Starting phenix.real_space_refine on Sun Jul 27 21:56:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bsv_30168/07_2025/7bsv_30168_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bsv_30168/07_2025/7bsv_30168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bsv_30168/07_2025/7bsv_30168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bsv_30168/07_2025/7bsv_30168.map" model { file = "/net/cci-nas-00/data/ceres_data/7bsv_30168/07_2025/7bsv_30168_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bsv_30168/07_2025/7bsv_30168_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 1 5.49 5 Mg 1 5.21 5 S 45 5.16 5 C 6081 2.51 5 N 1504 2.21 5 O 1702 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9339 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6596 Classifications: {'peptide': 815} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 792} Chain breaks: 3 Chain: "C" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2613 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 298} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 5.89, per 1000 atoms: 0.63 Number of scatterers: 9339 At special positions: 0 Unit cell: (101.26, 93.79, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 45 16.00 P 1 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1702 8.00 N 1504 7.00 C 6081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 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=1, symmetry=0 Links applied ALPHA1-4 " NAG B 1 " - " MAN B 2 " NAG-ASN " NAG C 401 " - " ASN C 180 " " NAG C 402 " - " ASN C 294 " " NAG C 403 " - " ASN C 107 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.0 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 46.3% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 54 through 64 removed outlier: 3.515A pdb=" N LYS A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.574A pdb=" N LEU A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 121 Proline residue: A 94 - end of helix removed outlier: 3.596A pdb=" N THR A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.681A pdb=" N ASN A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 314 removed outlier: 3.503A pdb=" N ASN A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.532A pdb=" N ASP A 320 " --> pdb=" O PRO A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.550A pdb=" N MET A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 356 through 371 removed outlier: 4.217A pdb=" N TYR A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET A 365 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.925A pdb=" N SER A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 400 removed outlier: 4.060A pdb=" N LEU A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN A 397 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLU A 398 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 666 removed outlier: 3.600A pdb=" N ILE A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 666 " --> pdb=" O ALA A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 686 removed outlier: 3.785A pdb=" N SER A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N CYS A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 720 removed outlier: 3.641A pdb=" N ASP A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 762 removed outlier: 3.910A pdb=" N LEU A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 781 removed outlier: 3.715A pdb=" N ILE A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 803 removed outlier: 3.519A pdb=" N ARG A 800 " --> pdb=" O ALA A 796 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 825 Processing helix chain 'A' and resid 853 through 860 removed outlier: 4.380A pdb=" N LYS A 857 " --> pdb=" O LYS A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 891 removed outlier: 3.621A pdb=" N ASN A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) Proline residue: A 887 - end of helix Processing helix chain 'A' and resid 892 through 894 No H-bonds generated for 'chain 'A' and resid 892 through 894' Processing helix chain 'A' and resid 904 through 911 Processing helix chain 'A' and resid 918 through 924 Processing helix chain 'A' and resid 931 through 936 Processing helix chain 'A' and resid 938 through 946 removed outlier: 3.536A pdb=" N LYS A 944 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 951 Processing helix chain 'A' and resid 952 through 978 removed outlier: 3.597A pdb=" N THR A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1015 removed outlier: 3.530A pdb=" N PHE A 995 " --> pdb=" O GLY A 991 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1041 removed outlier: 3.548A pdb=" N LEU A1030 " --> pdb=" O ILE A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1060 Processing helix chain 'A' and resid 1063 through 1077 removed outlier: 3.641A pdb=" N PHE A1075 " --> pdb=" O ILE A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1088 removed outlier: 3.573A pdb=" N VAL A1086 " --> pdb=" O ILE A1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 52 through 72 removed outlier: 3.641A pdb=" N GLY C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) Proline residue: C 63 - end of helix removed outlier: 3.555A pdb=" N SER C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 95 removed outlier: 3.796A pdb=" N LYS C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 95 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.688A pdb=" N LYS C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 152 removed outlier: 3.783A pdb=" N LEU C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 254 through 262 removed outlier: 3.738A pdb=" N ARG C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.640A pdb=" N PHE C 304 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 347 removed outlier: 3.538A pdb=" N LEU C 339 " --> pdb=" O ILE C 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 137 removed outlier: 4.175A pdb=" N TYR A 126 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL A 146 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA4, first strand: chain 'A' and resid 187 through 188 removed outlier: 3.955A pdb=" N TYR A 172 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 225 removed outlier: 3.530A pdb=" N LEU A 239 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 225 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 381 through 382 Processing sheet with id=AA7, first strand: chain 'A' and resid 390 through 391 Processing sheet with id=AA8, first strand: chain 'A' and resid 696 through 699 removed outlier: 6.131A pdb=" N GLU A 696 " --> pdb=" O GLY A 748 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ILE A 750 " --> pdb=" O GLU A 696 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 698 " --> pdb=" O ILE A 750 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ASP A 752 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL A 670 " --> pdb=" O VAL A 785 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N CYS A 787 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A 672 " --> pdb=" O CYS A 787 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR A 811 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE A 831 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N SER A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 81 removed outlier: 6.029A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 106 through 110 removed outlier: 3.514A pdb=" N PHE C 108 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 182 " --> pdb=" O THR C 296 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.93 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1465 1.30 - 1.43: 2578 1.43 - 1.56: 5449 1.56 - 1.68: 1 1.68 - 1.81: 71 Bond restraints: 9564 Sorted by residual: bond pdb=" F4 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.686 1.800 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.684 1.796 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.796 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.793 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C17 P5S A1103 " pdb=" O19 P5S A1103 " ideal model delta sigma weight residual 1.351 1.453 -0.102 2.00e-02 2.50e+03 2.60e+01 ... (remaining 9559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.20: 12962 14.20 - 28.41: 4 28.41 - 42.61: 0 42.61 - 56.81: 0 56.81 - 71.01: 2 Bond angle restraints: 12968 Sorted by residual: angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 179.69 -71.01 3.00e+00 1.11e-01 5.60e+02 angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 179.28 -69.65 3.00e+00 1.11e-01 5.39e+02 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 110.21 90.09 20.12 3.00e+00 1.11e-01 4.50e+01 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.59 89.52 20.07 3.00e+00 1.11e-01 4.48e+01 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.69 90.20 19.49 3.00e+00 1.11e-01 4.22e+01 ... (remaining 12963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.93: 5397 29.93 - 59.85: 294 59.85 - 89.78: 40 89.78 - 119.71: 6 119.71 - 149.64: 6 Dihedral angle restraints: 5743 sinusoidal: 2398 harmonic: 3345 Sorted by residual: dihedral pdb=" CA THR C 100 " pdb=" C THR C 100 " pdb=" N PRO C 101 " pdb=" CA PRO C 101 " ideal model delta harmonic sigma weight residual 180.00 121.36 58.64 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CB CYS C 91 " pdb=" SG CYS C 91 " pdb=" SG CYS C 104 " pdb=" CB CYS C 104 " ideal model delta sinusoidal sigma weight residual 93.00 153.74 -60.74 1 1.00e+01 1.00e-02 4.91e+01 dihedral pdb=" CA VAL C 99 " pdb=" C VAL C 99 " pdb=" N THR C 100 " pdb=" CA THR C 100 " ideal model delta harmonic sigma weight residual -180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 5740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 1462 0.148 - 0.295: 0 0.295 - 0.443: 0 0.443 - 0.591: 1 0.591 - 0.738: 2 Chirality restraints: 1465 Sorted by residual: chirality pdb=" C1 MAN B 2 " pdb=" O4 NAG B 1 " pdb=" C2 MAN B 2 " pdb=" O5 MAN B 2 " both_signs ideal model delta sigma weight residual False 2.40 1.91 0.49 2.00e-02 2.50e+03 6.00e+02 chirality pdb=" C1 NAG C 402 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 402 " pdb=" O5 NAG C 402 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" C1 NAG C 403 " pdb=" ND2 ASN C 107 " pdb=" C2 NAG C 403 " pdb=" O5 NAG C 403 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.18e+01 ... (remaining 1462 not shown) Planarity restraints: 1615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 403 " 0.342 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG C 403 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C 403 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG C 403 " -0.515 2.00e-02 2.50e+03 pdb=" O7 NAG C 403 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 107 " 0.124 2.00e-02 2.50e+03 2.34e-01 6.83e+02 pdb=" CG ASN C 107 " -0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN C 107 " 0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN C 107 " -0.417 2.00e-02 2.50e+03 pdb=" C1 NAG C 403 " 0.265 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " -0.068 2.00e-02 2.50e+03 5.76e-02 4.15e+01 pdb=" C7 NAG C 401 " 0.015 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " 0.019 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " 0.091 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.056 2.00e-02 2.50e+03 ... (remaining 1612 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 64 2.43 - 3.05: 6095 3.05 - 3.66: 13205 3.66 - 4.28: 22947 4.28 - 4.90: 37488 Nonbonded interactions: 79799 Sorted by model distance: nonbonded pdb=" F4 ALF A1101 " pdb="MG MG A1102 " model vdw 1.809 2.120 nonbonded pdb=" OG1 THR A 175 " pdb=" OD2 ASP A 179 " model vdw 2.042 3.040 nonbonded pdb=" O GLY C 84 " pdb=" OG1 THR C 85 " model vdw 2.054 3.040 nonbonded pdb=" O TYR A 188 " pdb=" ND2 ASN A 243 " model vdw 2.079 3.120 nonbonded pdb=" ND2 ASN C 216 " pdb=" O GLY C 251 " model vdw 2.101 3.120 ... (remaining 79794 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.570 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:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.747 9572 Z= 0.803 Angle : 1.186 71.014 12986 Z= 0.470 Chirality : 0.049 0.738 1465 Planarity : 0.008 0.292 1612 Dihedral : 19.273 149.635 3576 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 30.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.62 % Favored : 92.21 % Rotamer: Outliers : 6.19 % Allowed : 22.12 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -6.02 (0.17), residues: 1129 helix: -4.44 (0.12), residues: 497 sheet: -2.74 (0.37), residues: 166 loop : -3.76 (0.21), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 323 HIS 0.004 0.001 HIS A 929 PHE 0.014 0.001 PHE A 894 TYR 0.011 0.001 TYR A 324 ARG 0.002 0.000 ARG C 262 Details of bonding type rmsd link_NAG-ASN : bond 0.01419 ( 3) link_NAG-ASN : angle 10.44374 ( 9) link_ALPHA1-4 : bond 0.01875 ( 1) link_ALPHA1-4 : angle 7.57103 ( 3) hydrogen bonds : bond 0.29104 ( 362) hydrogen bonds : angle 12.10350 ( 1005) SS BOND : bond 0.00263 ( 3) SS BOND : angle 0.88274 ( 6) covalent geometry : bond 0.00520 ( 9564) covalent geometry : angle 1.14888 (12968) Misc. bond : bond 0.74735 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 144 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 135 ARG cc_start: 0.7850 (ptm-80) cc_final: 0.7524 (ptt180) REVERT: A 191 ARG cc_start: 0.7612 (mmm160) cc_final: 0.7011 (mmp-170) REVERT: A 256 LYS cc_start: 0.8835 (ptmm) cc_final: 0.8614 (pttp) REVERT: A 329 GLN cc_start: 0.8014 (tp40) cc_final: 0.7624 (mm-40) REVERT: A 676 ASP cc_start: 0.7872 (t0) cc_final: 0.7440 (t0) REVERT: A 703 LYS cc_start: 0.7720 (mtpm) cc_final: 0.6858 (mtmm) REVERT: A 774 ILE cc_start: 0.8693 (mt) cc_final: 0.8480 (mt) REVERT: A 926 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8127 (pp) REVERT: C 27 ARG cc_start: 0.6341 (OUTLIER) cc_final: 0.5779 (tpp80) REVERT: C 343 LEU cc_start: 0.8246 (pp) cc_final: 0.7948 (pt) outliers start: 63 outliers final: 21 residues processed: 195 average time/residue: 1.1454 time to fit residues: 239.6803 Evaluate side-chains 142 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 342 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.1980 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 106 GLN A 121 ASN A 226 ASN ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN A 392 ASN A 397 ASN A 764 GLN A 777 GLN A 819 ASN A 840 GLN A 862 HIS A 872 HIS C 36 GLN C 129 GLN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN C 298 ASN ** C 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.143133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.102937 restraints weight = 10166.201| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.77 r_work: 0.2885 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9572 Z= 0.177 Angle : 0.919 32.837 12986 Z= 0.409 Chirality : 0.047 0.463 1465 Planarity : 0.005 0.061 1612 Dihedral : 13.557 143.139 1428 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.29 % Favored : 93.62 % Rotamer: Outliers : 6.19 % Allowed : 20.55 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.21), residues: 1129 helix: -2.41 (0.18), residues: 498 sheet: -1.69 (0.39), residues: 157 loop : -2.90 (0.24), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 323 HIS 0.004 0.001 HIS A 864 PHE 0.015 0.002 PHE A 894 TYR 0.013 0.002 TYR A 324 ARG 0.003 0.000 ARG C 307 Details of bonding type rmsd link_NAG-ASN : bond 0.01453 ( 3) link_NAG-ASN : angle 4.27827 ( 9) link_ALPHA1-4 : bond 0.01862 ( 1) link_ALPHA1-4 : angle 4.79657 ( 3) hydrogen bonds : bond 0.04884 ( 362) hydrogen bonds : angle 5.73761 ( 1005) SS BOND : bond 0.00337 ( 3) SS BOND : angle 1.89760 ( 6) covalent geometry : bond 0.00416 ( 9564) covalent geometry : angle 0.90860 (12968) Misc. bond : bond 0.00127 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 135 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.7970 (ptm-80) cc_final: 0.7398 (tmt-80) REVERT: A 224 ARG cc_start: 0.7325 (ttm170) cc_final: 0.6648 (ttt90) REVERT: A 252 LYS cc_start: 0.8421 (mptt) cc_final: 0.8213 (mmtp) REVERT: A 256 LYS cc_start: 0.8749 (ptmm) cc_final: 0.8478 (pttp) REVERT: A 329 GLN cc_start: 0.8130 (tp40) cc_final: 0.7761 (mm-40) REVERT: A 364 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7980 (mp0) REVERT: A 703 LYS cc_start: 0.7518 (mtpm) cc_final: 0.6607 (mtmm) REVERT: A 717 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6457 (tm-30) REVERT: A 895 CYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8057 (p) REVERT: A 926 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8368 (pp) REVERT: A 928 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.6893 (mp10) REVERT: A 1074 ILE cc_start: 0.8747 (pt) cc_final: 0.8540 (mt) REVERT: C 343 LEU cc_start: 0.7590 (pp) cc_final: 0.7384 (pt) outliers start: 63 outliers final: 19 residues processed: 185 average time/residue: 1.0633 time to fit residues: 212.8389 Evaluate side-chains 140 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 234 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A 777 GLN C 142 GLN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN C 347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.144668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.104303 restraints weight = 10272.102| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.84 r_work: 0.2908 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9572 Z= 0.153 Angle : 0.869 31.454 12986 Z= 0.379 Chirality : 0.045 0.322 1465 Planarity : 0.004 0.064 1612 Dihedral : 11.551 134.913 1400 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.92 % Allowed : 22.12 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -2.61 (0.23), residues: 1129 helix: -1.07 (0.21), residues: 505 sheet: -1.00 (0.40), residues: 157 loop : -2.70 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.005 0.001 HIS A 114 PHE 0.016 0.001 PHE C 108 TYR 0.017 0.002 TYR A 318 ARG 0.003 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00735 ( 3) link_NAG-ASN : angle 2.87846 ( 9) link_ALPHA1-4 : bond 0.01189 ( 1) link_ALPHA1-4 : angle 3.99986 ( 3) hydrogen bonds : bond 0.04244 ( 362) hydrogen bonds : angle 5.14003 ( 1005) SS BOND : bond 0.00365 ( 3) SS BOND : angle 1.79011 ( 6) covalent geometry : bond 0.00363 ( 9564) covalent geometry : angle 0.86323 (12968) Misc. bond : bond 0.00162 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 128 time to evaluate : 0.971 Fit side-chains REVERT: A 44 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7264 (ttp-170) REVERT: A 135 ARG cc_start: 0.7973 (ptm-80) cc_final: 0.7393 (tmt-80) REVERT: A 252 LYS cc_start: 0.8322 (mptt) cc_final: 0.8104 (mmtp) REVERT: A 256 LYS cc_start: 0.8761 (ptmm) cc_final: 0.8520 (pttp) REVERT: A 329 GLN cc_start: 0.8090 (tp40) cc_final: 0.7632 (mm-40) REVERT: A 663 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8562 (mp) REVERT: A 703 LYS cc_start: 0.7519 (mtpm) cc_final: 0.6641 (mtmm) REVERT: A 717 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6536 (tm-30) REVERT: A 774 ILE cc_start: 0.8180 (mt) cc_final: 0.7908 (mp) REVERT: A 895 CYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7500 (m) REVERT: A 926 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8341 (pp) REVERT: A 928 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.7030 (mp10) REVERT: C 270 ARG cc_start: 0.8811 (mtt180) cc_final: 0.8315 (mtm-85) outliers start: 50 outliers final: 20 residues processed: 170 average time/residue: 1.1548 time to fit residues: 211.3392 Evaluate side-chains 140 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 339 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 60 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.145805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.104985 restraints weight = 10152.915| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.75 r_work: 0.2937 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9572 Z= 0.142 Angle : 0.851 31.147 12986 Z= 0.368 Chirality : 0.044 0.248 1465 Planarity : 0.004 0.073 1612 Dihedral : 10.591 126.388 1400 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.92 % Allowed : 23.21 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.18 % 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: -1.87 (0.24), residues: 1129 helix: -0.37 (0.22), residues: 509 sheet: -0.50 (0.42), residues: 157 loop : -2.50 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 323 HIS 0.005 0.001 HIS A 114 PHE 0.016 0.001 PHE C 108 TYR 0.014 0.001 TYR A 318 ARG 0.003 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00732 ( 3) link_NAG-ASN : angle 2.36326 ( 9) link_ALPHA1-4 : bond 0.01521 ( 1) link_ALPHA1-4 : angle 4.21371 ( 3) hydrogen bonds : bond 0.03933 ( 362) hydrogen bonds : angle 4.84625 ( 1005) SS BOND : bond 0.00386 ( 3) SS BOND : angle 3.15522 ( 6) covalent geometry : bond 0.00335 ( 9564) covalent geometry : angle 0.84434 (12968) Misc. bond : bond 0.00091 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 123 time to evaluate : 1.146 Fit side-chains REVERT: A 44 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7333 (ttp-170) REVERT: A 135 ARG cc_start: 0.8040 (ptm-80) cc_final: 0.7522 (tmt-80) REVERT: A 191 ARG cc_start: 0.7436 (mmm160) cc_final: 0.6542 (mmm160) REVERT: A 252 LYS cc_start: 0.8377 (mptt) cc_final: 0.8163 (mmtp) REVERT: A 256 LYS cc_start: 0.8771 (ptmm) cc_final: 0.8527 (pttp) REVERT: A 329 GLN cc_start: 0.8092 (tp40) cc_final: 0.7657 (mm-40) REVERT: A 663 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8560 (mp) REVERT: A 678 MET cc_start: 0.5468 (tmm) cc_final: 0.5161 (tpp) REVERT: A 717 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6727 (tm-30) REVERT: A 774 ILE cc_start: 0.8242 (mt) cc_final: 0.7968 (mp) REVERT: A 926 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8364 (pp) REVERT: A 928 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.7032 (mp10) REVERT: C 155 LYS cc_start: 0.8335 (mttp) cc_final: 0.7663 (pttm) REVERT: C 238 LYS cc_start: 0.8355 (mtmm) cc_final: 0.7916 (pttp) REVERT: C 270 ARG cc_start: 0.8812 (mtt180) cc_final: 0.8340 (mtm-85) outliers start: 50 outliers final: 18 residues processed: 161 average time/residue: 1.3226 time to fit residues: 229.0364 Evaluate side-chains 138 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 339 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A 777 GLN C 142 GLN C 144 ASN C 152 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.150743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.108598 restraints weight = 9983.164| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.89 r_work: 0.2972 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9572 Z= 0.127 Angle : 0.838 30.500 12986 Z= 0.359 Chirality : 0.043 0.224 1465 Planarity : 0.004 0.073 1612 Dihedral : 9.481 112.859 1397 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.11 % Allowed : 23.50 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.09 % 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: -1.39 (0.24), residues: 1129 helix: 0.12 (0.23), residues: 503 sheet: -0.39 (0.42), residues: 164 loop : -2.32 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 323 HIS 0.004 0.001 HIS A 114 PHE 0.015 0.001 PHE C 108 TYR 0.014 0.001 TYR A 324 ARG 0.003 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00647 ( 3) link_NAG-ASN : angle 2.20367 ( 9) link_ALPHA1-4 : bond 0.01998 ( 1) link_ALPHA1-4 : angle 4.32123 ( 3) hydrogen bonds : bond 0.03638 ( 362) hydrogen bonds : angle 4.63322 ( 1005) SS BOND : bond 0.00296 ( 3) SS BOND : angle 2.57556 ( 6) covalent geometry : bond 0.00296 ( 9564) covalent geometry : angle 0.83176 (12968) Misc. bond : bond 0.00082 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 119 time to evaluate : 1.030 Fit side-chains REVERT: A 44 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7232 (ttp-170) REVERT: A 90 THR cc_start: 0.8804 (p) cc_final: 0.8593 (p) REVERT: A 124 THR cc_start: 0.8520 (m) cc_final: 0.8233 (t) REVERT: A 135 ARG cc_start: 0.8014 (ptm-80) cc_final: 0.7598 (tmt-80) REVERT: A 191 ARG cc_start: 0.7422 (mmm160) cc_final: 0.6534 (mmm160) REVERT: A 252 LYS cc_start: 0.8370 (mptt) cc_final: 0.8162 (mmtp) REVERT: A 256 LYS cc_start: 0.8768 (ptmm) cc_final: 0.8506 (pttp) REVERT: A 329 GLN cc_start: 0.8100 (tp40) cc_final: 0.7703 (mm-40) REVERT: A 339 LYS cc_start: 0.7689 (tptp) cc_final: 0.7114 (ttpt) REVERT: A 678 MET cc_start: 0.5545 (tmm) cc_final: 0.5295 (tpp) REVERT: A 717 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6792 (tm-30) REVERT: A 721 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.5911 (mp0) REVERT: A 774 ILE cc_start: 0.8171 (mt) cc_final: 0.7890 (mp) REVERT: A 926 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8620 (pt) REVERT: A 928 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.6990 (mp10) REVERT: C 155 LYS cc_start: 0.8303 (mttp) cc_final: 0.7651 (pttm) REVERT: C 184 GLU cc_start: 0.7172 (pm20) cc_final: 0.6954 (mp0) REVERT: C 238 LYS cc_start: 0.8236 (mtmm) cc_final: 0.7892 (pttp) REVERT: C 262 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8091 (ttm170) REVERT: C 270 ARG cc_start: 0.8741 (mtt180) cc_final: 0.8215 (mtm-85) outliers start: 52 outliers final: 18 residues processed: 160 average time/residue: 1.1645 time to fit residues: 200.0719 Evaluate side-chains 141 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 721 GLU Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain C residue 343 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 105 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 101 optimal weight: 0.0870 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 386 ASN A 777 GLN C 36 GLN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.146059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.105972 restraints weight = 10147.464| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.73 r_work: 0.2950 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9572 Z= 0.148 Angle : 0.846 30.953 12986 Z= 0.364 Chirality : 0.044 0.229 1465 Planarity : 0.004 0.063 1612 Dihedral : 9.032 105.802 1396 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.42 % Allowed : 24.68 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.25), residues: 1129 helix: 0.14 (0.23), residues: 512 sheet: -0.17 (0.42), residues: 163 loop : -2.19 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.005 0.001 HIS A 114 PHE 0.016 0.001 PHE C 108 TYR 0.013 0.001 TYR A 311 ARG 0.004 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00668 ( 3) link_NAG-ASN : angle 2.20103 ( 9) link_ALPHA1-4 : bond 0.01633 ( 1) link_ALPHA1-4 : angle 5.02561 ( 3) hydrogen bonds : bond 0.03848 ( 362) hydrogen bonds : angle 4.57555 ( 1005) SS BOND : bond 0.00314 ( 3) SS BOND : angle 3.24196 ( 6) covalent geometry : bond 0.00356 ( 9564) covalent geometry : angle 0.83869 (12968) Misc. bond : bond 0.00098 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 1.064 Fit side-chains REVERT: A 124 THR cc_start: 0.8534 (m) cc_final: 0.8268 (t) REVERT: A 135 ARG cc_start: 0.7932 (ptm-80) cc_final: 0.7452 (tmt-80) REVERT: A 191 ARG cc_start: 0.7385 (mmm160) cc_final: 0.6492 (mmm160) REVERT: A 252 LYS cc_start: 0.8344 (mptt) cc_final: 0.8143 (mmtp) REVERT: A 255 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7445 (mp0) REVERT: A 329 GLN cc_start: 0.8151 (tp40) cc_final: 0.7770 (mm-40) REVERT: A 339 LYS cc_start: 0.7804 (tptp) cc_final: 0.7180 (ttpt) REVERT: A 678 MET cc_start: 0.5633 (tmm) cc_final: 0.5275 (tpp) REVERT: A 721 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.5935 (mp0) REVERT: A 774 ILE cc_start: 0.8161 (mt) cc_final: 0.7895 (mp) REVERT: A 926 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8384 (pp) REVERT: A 928 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.7201 (mp10) REVERT: C 155 LYS cc_start: 0.8320 (mttp) cc_final: 0.7639 (pttm) REVERT: C 184 GLU cc_start: 0.7197 (pm20) cc_final: 0.6876 (mp0) REVERT: C 238 LYS cc_start: 0.8228 (mtmm) cc_final: 0.7840 (pttp) REVERT: C 262 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8220 (ttm110) REVERT: C 270 ARG cc_start: 0.8774 (mtt180) cc_final: 0.8236 (mtm-85) REVERT: C 290 ARG cc_start: 0.7827 (mtp180) cc_final: 0.7371 (mtm110) outliers start: 45 outliers final: 16 residues processed: 160 average time/residue: 1.1816 time to fit residues: 202.9283 Evaluate side-chains 139 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 721 GLU Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 343 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.0980 chunk 104 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 66 optimal weight: 0.0980 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A 769 ASN A 777 GLN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.148506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.108917 restraints weight = 10137.894| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.75 r_work: 0.3011 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9572 Z= 0.116 Angle : 0.832 30.059 12986 Z= 0.356 Chirality : 0.043 0.228 1465 Planarity : 0.004 0.067 1612 Dihedral : 8.435 92.728 1393 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.13 % Allowed : 25.37 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -0.96 (0.25), residues: 1129 helix: 0.36 (0.23), residues: 511 sheet: 0.06 (0.44), residues: 156 loop : -2.04 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 323 HIS 0.004 0.001 HIS A 114 PHE 0.015 0.001 PHE C 108 TYR 0.015 0.001 TYR A 324 ARG 0.006 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 3) link_NAG-ASN : angle 2.19979 ( 9) link_ALPHA1-4 : bond 0.01558 ( 1) link_ALPHA1-4 : angle 4.78832 ( 3) hydrogen bonds : bond 0.03498 ( 362) hydrogen bonds : angle 4.46989 ( 1005) SS BOND : bond 0.00297 ( 3) SS BOND : angle 2.58605 ( 6) covalent geometry : bond 0.00272 ( 9564) covalent geometry : angle 0.82559 (12968) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 1.080 Fit side-chains REVERT: A 109 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: A 124 THR cc_start: 0.8531 (m) cc_final: 0.8277 (t) REVERT: A 135 ARG cc_start: 0.7865 (ptm-80) cc_final: 0.7400 (tmt-80) REVERT: A 191 ARG cc_start: 0.7404 (mmm160) cc_final: 0.6491 (mmm160) REVERT: A 224 ARG cc_start: 0.7093 (ttm170) cc_final: 0.6509 (ttt90) REVERT: A 252 LYS cc_start: 0.8334 (mptt) cc_final: 0.8076 (mmtp) REVERT: A 329 GLN cc_start: 0.8089 (tp40) cc_final: 0.7643 (mm-40) REVERT: A 339 LYS cc_start: 0.7759 (tptp) cc_final: 0.7162 (ttpt) REVERT: A 774 ILE cc_start: 0.8151 (mt) cc_final: 0.7867 (mp) REVERT: A 926 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8609 (pt) REVERT: A 928 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.6964 (mp10) REVERT: C 155 LYS cc_start: 0.8248 (mttp) cc_final: 0.7597 (pttm) REVERT: C 184 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: C 238 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7736 (pttp) REVERT: C 262 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8166 (ttm110) REVERT: C 270 ARG cc_start: 0.8682 (mtt180) cc_final: 0.8309 (mtm-85) REVERT: C 290 ARG cc_start: 0.7785 (mtp180) cc_final: 0.7382 (mtm110) outliers start: 42 outliers final: 15 residues processed: 154 average time/residue: 1.1366 time to fit residues: 189.3397 Evaluate side-chains 138 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 343 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A 777 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.144390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.103622 restraints weight = 10311.089| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.74 r_work: 0.2920 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9572 Z= 0.198 Angle : 0.881 32.025 12986 Z= 0.383 Chirality : 0.047 0.232 1465 Planarity : 0.004 0.061 1612 Dihedral : 8.886 107.451 1393 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.38 % Favored : 93.53 % Rotamer: Outliers : 3.54 % Allowed : 25.76 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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 (0.25), residues: 1129 helix: 0.20 (0.23), residues: 506 sheet: 0.02 (0.43), residues: 163 loop : -2.03 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 236 HIS 0.005 0.001 HIS A 114 PHE 0.017 0.002 PHE C 108 TYR 0.015 0.002 TYR A 311 ARG 0.006 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00671 ( 3) link_NAG-ASN : angle 2.26866 ( 9) link_ALPHA1-4 : bond 0.01235 ( 1) link_ALPHA1-4 : angle 5.30757 ( 3) hydrogen bonds : bond 0.04160 ( 362) hydrogen bonds : angle 4.60805 ( 1005) SS BOND : bond 0.00398 ( 3) SS BOND : angle 3.04521 ( 6) covalent geometry : bond 0.00485 ( 9564) covalent geometry : angle 0.87310 (12968) Misc. bond : bond 0.00173 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 1.060 Fit side-chains REVERT: A 124 THR cc_start: 0.8562 (m) cc_final: 0.8317 (t) REVERT: A 135 ARG cc_start: 0.7936 (ptm-80) cc_final: 0.7485 (tmt-80) REVERT: A 191 ARG cc_start: 0.7360 (mmm160) cc_final: 0.6432 (mmm160) REVERT: A 224 ARG cc_start: 0.7189 (ttm170) cc_final: 0.6585 (ttt90) REVERT: A 252 LYS cc_start: 0.8367 (mptt) cc_final: 0.8089 (mmtp) REVERT: A 329 GLN cc_start: 0.8230 (tp40) cc_final: 0.7819 (mm-40) REVERT: A 746 GLU cc_start: 0.4539 (OUTLIER) cc_final: 0.4223 (tt0) REVERT: A 774 ILE cc_start: 0.8250 (mt) cc_final: 0.7972 (mp) REVERT: A 926 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8417 (pp) REVERT: A 928 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: C 155 LYS cc_start: 0.8358 (mttp) cc_final: 0.7674 (pttm) REVERT: C 238 LYS cc_start: 0.8270 (mtmm) cc_final: 0.7844 (pttp) REVERT: C 262 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8265 (ttm110) REVERT: C 270 ARG cc_start: 0.8856 (mtt180) cc_final: 0.8376 (mtm-85) REVERT: C 290 ARG cc_start: 0.7847 (mtp180) cc_final: 0.7354 (mtm110) outliers start: 36 outliers final: 16 residues processed: 146 average time/residue: 1.3880 time to fit residues: 217.6277 Evaluate side-chains 139 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 343 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.0980 chunk 75 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A 777 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.150000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.110025 restraints weight = 10115.367| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.81 r_work: 0.3016 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9572 Z= 0.115 Angle : 0.839 30.086 12986 Z= 0.357 Chirality : 0.044 0.263 1465 Planarity : 0.004 0.068 1612 Dihedral : 8.354 90.325 1393 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.95 % Allowed : 26.55 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.25), residues: 1129 helix: 0.57 (0.23), residues: 499 sheet: 0.11 (0.44), residues: 154 loop : -1.99 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 323 HIS 0.004 0.001 HIS A 114 PHE 0.015 0.001 PHE C 108 TYR 0.015 0.001 TYR A 324 ARG 0.007 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 3) link_NAG-ASN : angle 2.21987 ( 9) link_ALPHA1-4 : bond 0.01291 ( 1) link_ALPHA1-4 : angle 4.82600 ( 3) hydrogen bonds : bond 0.03527 ( 362) hydrogen bonds : angle 4.44039 ( 1005) SS BOND : bond 0.00241 ( 3) SS BOND : angle 2.48006 ( 6) covalent geometry : bond 0.00268 ( 9564) covalent geometry : angle 0.83284 (12968) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 1.002 Fit side-chains REVERT: A 109 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: A 124 THR cc_start: 0.8520 (m) cc_final: 0.8258 (t) REVERT: A 135 ARG cc_start: 0.7857 (ptm-80) cc_final: 0.7434 (tmt-80) REVERT: A 191 ARG cc_start: 0.7415 (mmm160) cc_final: 0.6501 (mmm160) REVERT: A 224 ARG cc_start: 0.7147 (ttm170) cc_final: 0.6488 (ttt90) REVERT: A 252 LYS cc_start: 0.8344 (mptt) cc_final: 0.8011 (mmtm) REVERT: A 329 GLN cc_start: 0.8113 (tp40) cc_final: 0.7687 (mm-40) REVERT: A 339 LYS cc_start: 0.7808 (tptp) cc_final: 0.7182 (ttpt) REVERT: A 746 GLU cc_start: 0.4511 (OUTLIER) cc_final: 0.4164 (tt0) REVERT: A 774 ILE cc_start: 0.8089 (mt) cc_final: 0.7802 (mp) REVERT: A 926 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8630 (pt) REVERT: A 928 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7066 (mp10) REVERT: C 155 LYS cc_start: 0.8257 (mttp) cc_final: 0.7614 (pttm) REVERT: C 238 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7725 (pttp) REVERT: C 262 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8209 (ttm110) REVERT: C 270 ARG cc_start: 0.8682 (mtt180) cc_final: 0.8292 (mtm-85) outliers start: 30 outliers final: 13 residues processed: 143 average time/residue: 1.3352 time to fit residues: 205.2829 Evaluate side-chains 137 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 24 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 26 optimal weight: 0.0270 chunk 43 optimal weight: 0.0030 chunk 83 optimal weight: 0.0980 overall best weight: 0.3248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.154635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.112623 restraints weight = 10049.688| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.85 r_work: 0.3035 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 9572 Z= 0.105 Angle : 0.824 29.908 12986 Z= 0.349 Chirality : 0.043 0.232 1465 Planarity : 0.004 0.061 1612 Dihedral : 7.894 81.236 1393 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.77 % Allowed : 28.32 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -0.45 (0.26), residues: 1129 helix: 0.83 (0.24), residues: 499 sheet: 0.20 (0.44), residues: 155 loop : -1.71 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.004 0.001 HIS A 114 PHE 0.014 0.001 PHE C 108 TYR 0.015 0.001 TYR A 324 ARG 0.009 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 3) link_NAG-ASN : angle 2.13998 ( 9) link_ALPHA1-4 : bond 0.01217 ( 1) link_ALPHA1-4 : angle 4.73920 ( 3) hydrogen bonds : bond 0.03257 ( 362) hydrogen bonds : angle 4.31991 ( 1005) SS BOND : bond 0.00266 ( 3) SS BOND : angle 2.29219 ( 6) covalent geometry : bond 0.00243 ( 9564) covalent geometry : angle 0.81831 (12968) Misc. bond : bond 0.00039 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: A 124 THR cc_start: 0.8434 (m) cc_final: 0.8200 (t) REVERT: A 135 ARG cc_start: 0.7802 (ptm-80) cc_final: 0.7452 (tmt-80) REVERT: A 191 ARG cc_start: 0.7435 (mmm160) cc_final: 0.6557 (mmm160) REVERT: A 215 GLN cc_start: 0.8460 (pt0) cc_final: 0.8156 (pm20) REVERT: A 224 ARG cc_start: 0.7214 (ttm170) cc_final: 0.6675 (ttt90) REVERT: A 329 GLN cc_start: 0.8130 (tp40) cc_final: 0.7814 (mm-40) REVERT: A 339 LYS cc_start: 0.7814 (tptp) cc_final: 0.7220 (ttmt) REVERT: A 746 GLU cc_start: 0.4421 (OUTLIER) cc_final: 0.4004 (tt0) REVERT: A 774 ILE cc_start: 0.8123 (mt) cc_final: 0.7838 (mp) REVERT: A 926 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8663 (pt) REVERT: A 928 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.7040 (mp10) REVERT: A 961 PHE cc_start: 0.8657 (m-10) cc_final: 0.8426 (m-10) REVERT: C 155 LYS cc_start: 0.8240 (mttp) cc_final: 0.7630 (pttm) REVERT: C 238 LYS cc_start: 0.8015 (mtmm) cc_final: 0.7661 (ptpp) REVERT: C 262 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8225 (ttm110) REVERT: C 270 ARG cc_start: 0.8554 (mtt180) cc_final: 0.8303 (mtm-85) REVERT: C 290 ARG cc_start: 0.7832 (mtp-110) cc_final: 0.7355 (mtm110) outliers start: 18 outliers final: 11 residues processed: 141 average time/residue: 1.5931 time to fit residues: 241.4968 Evaluate side-chains 137 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain C residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 40 optimal weight: 0.0170 chunk 27 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN C 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.151649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.111727 restraints weight = 9976.912| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.71 r_work: 0.3001 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9572 Z= 0.126 Angle : 0.834 31.269 12986 Z= 0.357 Chirality : 0.044 0.247 1465 Planarity : 0.004 0.065 1612 Dihedral : 8.019 82.406 1393 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.97 % Allowed : 28.22 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -0.41 (0.26), residues: 1129 helix: 0.88 (0.23), residues: 498 sheet: 0.22 (0.44), residues: 155 loop : -1.72 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.004 0.001 HIS A 114 PHE 0.015 0.001 PHE C 108 TYR 0.012 0.001 TYR C 121 ARG 0.012 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 3) link_NAG-ASN : angle 2.06729 ( 9) link_ALPHA1-4 : bond 0.01224 ( 1) link_ALPHA1-4 : angle 4.76385 ( 3) hydrogen bonds : bond 0.03525 ( 362) hydrogen bonds : angle 4.27945 ( 1005) SS BOND : bond 0.00252 ( 3) SS BOND : angle 2.20200 ( 6) covalent geometry : bond 0.00301 ( 9564) covalent geometry : angle 0.82825 (12968) Misc. bond : bond 0.00110 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7524.49 seconds wall clock time: 133 minutes 48.28 seconds (8028.28 seconds total)