Starting phenix.real_space_refine on Sat Jun 7 23:37:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kk6_62383/06_2025/9kk6_62383.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kk6_62383/06_2025/9kk6_62383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kk6_62383/06_2025/9kk6_62383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kk6_62383/06_2025/9kk6_62383.map" model { file = "/net/cci-nas-00/data/ceres_data/9kk6_62383/06_2025/9kk6_62383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kk6_62383/06_2025/9kk6_62383.cif" } resolution = 3.7 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= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians V 2 8.30 5 P 4 5.49 5 Mg 2 5.21 5 S 37 5.16 5 C 5792 2.51 5 N 1533 2.21 5 O 1696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9066 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1170, 9000 Classifications: {'peptide': 1170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 1140} Chain breaks: 1 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {' MG': 2, 'ADP': 2, 'VO4': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 5.84, per 1000 atoms: 0.64 Number of scatterers: 9066 At special positions: 0 Unit cell: (78.66, 80.37, 141.075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 2 22.97 S 37 16.00 P 4 15.00 Mg 2 11.99 O 1696 8.00 N 1533 7.00 C 5792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 5 sheets defined 70.6% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 34 through 67 removed outlier: 4.568A pdb=" N MET A 55 " --> pdb=" O HIS A 51 " (cutoff:3.500A) Proline residue: A 56 - end of helix removed outlier: 4.305A pdb=" N GLN A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.905A pdb=" N ASN A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 128 removed outlier: 3.758A pdb=" N MET A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 138 removed outlier: 3.804A pdb=" N PHE A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 137 " --> pdb=" O GLY A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 159 removed outlier: 3.518A pdb=" N ASP A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 184 removed outlier: 4.174A pdb=" N GLY A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 194 removed outlier: 3.967A pdb=" N ALA A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 233 removed outlier: 4.213A pdb=" N ILE A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A 233 " --> pdb=" O GLN A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.570A pdb=" N ILE A 254 " --> pdb=" O TYR A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 297 removed outlier: 4.400A pdb=" N LYS A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 344 removed outlier: 4.700A pdb=" N SER A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASN A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 414 removed outlier: 4.078A pdb=" N VAL A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 442 Processing helix chain 'A' and resid 456 through 463 Processing helix chain 'A' and resid 469 through 480 Processing helix chain 'A' and resid 482 through 488 Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.641A pdb=" N GLY A 501 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 521 removed outlier: 3.615A pdb=" N LYS A 520 " --> pdb=" O ARG A 516 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 550 Processing helix chain 'A' and resid 584 through 592 removed outlier: 3.761A pdb=" N LYS A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 607 removed outlier: 3.531A pdb=" N LEU A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 679 Processing helix chain 'A' and resid 683 through 718 removed outlier: 3.658A pdb=" N SER A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY A 701 " --> pdb=" O SER A 697 " (cutoff:3.500A) Proline residue: A 702 - end of helix removed outlier: 4.225A pdb=" N ALA A 705 " --> pdb=" O GLY A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 774 Processing helix chain 'A' and resid 775 through 780 removed outlier: 3.933A pdb=" N PHE A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 829 removed outlier: 3.653A pdb=" N ALA A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA A 798 " --> pdb=" O ALA A 794 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER A 809 " --> pdb=" O ALA A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 838 Processing helix chain 'A' and resid 839 through 878 removed outlier: 3.658A pdb=" N LEU A 843 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 855 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 856 " --> pdb=" O LEU A 852 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE A 857 " --> pdb=" O SER A 853 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 859 " --> pdb=" O LYS A 855 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP A 860 " --> pdb=" O GLY A 856 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A 861 " --> pdb=" O PHE A 857 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 863 " --> pdb=" O GLY A 859 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 885 Processing helix chain 'A' and resid 887 through 942 removed outlier: 4.701A pdb=" N VAL A 901 " --> pdb=" O HIS A 897 " (cutoff:3.500A) Proline residue: A 902 - end of helix removed outlier: 3.698A pdb=" N TYR A 908 " --> pdb=" O LYS A 904 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A 928 " --> pdb=" O LEU A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.580A pdb=" N VAL A 949 " --> pdb=" O THR A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 975 Proline residue: A 971 - end of helix Processing helix chain 'A' and resid 976 through 989 Processing helix chain 'A' and resid 1052 through 1059 removed outlier: 3.552A pdb=" N ALA A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1087 removed outlier: 3.661A pdb=" N LEU A1084 " --> pdb=" O ASN A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1107 Processing helix chain 'A' and resid 1114 through 1125 Processing helix chain 'A' and resid 1127 through 1134 Processing helix chain 'A' and resid 1136 through 1140 removed outlier: 4.251A pdb=" N THR A1140 " --> pdb=" O GLY A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1166 Processing helix chain 'A' and resid 1183 through 1195 Processing helix chain 'A' and resid 1196 through 1198 No H-bonds generated for 'chain 'A' and resid 1196 through 1198' Processing helix chain 'A' and resid 1229 through 1236 Processing helix chain 'A' and resid 1239 through 1252 Processing sheet with id=AA1, first strand: chain 'A' and resid 383 through 390 removed outlier: 6.888A pdb=" N ARG A 384 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR A 371 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N PHE A 386 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 368 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN A 423 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL A 370 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N SER A 421 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 443 through 446 removed outlier: 6.326A pdb=" N LEU A 525 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL A 558 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU A 527 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR A 395 " --> pdb=" O SER A 570 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ALA A 572 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ALA A 397 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE A 574 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL A 399 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY A 583 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLU A 581 " --> pdb=" O VAL A 573 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1028 through 1031 removed outlier: 3.800A pdb=" N PHE A1017 " --> pdb=" O PHE A1028 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP A1030 " --> pdb=" O VAL A1015 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A1015 " --> pdb=" O ASP A1030 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1028 through 1031 removed outlier: 3.800A pdb=" N PHE A1017 " --> pdb=" O PHE A1028 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP A1030 " --> pdb=" O VAL A1015 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A1015 " --> pdb=" O ASP A1030 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A1015 " --> pdb=" O ALA A1066 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA A1066 " --> pdb=" O VAL A1015 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1088 through 1090 removed outlier: 6.994A pdb=" N GLY A1089 " --> pdb=" O LEU A1171 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1782 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.33 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 2978 1.36 - 1.50: 2377 1.50 - 1.64: 3807 1.64 - 1.77: 0 1.77 - 1.91: 73 Bond restraints: 9235 Sorted by residual: bond pdb=" C PHE A 840 " pdb=" N PRO A 841 " ideal model delta sigma weight residual 1.334 1.356 -0.021 1.51e-02 4.39e+03 2.02e+00 bond pdb=" C ASP A 351 " pdb=" N PRO A 352 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.50e+00 bond pdb=" CB ASP A 418 " pdb=" CG ASP A 418 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.38e+00 bond pdb=" CA GLY A 363 " pdb=" C GLY A 363 " ideal model delta sigma weight residual 1.514 1.531 -0.016 1.41e-02 5.03e+03 1.34e+00 bond pdb=" C4 ADP A1304 " pdb=" C5 ADP A1304 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.20e+00 ... (remaining 9230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 12197 1.64 - 3.28: 233 3.28 - 4.93: 59 4.93 - 6.57: 17 6.57 - 8.21: 3 Bond angle restraints: 12509 Sorted by residual: angle pdb=" C THR A 945 " pdb=" N PHE A 946 " pdb=" CA PHE A 946 " ideal model delta sigma weight residual 120.54 124.84 -4.30 1.35e+00 5.49e-01 1.01e+01 angle pdb=" N ILE A1216 " pdb=" CA ILE A1216 " pdb=" C ILE A1216 " ideal model delta sigma weight residual 109.34 115.80 -6.46 2.08e+00 2.31e-01 9.63e+00 angle pdb=" N ASP A 351 " pdb=" CA ASP A 351 " pdb=" C ASP A 351 " ideal model delta sigma weight residual 109.81 116.42 -6.61 2.21e+00 2.05e-01 8.95e+00 angle pdb=" C TYR A 717 " pdb=" N THR A 718 " pdb=" CA THR A 718 " ideal model delta sigma weight residual 121.54 126.97 -5.43 1.91e+00 2.74e-01 8.07e+00 angle pdb=" CB MET A 711 " pdb=" CG MET A 711 " pdb=" SD MET A 711 " ideal model delta sigma weight residual 112.70 120.91 -8.21 3.00e+00 1.11e-01 7.49e+00 ... (remaining 12504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.27: 5226 28.27 - 56.54: 204 56.54 - 84.81: 23 84.81 - 113.08: 3 113.08 - 141.35: 2 Dihedral angle restraints: 5458 sinusoidal: 2109 harmonic: 3349 Sorted by residual: dihedral pdb=" O2A ADP A1304 " pdb=" O3A ADP A1304 " pdb=" PA ADP A1304 " pdb=" PB ADP A1304 " ideal model delta sinusoidal sigma weight residual -60.00 81.36 -141.35 1 2.00e+01 2.50e-03 4.27e+01 dihedral pdb=" O2A ADP A1302 " pdb=" O3A ADP A1302 " pdb=" PA ADP A1302 " pdb=" PB ADP A1302 " ideal model delta sinusoidal sigma weight residual -60.00 81.30 -141.30 1 2.00e+01 2.50e-03 4.27e+01 dihedral pdb=" CA ASP A 547 " pdb=" C ASP A 547 " pdb=" N ARG A 548 " pdb=" CA ARG A 548 " ideal model delta harmonic sigma weight residual 180.00 153.91 26.09 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 5455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1340 0.074 - 0.149: 95 0.149 - 0.223: 0 0.223 - 0.297: 2 0.297 - 0.371: 1 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CG LEU A 696 " pdb=" CB LEU A 696 " pdb=" CD1 LEU A 696 " pdb=" CD2 LEU A 696 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CG LEU A 187 " pdb=" CB LEU A 187 " pdb=" CD1 LEU A 187 " pdb=" CD2 LEU A 187 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ASP A 351 " pdb=" N ASP A 351 " pdb=" C ASP A 351 " pdb=" CB ASP A 351 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 1435 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 351 " -0.026 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO A 352 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 352 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 352 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 901 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO A 902 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 902 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 902 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A1236 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.64e+00 pdb=" N PRO A1237 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A1237 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A1237 " 0.018 5.00e-02 4.00e+02 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 75 2.60 - 3.18: 8299 3.18 - 3.75: 14018 3.75 - 4.33: 18330 4.33 - 4.90: 30584 Nonbonded interactions: 71306 Sorted by model distance: nonbonded pdb=" OG SER A 407 " pdb="MG MG A1305 " model vdw 2.031 2.170 nonbonded pdb=" O3 VO4 A1301 " pdb="MG MG A1305 " model vdw 2.098 2.170 nonbonded pdb=" O3 VO4 A1303 " pdb="MG MG A1306 " model vdw 2.111 2.170 nonbonded pdb=" OE1 GLN A 448 " pdb="MG MG A1305 " model vdw 2.169 2.170 nonbonded pdb=" OG1 THR A 469 " pdb=" OE1 GLU A 472 " model vdw 2.207 3.040 ... (remaining 71301 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.970 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 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 : 0.003 0.038 9235 Z= 0.133 Angle : 0.620 8.211 12509 Z= 0.333 Chirality : 0.041 0.371 1438 Planarity : 0.003 0.038 1584 Dihedral : 15.108 141.354 3320 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 1.23 (0.26), residues: 1166 helix: 2.28 (0.19), residues: 754 sheet: -0.88 (0.82), residues: 45 loop : -2.28 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 684 HIS 0.002 0.000 HIS A 77 PHE 0.014 0.001 PHE A 752 TYR 0.010 0.001 TYR A 205 ARG 0.011 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.17983 ( 602) hydrogen bonds : angle 5.10926 ( 1782) covalent geometry : bond 0.00263 ( 9235) covalent geometry : angle 0.61961 (12509) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1983 time to fit residues: 46.9088 Evaluate side-chains 136 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.0980 chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 0.0980 chunk 68 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 GLN ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 GLN A1148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.164750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.136513 restraints weight = 12792.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.139545 restraints weight = 8022.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.141661 restraints weight = 5956.597| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9235 Z= 0.157 Angle : 0.626 7.966 12509 Z= 0.325 Chirality : 0.040 0.229 1438 Planarity : 0.004 0.043 1584 Dihedral : 7.256 141.467 1293 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 1.15 % Allowed : 10.17 % Favored : 88.68 % 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: 1.34 (0.26), residues: 1166 helix: 2.36 (0.19), residues: 782 sheet: -0.80 (0.82), residues: 39 loop : -2.61 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 185 HIS 0.007 0.001 HIS A 77 PHE 0.029 0.002 PHE A 946 TYR 0.018 0.001 TYR A 740 ARG 0.006 0.000 ARG A 762 Details of bonding type rmsd hydrogen bonds : bond 0.06276 ( 602) hydrogen bonds : angle 4.07886 ( 1782) covalent geometry : bond 0.00338 ( 9235) covalent geometry : angle 0.62580 (12509) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 1.053 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 142 average time/residue: 0.2027 time to fit residues: 41.5753 Evaluate side-chains 131 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 931 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 70 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 0.3980 chunk 79 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 560 HIS ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.155085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.126828 restraints weight = 13296.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.129764 restraints weight = 8377.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.131725 restraints weight = 6232.909| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9235 Z= 0.217 Angle : 0.681 6.950 12509 Z= 0.358 Chirality : 0.042 0.192 1438 Planarity : 0.004 0.044 1584 Dihedral : 7.445 143.050 1293 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 3.04 % Allowed : 12.89 % Favored : 84.07 % 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: 0.87 (0.25), residues: 1166 helix: 2.02 (0.18), residues: 777 sheet: -1.46 (0.72), residues: 45 loop : -2.69 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 684 HIS 0.005 0.001 HIS A 560 PHE 0.026 0.002 PHE A 946 TYR 0.023 0.002 TYR A 463 ARG 0.005 0.001 ARG A 762 Details of bonding type rmsd hydrogen bonds : bond 0.07317 ( 602) hydrogen bonds : angle 4.28335 ( 1782) covalent geometry : bond 0.00497 ( 9235) covalent geometry : angle 0.68106 (12509) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 688 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7899 (mp) REVERT: A 1192 GLU cc_start: 0.7685 (tp30) cc_final: 0.7393 (tp30) outliers start: 29 outliers final: 22 residues processed: 161 average time/residue: 0.1949 time to fit residues: 45.2688 Evaluate side-chains 155 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 752 PHE Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1140 THR Chi-restraints excluded: chain A residue 1216 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 2 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 113 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS A 77 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.162615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.135680 restraints weight = 12908.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.136993 restraints weight = 8147.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.139028 restraints weight = 6264.981| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9235 Z= 0.133 Angle : 0.594 8.217 12509 Z= 0.309 Chirality : 0.038 0.158 1438 Planarity : 0.003 0.040 1584 Dihedral : 7.249 143.040 1293 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.31 % Allowed : 16.77 % Favored : 80.92 % 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: 1.25 (0.26), residues: 1166 helix: 2.37 (0.19), residues: 779 sheet: -1.45 (0.73), residues: 46 loop : -2.73 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 830 HIS 0.003 0.001 HIS A 585 PHE 0.026 0.001 PHE A 946 TYR 0.014 0.001 TYR A 86 ARG 0.004 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.05695 ( 602) hydrogen bonds : angle 3.89528 ( 1782) covalent geometry : bond 0.00256 ( 9235) covalent geometry : angle 0.59370 (12509) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 69 PHE cc_start: 0.5740 (t80) cc_final: 0.5518 (t80) REVERT: A 270 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7694 (mp) REVERT: A 339 MET cc_start: 0.7668 (tpp) cc_final: 0.7462 (ttt) REVERT: A 459 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7448 (tm-30) REVERT: A 684 TRP cc_start: 0.7907 (p90) cc_final: 0.7064 (p-90) REVERT: A 688 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.8006 (mp) REVERT: A 1192 GLU cc_start: 0.7859 (tp30) cc_final: 0.7476 (tp30) outliers start: 22 outliers final: 9 residues processed: 148 average time/residue: 0.2109 time to fit residues: 44.7410 Evaluate side-chains 137 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 1006 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 109 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.156353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128030 restraints weight = 13083.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.130875 restraints weight = 8017.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.132938 restraints weight = 5900.135| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9235 Z= 0.197 Angle : 0.675 9.981 12509 Z= 0.349 Chirality : 0.042 0.270 1438 Planarity : 0.004 0.050 1584 Dihedral : 7.356 145.129 1293 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 3.04 % Allowed : 17.92 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.98 (0.25), residues: 1166 helix: 2.17 (0.19), residues: 775 sheet: -1.73 (0.71), residues: 46 loop : -2.76 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 684 HIS 0.004 0.001 HIS A 81 PHE 0.026 0.002 PHE A 58 TYR 0.012 0.002 TYR A 463 ARG 0.004 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.06785 ( 602) hydrogen bonds : angle 4.11748 ( 1782) covalent geometry : bond 0.00451 ( 9235) covalent geometry : angle 0.67502 (12509) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7493 (tm-30) REVERT: A 688 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.8014 (mp) REVERT: A 1192 GLU cc_start: 0.7809 (tp30) cc_final: 0.7452 (tp30) REVERT: A 1218 VAL cc_start: 0.7186 (OUTLIER) cc_final: 0.6904 (t) outliers start: 29 outliers final: 18 residues processed: 160 average time/residue: 0.2079 time to fit residues: 47.3228 Evaluate side-chains 154 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 752 PHE Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1218 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.157224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129878 restraints weight = 12995.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.132044 restraints weight = 8532.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.134401 restraints weight = 5690.498| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9235 Z= 0.169 Angle : 0.630 6.397 12509 Z= 0.329 Chirality : 0.040 0.216 1438 Planarity : 0.004 0.050 1584 Dihedral : 7.375 144.233 1293 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 3.04 % Allowed : 18.45 % Favored : 78.51 % 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: 0.94 (0.25), residues: 1166 helix: 2.15 (0.19), residues: 776 sheet: -1.66 (0.71), residues: 46 loop : -2.84 (0.29), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 684 HIS 0.003 0.001 HIS A 77 PHE 0.026 0.002 PHE A 946 TYR 0.013 0.001 TYR A 86 ARG 0.004 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.06443 ( 602) hydrogen bonds : angle 4.05826 ( 1782) covalent geometry : bond 0.00376 ( 9235) covalent geometry : angle 0.63029 (12509) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7620 (tm-30) REVERT: A 688 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8044 (mp) REVERT: A 1145 ARG cc_start: 0.8532 (mmm160) cc_final: 0.7959 (tpt170) REVERT: A 1188 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8061 (mt0) REVERT: A 1192 GLU cc_start: 0.7829 (tp30) cc_final: 0.7456 (tp30) REVERT: A 1218 VAL cc_start: 0.7032 (OUTLIER) cc_final: 0.6750 (t) outliers start: 29 outliers final: 18 residues processed: 152 average time/residue: 0.2145 time to fit residues: 46.5594 Evaluate side-chains 149 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 752 PHE Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1218 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 37 optimal weight: 0.0040 chunk 82 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 35 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.158164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.130428 restraints weight = 13060.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.133793 restraints weight = 8240.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.135046 restraints weight = 6123.838| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9235 Z= 0.154 Angle : 0.628 7.010 12509 Z= 0.324 Chirality : 0.039 0.195 1438 Planarity : 0.004 0.048 1584 Dihedral : 7.370 145.452 1293 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.62 % Allowed : 19.50 % Favored : 77.88 % 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: 0.95 (0.25), residues: 1166 helix: 2.15 (0.19), residues: 778 sheet: -1.51 (0.73), residues: 46 loop : -2.87 (0.29), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 830 HIS 0.003 0.001 HIS A1230 PHE 0.027 0.002 PHE A 27 TYR 0.013 0.001 TYR A 86 ARG 0.006 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.06258 ( 602) hydrogen bonds : angle 4.02439 ( 1782) covalent geometry : bond 0.00334 ( 9235) covalent geometry : angle 0.62763 (12509) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 418 ASP cc_start: 0.7965 (p0) cc_final: 0.7731 (p0) REVERT: A 459 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7568 (tm-30) REVERT: A 688 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7890 (mp) REVERT: A 848 PHE cc_start: 0.6501 (OUTLIER) cc_final: 0.6227 (m-80) REVERT: A 1145 ARG cc_start: 0.8462 (mmm160) cc_final: 0.7905 (tpp-160) REVERT: A 1192 GLU cc_start: 0.7751 (tp30) cc_final: 0.7410 (tp30) REVERT: A 1218 VAL cc_start: 0.7025 (OUTLIER) cc_final: 0.6772 (t) outliers start: 25 outliers final: 18 residues processed: 155 average time/residue: 0.2157 time to fit residues: 46.8313 Evaluate side-chains 152 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 752 PHE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 848 PHE Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1218 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 101 optimal weight: 0.0010 chunk 41 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.162065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.133659 restraints weight = 13217.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.137606 restraints weight = 8026.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.139151 restraints weight = 5707.596| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9235 Z= 0.131 Angle : 0.619 10.303 12509 Z= 0.317 Chirality : 0.039 0.176 1438 Planarity : 0.003 0.046 1584 Dihedral : 7.330 145.881 1293 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.31 % Allowed : 19.92 % Favored : 77.78 % 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: 1.20 (0.26), residues: 1166 helix: 2.35 (0.19), residues: 773 sheet: -1.40 (0.74), residues: 46 loop : -2.74 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 830 HIS 0.003 0.001 HIS A1230 PHE 0.029 0.001 PHE A 27 TYR 0.017 0.001 TYR A 86 ARG 0.007 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.05422 ( 602) hydrogen bonds : angle 3.86719 ( 1782) covalent geometry : bond 0.00261 ( 9235) covalent geometry : angle 0.61938 (12509) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7420 (tm-30) REVERT: A 684 TRP cc_start: 0.7915 (p90) cc_final: 0.7110 (p-90) REVERT: A 688 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7720 (mp) REVERT: A 689 MET cc_start: 0.7638 (ttt) cc_final: 0.7146 (ttm) REVERT: A 1145 ARG cc_start: 0.8341 (mmm160) cc_final: 0.7792 (tpp-160) REVERT: A 1188 GLN cc_start: 0.8305 (tm-30) cc_final: 0.8075 (mt0) REVERT: A 1192 GLU cc_start: 0.7757 (tp30) cc_final: 0.7391 (tp30) REVERT: A 1218 VAL cc_start: 0.6866 (OUTLIER) cc_final: 0.6611 (t) outliers start: 22 outliers final: 15 residues processed: 151 average time/residue: 0.2101 time to fit residues: 44.9007 Evaluate side-chains 145 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 752 PHE Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 1218 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 104 optimal weight: 0.0470 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.161308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.132924 restraints weight = 12973.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.136043 restraints weight = 7854.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.138234 restraints weight = 5686.766| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9235 Z= 0.134 Angle : 0.617 7.895 12509 Z= 0.316 Chirality : 0.039 0.171 1438 Planarity : 0.003 0.046 1584 Dihedral : 7.290 146.270 1293 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 2.41 % Allowed : 20.23 % Favored : 77.36 % 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: 1.19 (0.26), residues: 1166 helix: 2.33 (0.19), residues: 780 sheet: -1.37 (0.75), residues: 46 loop : -2.81 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 830 HIS 0.003 0.001 HIS A1230 PHE 0.027 0.001 PHE A 27 TYR 0.014 0.001 TYR A 86 ARG 0.007 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.05491 ( 602) hydrogen bonds : angle 3.86642 ( 1782) covalent geometry : bond 0.00279 ( 9235) covalent geometry : angle 0.61717 (12509) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 64 GLN cc_start: 0.7001 (tm-30) cc_final: 0.6655 (tm-30) REVERT: A 459 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7482 (tm-30) REVERT: A 684 TRP cc_start: 0.7883 (p90) cc_final: 0.7133 (p-90) REVERT: A 688 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7663 (mp) REVERT: A 848 PHE cc_start: 0.6466 (OUTLIER) cc_final: 0.6168 (m-80) REVERT: A 1145 ARG cc_start: 0.8345 (mmm160) cc_final: 0.7785 (tpp-160) REVERT: A 1192 GLU cc_start: 0.7736 (tp30) cc_final: 0.7381 (tp30) REVERT: A 1218 VAL cc_start: 0.6883 (OUTLIER) cc_final: 0.6664 (t) outliers start: 23 outliers final: 17 residues processed: 143 average time/residue: 0.2162 time to fit residues: 43.5221 Evaluate side-chains 145 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 752 PHE Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 848 PHE Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 43 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 38 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.154005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126638 restraints weight = 13337.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.127870 restraints weight = 8734.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.129189 restraints weight = 7070.894| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9235 Z= 0.205 Angle : 0.701 8.902 12509 Z= 0.360 Chirality : 0.042 0.176 1438 Planarity : 0.004 0.047 1584 Dihedral : 7.405 143.264 1293 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 2.52 % Allowed : 20.23 % Favored : 77.25 % 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: 0.82 (0.25), residues: 1166 helix: 2.03 (0.19), residues: 775 sheet: -1.34 (0.74), residues: 45 loop : -2.85 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 684 HIS 0.004 0.001 HIS A 81 PHE 0.028 0.002 PHE A 27 TYR 0.015 0.002 TYR A 205 ARG 0.009 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.07032 ( 602) hydrogen bonds : angle 4.21086 ( 1782) covalent geometry : bond 0.00472 ( 9235) covalent geometry : angle 0.70057 (12509) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7365 (tm-30) REVERT: A 463 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.7180 (m-80) REVERT: A 688 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7799 (mp) REVERT: A 689 MET cc_start: 0.7586 (ttm) cc_final: 0.7207 (ttm) REVERT: A 848 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.6348 (m-80) REVERT: A 851 GLN cc_start: 0.7638 (tm-30) cc_final: 0.7346 (tm-30) REVERT: A 1145 ARG cc_start: 0.8451 (mmm160) cc_final: 0.7801 (tpp-160) REVERT: A 1192 GLU cc_start: 0.7949 (tp30) cc_final: 0.7582 (tp30) REVERT: A 1218 VAL cc_start: 0.7053 (OUTLIER) cc_final: 0.6829 (t) outliers start: 24 outliers final: 18 residues processed: 157 average time/residue: 0.2087 time to fit residues: 46.4525 Evaluate side-chains 159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 740 TYR Chi-restraints excluded: chain A residue 752 PHE Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 848 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.160169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131955 restraints weight = 13018.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.135061 restraints weight = 7866.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137246 restraints weight = 5730.991| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9235 Z= 0.140 Angle : 0.641 8.595 12509 Z= 0.330 Chirality : 0.039 0.259 1438 Planarity : 0.004 0.051 1584 Dihedral : 7.315 143.726 1293 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 2.31 % Allowed : 20.34 % Favored : 77.36 % 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: 1.08 (0.26), residues: 1166 helix: 2.26 (0.19), residues: 775 sheet: -1.29 (0.75), residues: 46 loop : -2.81 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 830 HIS 0.003 0.001 HIS A1230 PHE 0.023 0.001 PHE A 673 TYR 0.016 0.001 TYR A 86 ARG 0.007 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.05792 ( 602) hydrogen bonds : angle 3.94083 ( 1782) covalent geometry : bond 0.00286 ( 9235) covalent geometry : angle 0.64102 (12509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2818.79 seconds wall clock time: 50 minutes 38.74 seconds (3038.74 seconds total)