z= 0.405 Angle : 0.651 7.284 13184 Z= 0.356 Chirality : 0.044 0.225 1524 Planarity : 0.005 0.054 1639 Dihedral : 5.937 86.865 1349 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.90 % Allowed : 13.26 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.24), residues: 1180 helix: 0.79 (0.18), residues: 771 sheet: -0.11 (0.58), residues: 61 loop : 0.46 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 947 HIS 0.013 0.002 HIS A 153 PHE 0.020 0.002 PHE A 485 TYR 0.018 0.002 TYR A 728 ARG 0.007 0.001 ARG A 951 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6850 (m-30) REVERT: A 763 TRP cc_start: 0.7690 (OUTLIER) cc_final: 0.7446 (t60) REVERT: A 801 MET cc_start: 0.8477 (ttp) cc_final: 0.8240 (ttm) REVERT: A 1045 ASN cc_start: 0.8425 (t0) cc_final: 0.8035 (t0) REVERT: A 1084 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7204 (tp) REVERT: A 1133 LYS cc_start: 0.5665 (mmtt) cc_final: 0.5239 (tmtm) REVERT: A 1166 MET cc_start: 0.5085 (OUTLIER) cc_final: 0.4848 (ppp) outliers start: 30 outliers final: 15 residues processed: 93 average time/residue: 1.7116 time to fit residues: 175.9336 Evaluate side-chains 89 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 763 TRP Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 886 SER Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1256 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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: 0.7829 moved from start: 0.7944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9722 Z= 0.281 Angle : 0.555 6.708 13184 Z= 0.301 Chirality : 0.040 0.157 1524 Planarity : 0.004 0.050 1639 Dihedral : 5.363 76.446 1349 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.81 % Allowed : 14.33 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.21 (0.24), residues: 1180 helix: 1.14 (0.18), residues: 772 sheet: -0.21 (0.59), residues: 61 loop : 0.48 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 947 HIS 0.010 0.002 HIS A 153 PHE 0.020 0.002 PHE A 352 TYR 0.016 0.002 TYR A 728 ARG 0.002 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.7297 (mppt) cc_final: 0.6781 (ttpt) REVERT: A 270 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6764 (m-30) REVERT: A 763 TRP cc_start: 0.7676 (OUTLIER) cc_final: 0.7363 (t60) REVERT: A 801 MET cc_start: 0.8440 (ttp) cc_final: 0.8237 (ttm) REVERT: A 1045 ASN cc_start: 0.8448 (t0) cc_final: 0.8046 (t0) REVERT: A 1133 LYS cc_start: 0.5660 (mmtt) cc_final: 0.5277 (tmtm) REVERT: A 1183 GLN cc_start: 0.7839 (mt0) cc_final: 0.7595 (mt0) outliers start: 29 outliers final: 18 residues processed: 91 average time/residue: 1.6354 time to fit residues: 167.9543 Evaluate side-chains 92 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 763 TRP Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 886 SER Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.8095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9722 Z= 0.173 Angle : 0.498 6.616 13184 Z= 0.268 Chirality : 0.038 0.148 1524 Planarity : 0.004 0.047 1639 Dihedral : 4.929 69.905 1349 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.13 % Allowed : 15.30 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.73 (0.24), residues: 1180 helix: 1.59 (0.19), residues: 770 sheet: 0.08 (0.62), residues: 55 loop : 0.53 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 947 HIS 0.007 0.001 HIS A 153 PHE 0.014 0.001 PHE A 156 TYR 0.013 0.001 TYR A 728 ARG 0.002 0.000 ARG A 951 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1045 ASN cc_start: 0.8478 (t0) cc_final: 0.8093 (t0) REVERT: A 1133 LYS cc_start: 0.5606 (mmtt) cc_final: 0.5170 (tmtm) REVERT: A 1183 GLN cc_start: 0.7913 (mt0) cc_final: 0.7704 (mt0) outliers start: 22 outliers final: 17 residues processed: 86 average time/residue: 1.7263 time to fit residues: 168.3138 Evaluate side-chains 88 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 886 SER Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1256 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 96 optimal weight: 9.9990 chunk 63 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.8323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9722 Z= 0.212 Angle : 0.513 6.722 13184 Z= 0.277 Chirality : 0.038 0.148 1524 Planarity : 0.004 0.047 1639 Dihedral : 5.006 74.436 1349 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.23 % Allowed : 14.91 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.76 (0.24), residues: 1180 helix: 1.66 (0.18), residues: 769 sheet: 0.04 (0.63), residues: 55 loop : 0.43 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 947 HIS 0.014 0.002 HIS A 35 PHE 0.019 0.002 PHE A 352 TYR 0.013 0.001 TYR A 728 ARG 0.002 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1045 ASN cc_start: 0.8497 (t0) cc_final: 0.8141 (t0) REVERT: A 1183 GLN cc_start: 0.7842 (mt0) cc_final: 0.7638 (mt0) outliers start: 23 outliers final: 19 residues processed: 88 average time/residue: 1.5658 time to fit residues: 159.0365 Evaluate side-chains 91 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 886 SER Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1256 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 72 optimal weight: 0.0770 chunk 77 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.8405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9722 Z= 0.139 Angle : 0.462 6.236 13184 Z= 0.247 Chirality : 0.037 0.148 1524 Planarity : 0.003 0.044 1639 Dihedral : 4.542 63.677 1349 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.84 % Allowed : 15.30 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.25), residues: 1180 helix: 1.94 (0.19), residues: 779 sheet: -0.29 (0.59), residues: 65 loop : 0.61 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 947 HIS 0.012 0.001 HIS A 35 PHE 0.013 0.001 PHE A 939 TYR 0.011 0.001 TYR A 728 ARG 0.003 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.7348 (ptpt) cc_final: 0.7030 (ptmm) REVERT: A 1045 ASN cc_start: 0.8493 (t0) cc_final: 0.8134 (t0) REVERT: A 1183 GLN cc_start: 0.7844 (mt0) cc_final: 0.7608 (mt0) outliers start: 19 outliers final: 13 residues processed: 86 average time/residue: 1.5335 time to fit residues: 150.1844 Evaluate side-chains 84 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 886 SER Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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: 0.7837 moved from start: 0.8590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9722 Z= 0.265 Angle : 0.532 5.797 13184 Z= 0.290 Chirality : 0.040 0.154 1524 Planarity : 0.004 0.048 1639 Dihedral : 5.089 77.247 1349 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.65 % Allowed : 15.68 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.79 (0.25), residues: 1180 helix: 1.70 (0.18), residues: 770 sheet: -0.65 (0.58), residues: 71 loop : 0.63 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 947 HIS 0.012 0.002 HIS A 35 PHE 0.020 0.002 PHE A 352 TYR 0.015 0.001 TYR A 728 ARG 0.002 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1045 ASN cc_start: 0.8467 (t0) cc_final: 0.8103 (t0) outliers start: 17 outliers final: 14 residues processed: 78 average time/residue: 1.5466 time to fit residues: 138.2042 Evaluate side-chains 82 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 886 SER Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.8707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9722 Z= 0.233 Angle : 0.511 5.424 13184 Z= 0.278 Chirality : 0.039 0.146 1524 Planarity : 0.004 0.046 1639 Dihedral : 5.076 77.825 1349 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.45 % Allowed : 15.97 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.78 (0.25), residues: 1180 helix: 1.72 (0.18), residues: 770 sheet: -0.68 (0.60), residues: 66 loop : 0.52 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 947 HIS 0.013 0.002 HIS A 35 PHE 0.019 0.002 PHE A 352 TYR 0.014 0.001 TYR A 728 ARG 0.002 0.000 ARG A 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 909 GLN cc_start: 0.7562 (mp10) cc_final: 0.7182 (mp10) REVERT: A 1045 ASN cc_start: 0.8448 (t0) cc_final: 0.8111 (t0) REVERT: A 1183 GLN cc_start: 0.7505 (mt0) cc_final: 0.7224 (mp-120) REVERT: A 1193 ARG cc_start: 0.6496 (mtp180) cc_final: 0.5739 (mmm-85) REVERT: A 1222 LYS cc_start: 0.7278 (mmmt) cc_final: 0.6151 (tmtt) REVERT: A 1248 ASP cc_start: 0.5120 (t0) cc_final: 0.4919 (t0) REVERT: A 1272 MET cc_start: 0.4398 (mtt) cc_final: 0.3608 (mmm) outliers start: 15 outliers final: 14 residues processed: 84 average time/residue: 1.6910 time to fit residues: 160.2469 Evaluate side-chains 86 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 886 SER Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.203940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.134090 restraints weight = 34547.978| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.44 r_work: 0.3636 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.8880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9722 Z= 0.272 Angle : 0.545 6.735 13184 Z= 0.295 Chirality : 0.040 0.149 1524 Planarity : 0.004 0.047 1639 Dihedral : 5.332 83.584 1349 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.45 % Allowed : 15.88 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.60 (0.24), residues: 1180 helix: 1.58 (0.18), residues: 770 sheet: -0.64 (0.61), residues: 66 loop : 0.41 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 947 HIS 0.008 0.002 HIS A 35 PHE 0.019 0.002 PHE A 156 TYR 0.015 0.001 TYR A 728 ARG 0.006 0.000 ARG A 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5889.83 seconds wall clock time: 214 minutes 57.00 seconds (12897.00 seconds total)