Starting phenix.real_space_refine on Wed Feb 4 08:03:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vnt_65217/02_2026/9vnt_65217_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vnt_65217/02_2026/9vnt_65217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vnt_65217/02_2026/9vnt_65217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vnt_65217/02_2026/9vnt_65217.map" model { file = "/net/cci-nas-00/data/ceres_data/9vnt_65217/02_2026/9vnt_65217_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vnt_65217/02_2026/9vnt_65217_trim.cif" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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 6004 2.51 5 N 1479 2.21 5 O 1670 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 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9205 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6509 Classifications: {'peptide': 805} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 782} Chain breaks: 4 Chain: "C" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2582 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 294} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.03, per 1000 atoms: 0.22 Number of scatterers: 9205 At special positions: 0 Unit cell: (75.2, 100.768, 162.432, 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 1670 8.00 N 1479 7.00 C 6004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 197 " distance=2.04 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=2.04 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 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 306.1 milliseconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 7 sheets defined 48.8% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 92 through 121 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 Processing helix chain 'A' and resid 282 through 314 Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 356 through 377 removed outlier: 4.235A pdb=" N TYR A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE A 372 " --> pdb=" O PHE A 368 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 374 " --> pdb=" O GLY A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 381 removed outlier: 3.536A pdb=" N TYR A 381 " --> pdb=" O LYS A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 378 through 381' Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 655 through 666 Processing helix chain 'A' and resid 677 through 688 removed outlier: 3.639A pdb=" N SER A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 720 removed outlier: 3.582A pdb=" N ASP A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 762 Processing helix chain 'A' and resid 770 through 781 Processing helix chain 'A' and resid 791 through 804 removed outlier: 3.639A pdb=" N ALA A 796 " --> pdb=" O PRO A 792 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 799 " --> pdb=" O LYS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 819 No H-bonds generated for 'chain 'A' and resid 817 through 819' Processing helix chain 'A' and resid 820 through 827 Processing helix chain 'A' and resid 839 through 844 Processing helix chain 'A' and resid 854 through 861 Processing helix chain 'A' and resid 861 through 891 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 917 through 927 removed outlier: 3.639A pdb=" N LEU A 921 " --> pdb=" O SER A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 938 Processing helix chain 'A' and resid 939 through 946 removed outlier: 3.501A pdb=" N MET A 943 " --> pdb=" O ARG A 940 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 945 " --> pdb=" O TYR A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 951 Processing helix chain 'A' and resid 952 through 978 removed outlier: 3.706A pdb=" N THR A 974 " --> pdb=" O PHE A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1015 Processing helix chain 'A' and resid 1019 through 1041 removed outlier: 3.692A pdb=" N LEU A1030 " --> pdb=" O ILE A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1061 Processing helix chain 'A' and resid 1063 through 1088 Proline residue: A1080 - end of helix Processing helix chain 'C' and resid 50 through 54 removed outlier: 3.664A pdb=" N ILE C 53 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 74 removed outlier: 3.801A pdb=" N ILE C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) Proline residue: C 63 - end of helix removed outlier: 3.525A pdb=" N SER C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.723A pdb=" N LYS C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 146 through 151 removed outlier: 4.067A pdb=" N LEU C 151 " --> pdb=" O SER C 147 " (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 239 through 243 removed outlier: 3.585A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 removed outlier: 4.102A pdb=" N ASN C 250 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 323 through 333 Processing helix chain 'C' and resid 333 through 348 removed outlier: 3.758A pdb=" N PHE C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU C 339 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.917A pdb=" N GLY A 223 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 137 removed outlier: 4.677A pdb=" N VAL A 146 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 260 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU A 161 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 262 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU A 159 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.720A pdb=" N TYR A 172 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.497A pdb=" N THR A 811 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE A 831 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N SER A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE A 833 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLY A 815 " --> pdb=" O ILE A 833 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 406 " --> pdb=" O TRP A 671 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU A 673 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N THR A 408 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL A 670 " --> pdb=" O VAL A 785 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N CYS A 787 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A 672 " --> pdb=" O CYS A 787 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR A 747 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N LEU A 786 " --> pdb=" O TYR A 747 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU A 749 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N CYS A 788 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE A 751 " --> pdb=" O CYS A 788 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP A 752 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 81 removed outlier: 3.758A pdb=" N ARG C 307 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL C 118 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU C 275 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N MET C 120 " --> pdb=" O TYR C 273 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 110 removed outlier: 4.605A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C 182 " --> pdb=" O THR C 296 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 162 through 163 412 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 2669 1.34 - 1.48: 2659 1.48 - 1.62: 4032 1.62 - 1.77: 1 1.77 - 1.91: 68 Bond restraints: 9429 Sorted by residual: bond pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.910 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" F4 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.686 1.487 0.199 2.00e-02 2.50e+03 9.94e+01 bond pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.547 0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" CG PRO C 52 " pdb=" CD PRO C 52 " ideal model delta sigma weight residual 1.503 1.318 0.185 3.40e-02 8.65e+02 2.95e+01 bond pdb=" C20 P5S A1103 " pdb=" C21 P5S A1103 " ideal model delta sigma weight residual 1.540 1.478 0.062 2.00e-02 2.50e+03 9.46e+00 ... (remaining 9424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.39: 12777 13.39 - 26.79: 2 26.79 - 40.18: 1 40.18 - 53.58: 0 53.58 - 66.97: 2 Bond angle restraints: 12782 Sorted by residual: angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 176.60 -66.97 3.00e+00 1.11e-01 4.98e+02 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 163.90 -55.22 3.00e+00 1.11e-01 3.39e+02 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.02 78.30 30.72 3.00e+00 1.11e-01 1.05e+02 angle pdb=" N PRO C 52 " pdb=" CD PRO C 52 " pdb=" CG PRO C 52 " ideal model delta sigma weight residual 103.20 88.69 14.51 1.50e+00 4.44e-01 9.35e+01 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 110.21 85.60 24.61 3.00e+00 1.11e-01 6.73e+01 ... (remaining 12777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 5364 34.96 - 69.93: 263 69.93 - 104.89: 19 104.89 - 139.86: 3 139.86 - 174.82: 1 Dihedral angle restraints: 5650 sinusoidal: 2350 harmonic: 3300 Sorted by residual: dihedral pdb=" CA GLU C 158 " pdb=" C GLU C 158 " pdb=" N PRO C 159 " pdb=" CA PRO C 159 " ideal model delta harmonic sigma weight residual 180.00 135.23 44.77 0 5.00e+00 4.00e-02 8.02e+01 dihedral pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " pdb=" SG CYS C 102 " pdb=" CB CYS C 102 " ideal model delta sinusoidal sigma weight residual 93.00 156.75 -63.75 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CA PHE A 894 " pdb=" C PHE A 894 " pdb=" N CYS A 895 " pdb=" CA CYS A 895 " ideal model delta harmonic sigma weight residual 180.00 154.83 25.17 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 5647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 835 0.032 - 0.064: 437 0.064 - 0.096: 123 0.096 - 0.128: 44 0.128 - 0.160: 6 Chirality restraints: 1445 Sorted by residual: chirality pdb=" C1 MAN B 3 " pdb=" O4 NAG B 2 " pdb=" C2 MAN B 3 " pdb=" O5 MAN B 3 " both_signs ideal model delta sigma weight residual False 2.40 2.38 0.02 2.00e-02 2.50e+03 1.18e+00 chirality pdb=" CA THR C 100 " pdb=" N THR C 100 " pdb=" C THR C 100 " pdb=" CB THR C 100 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CB ILE C 335 " pdb=" CA ILE C 335 " pdb=" CG1 ILE C 335 " pdb=" CG2 ILE C 335 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 1442 not shown) Planarity restraints: 1587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 158 " 0.082 5.00e-02 4.00e+02 1.26e-01 2.53e+01 pdb=" N PRO C 159 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO C 159 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO C 159 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 84 " -0.045 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO A 85 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 954 " 0.038 5.00e-02 4.00e+02 5.85e-02 5.47e+00 pdb=" N PRO A 955 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 955 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 955 " 0.032 5.00e-02 4.00e+02 ... (remaining 1584 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 15 2.29 - 2.94: 4038 2.94 - 3.59: 13098 3.59 - 4.25: 22768 4.25 - 4.90: 38289 Nonbonded interactions: 78208 Sorted by model distance: nonbonded pdb=" F3 ALF A1101 " pdb="MG MG A1102 " model vdw 1.636 2.120 nonbonded pdb=" OD2 ASP A 409 " pdb=" F3 ALF A1101 " model vdw 1.864 2.990 nonbonded pdb=" O THR A 411 " pdb="MG MG A1102 " model vdw 2.128 2.170 nonbonded pdb=" OD1 ASP A 816 " pdb="MG MG A1102 " model vdw 2.136 2.170 nonbonded pdb=" O GLY A 370 " pdb=" OH TYR A 866 " model vdw 2.162 3.040 ... (remaining 78203 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: 7.470 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 8.140 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 : 0.008 0.490 9438 Z= 0.573 Angle : 1.175 66.969 12802 Z= 0.564 Chirality : 0.042 0.160 1445 Planarity : 0.006 0.126 1585 Dihedral : 19.495 174.819 3508 Min Nonbonded Distance : 1.636 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.79 % Allowed : 27.42 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.25), residues: 1109 helix: -0.00 (0.23), residues: 506 sheet: 0.15 (0.42), residues: 161 loop : -1.64 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 714 TYR 0.016 0.001 TYR A 324 PHE 0.018 0.002 PHE A1035 TRP 0.014 0.002 TRP A 323 HIS 0.005 0.001 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 9429) covalent geometry : angle 1.17299 (12782) SS BOND : bond 0.00441 ( 4) SS BOND : angle 2.03719 ( 8) hydrogen bonds : bond 0.19579 ( 412) hydrogen bonds : angle 6.51201 ( 1164) Misc. bond : bond 0.48965 ( 1) link_ALPHA1-4 : bond 0.00543 ( 1) link_ALPHA1-4 : angle 2.96036 ( 3) link_BETA1-4 : bond 0.00365 ( 1) link_BETA1-4 : angle 1.20679 ( 3) link_NAG-ASN : bond 0.00260 ( 2) link_NAG-ASN : angle 2.36444 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 699 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7710 (mt-10) REVERT: C 338 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7696 (tt) outliers start: 28 outliers final: 19 residues processed: 128 average time/residue: 0.5566 time to fit residues: 75.8242 Evaluate side-chains 116 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 275 GLN A 761 ASN C 216 ASN C 222 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.116135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.093197 restraints weight = 12017.646| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.73 r_work: 0.3021 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9438 Z= 0.142 Angle : 0.846 31.830 12802 Z= 0.373 Chirality : 0.043 0.141 1445 Planarity : 0.006 0.103 1585 Dihedral : 12.913 164.677 1384 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.39 % Allowed : 23.83 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.25), residues: 1109 helix: 0.65 (0.23), residues: 504 sheet: 0.84 (0.44), residues: 146 loop : -1.63 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 290 TYR 0.015 0.002 TYR A 324 PHE 0.018 0.002 PHE A 894 TRP 0.013 0.002 TRP A 323 HIS 0.003 0.001 HIS A 872 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9429) covalent geometry : angle 0.84319 (12782) SS BOND : bond 0.01055 ( 4) SS BOND : angle 1.70658 ( 8) hydrogen bonds : bond 0.05039 ( 412) hydrogen bonds : angle 4.77148 ( 1164) Misc. bond : bond 0.00045 ( 1) link_ALPHA1-4 : bond 0.01246 ( 1) link_ALPHA1-4 : angle 3.35487 ( 3) link_BETA1-4 : bond 0.00158 ( 1) link_BETA1-4 : angle 1.06356 ( 3) link_NAG-ASN : bond 0.00393 ( 2) link_NAG-ASN : angle 1.97802 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 67 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8475 (mt) REVERT: A 210 GLU cc_start: 0.8220 (tp30) cc_final: 0.7824 (mt-10) REVERT: A 699 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8172 (mt-10) REVERT: A 843 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7587 (ptt90) REVERT: C 51 LEU cc_start: 0.8160 (tt) cc_final: 0.7746 (tp) REVERT: C 86 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7037 (pm20) REVERT: C 115 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7172 (mm-30) REVERT: C 342 VAL cc_start: 0.7657 (OUTLIER) cc_final: 0.7402 (p) outliers start: 44 outliers final: 13 residues processed: 141 average time/residue: 0.5881 time to fit residues: 88.5716 Evaluate side-chains 119 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 329 GLN ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.089651 restraints weight = 11991.181| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.73 r_work: 0.2964 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9438 Z= 0.200 Angle : 0.866 31.339 12802 Z= 0.388 Chirality : 0.045 0.149 1445 Planarity : 0.006 0.100 1585 Dihedral : 12.051 134.493 1369 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 5.18 % Allowed : 20.84 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.25), residues: 1109 helix: 0.75 (0.23), residues: 506 sheet: 0.93 (0.43), residues: 147 loop : -1.56 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 44 TYR 0.018 0.002 TYR A 311 PHE 0.019 0.002 PHE A 894 TRP 0.014 0.002 TRP A 323 HIS 0.004 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 9429) covalent geometry : angle 0.86216 (12782) SS BOND : bond 0.00608 ( 4) SS BOND : angle 1.47305 ( 8) hydrogen bonds : bond 0.05476 ( 412) hydrogen bonds : angle 4.65130 ( 1164) Misc. bond : bond 0.00081 ( 1) link_ALPHA1-4 : bond 0.01413 ( 1) link_ALPHA1-4 : angle 3.63414 ( 3) link_BETA1-4 : bond 0.00410 ( 1) link_BETA1-4 : angle 1.92818 ( 3) link_NAG-ASN : bond 0.00769 ( 2) link_NAG-ASN : angle 2.44735 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 92 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7804 (ttp-170) REVERT: A 67 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8485 (mt) REVERT: A 699 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8229 (mt-10) REVERT: A 746 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.5366 (tt0) REVERT: C 51 LEU cc_start: 0.8165 (tt) cc_final: 0.7831 (tp) REVERT: C 76 ARG cc_start: 0.7944 (mmm160) cc_final: 0.7690 (mmm160) REVERT: C 86 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7044 (pm20) REVERT: C 111 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: C 228 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7512 (mtpm) REVERT: C 309 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7860 (mtm180) REVERT: C 342 VAL cc_start: 0.7701 (OUTLIER) cc_final: 0.7322 (p) outliers start: 52 outliers final: 21 residues processed: 132 average time/residue: 0.5261 time to fit residues: 74.2552 Evaluate side-chains 118 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 343 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 0.0670 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN A 819 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.091142 restraints weight = 12115.447| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.74 r_work: 0.2986 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9438 Z= 0.149 Angle : 0.824 30.380 12802 Z= 0.361 Chirality : 0.042 0.156 1445 Planarity : 0.005 0.091 1585 Dihedral : 11.032 125.982 1365 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.99 % Allowed : 21.54 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.25), residues: 1109 helix: 1.02 (0.23), residues: 505 sheet: 1.01 (0.43), residues: 147 loop : -1.53 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 290 TYR 0.016 0.002 TYR A 324 PHE 0.017 0.001 PHE A 894 TRP 0.014 0.002 TRP A 323 HIS 0.003 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9429) covalent geometry : angle 0.82067 (12782) SS BOND : bond 0.00485 ( 4) SS BOND : angle 1.08948 ( 8) hydrogen bonds : bond 0.04721 ( 412) hydrogen bonds : angle 4.46255 ( 1164) Misc. bond : bond 0.00061 ( 1) link_ALPHA1-4 : bond 0.01425 ( 1) link_ALPHA1-4 : angle 3.53214 ( 3) link_BETA1-4 : bond 0.00024 ( 1) link_BETA1-4 : angle 1.39541 ( 3) link_NAG-ASN : bond 0.00548 ( 2) link_NAG-ASN : angle 2.26300 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 93 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8131 (ttp80) cc_final: 0.7912 (ptm-80) REVERT: A 67 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8464 (mt) REVERT: A 256 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8259 (ttpt) REVERT: A 699 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8210 (mt-10) REVERT: A 746 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.5356 (tt0) REVERT: C 51 LEU cc_start: 0.8095 (tt) cc_final: 0.7758 (tp) REVERT: C 115 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7089 (mm-30) REVERT: C 155 LYS cc_start: 0.8981 (ptmm) cc_final: 0.8605 (ttpp) REVERT: C 278 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6760 (tpm170) REVERT: C 309 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7803 (mtm180) outliers start: 50 outliers final: 20 residues processed: 132 average time/residue: 0.6535 time to fit residues: 91.9195 Evaluate side-chains 117 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 278 ARG Chi-restraints excluded: chain C residue 309 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN A 819 ASN A 899 GLN C 322 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.090604 restraints weight = 12019.414| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.73 r_work: 0.2978 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9438 Z= 0.158 Angle : 0.829 30.408 12802 Z= 0.363 Chirality : 0.043 0.166 1445 Planarity : 0.005 0.093 1585 Dihedral : 10.852 129.154 1362 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.08 % Allowed : 21.04 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.25), residues: 1109 helix: 1.14 (0.23), residues: 504 sheet: 1.06 (0.42), residues: 147 loop : -1.49 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 290 TYR 0.016 0.002 TYR A 311 PHE 0.016 0.002 PHE A 894 TRP 0.014 0.002 TRP A 323 HIS 0.003 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9429) covalent geometry : angle 0.82548 (12782) SS BOND : bond 0.00489 ( 4) SS BOND : angle 1.08106 ( 8) hydrogen bonds : bond 0.04838 ( 412) hydrogen bonds : angle 4.42473 ( 1164) Misc. bond : bond 0.00058 ( 1) link_ALPHA1-4 : bond 0.01420 ( 1) link_ALPHA1-4 : angle 3.57798 ( 3) link_BETA1-4 : bond 0.00169 ( 1) link_BETA1-4 : angle 1.53930 ( 3) link_NAG-ASN : bond 0.00628 ( 2) link_NAG-ASN : angle 2.42692 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 89 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 67 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8457 (mt) REVERT: A 210 GLU cc_start: 0.8272 (tp30) cc_final: 0.7870 (mt-10) REVERT: A 256 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8067 (ttpt) REVERT: A 699 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8203 (mt-10) REVERT: A 746 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.5391 (tt0) REVERT: C 51 LEU cc_start: 0.8083 (tt) cc_final: 0.7760 (tp) REVERT: C 86 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7040 (pm20) REVERT: C 115 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7093 (mm-30) REVERT: C 155 LYS cc_start: 0.8993 (ptmm) cc_final: 0.8623 (ttpp) REVERT: C 228 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7373 (mtpm) REVERT: C 309 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7852 (mtm180) outliers start: 51 outliers final: 25 residues processed: 131 average time/residue: 0.6006 time to fit residues: 83.8360 Evaluate side-chains 122 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 342 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 73 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 97 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 819 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.089560 restraints weight = 12048.636| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.74 r_work: 0.2963 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9438 Z= 0.176 Angle : 0.840 29.979 12802 Z= 0.371 Chirality : 0.044 0.172 1445 Planarity : 0.005 0.091 1585 Dihedral : 10.946 131.946 1362 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.89 % Allowed : 21.93 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.25), residues: 1109 helix: 1.13 (0.23), residues: 504 sheet: 1.11 (0.41), residues: 147 loop : -1.44 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 44 TYR 0.017 0.002 TYR A 311 PHE 0.017 0.002 PHE A 894 TRP 0.014 0.002 TRP A 323 HIS 0.003 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 9429) covalent geometry : angle 0.83618 (12782) SS BOND : bond 0.00546 ( 4) SS BOND : angle 1.13316 ( 8) hydrogen bonds : bond 0.05045 ( 412) hydrogen bonds : angle 4.44615 ( 1164) Misc. bond : bond 0.00052 ( 1) link_ALPHA1-4 : bond 0.01418 ( 1) link_ALPHA1-4 : angle 3.61197 ( 3) link_BETA1-4 : bond 0.00230 ( 1) link_BETA1-4 : angle 1.71192 ( 3) link_NAG-ASN : bond 0.00725 ( 2) link_NAG-ASN : angle 2.57174 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 87 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8485 (mt) REVERT: A 210 GLU cc_start: 0.8260 (tp30) cc_final: 0.7864 (mt-10) REVERT: A 228 TYR cc_start: 0.8169 (m-80) cc_final: 0.7967 (m-80) REVERT: A 699 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8212 (mt-10) REVERT: A 722 TYR cc_start: 0.7015 (OUTLIER) cc_final: 0.6578 (t80) REVERT: A 746 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.5412 (tt0) REVERT: C 86 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7072 (pm20) REVERT: C 115 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7212 (mm-30) REVERT: C 155 LYS cc_start: 0.8971 (ptmm) cc_final: 0.8611 (ttpp) REVERT: C 228 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7361 (mtpm) REVERT: C 309 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7858 (mtm180) outliers start: 49 outliers final: 26 residues processed: 126 average time/residue: 0.5876 time to fit residues: 79.3956 Evaluate side-chains 118 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 84 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 722 TYR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 309 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 0.1980 chunk 96 optimal weight: 0.0980 chunk 101 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 82 optimal weight: 0.0070 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 819 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.116874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.094260 restraints weight = 12050.172| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.73 r_work: 0.3036 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9438 Z= 0.107 Angle : 0.789 29.966 12802 Z= 0.337 Chirality : 0.041 0.191 1445 Planarity : 0.004 0.083 1585 Dihedral : 10.187 132.166 1362 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.99 % Allowed : 23.73 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.25), residues: 1109 helix: 1.35 (0.23), residues: 514 sheet: 0.78 (0.40), residues: 161 loop : -1.37 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 44 TYR 0.017 0.001 TYR A 324 PHE 0.012 0.001 PHE A 894 TRP 0.016 0.001 TRP A 323 HIS 0.002 0.001 HIS A 872 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9429) covalent geometry : angle 0.78582 (12782) SS BOND : bond 0.00375 ( 4) SS BOND : angle 0.71928 ( 8) hydrogen bonds : bond 0.03854 ( 412) hydrogen bonds : angle 4.21906 ( 1164) Misc. bond : bond 0.00036 ( 1) link_ALPHA1-4 : bond 0.01489 ( 1) link_ALPHA1-4 : angle 3.44068 ( 3) link_BETA1-4 : bond 0.00364 ( 1) link_BETA1-4 : angle 0.82501 ( 3) link_NAG-ASN : bond 0.00426 ( 2) link_NAG-ASN : angle 2.14459 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8109 (ptpt) REVERT: A 67 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8429 (mt) REVERT: A 210 GLU cc_start: 0.8199 (tp30) cc_final: 0.7781 (mp0) REVERT: A 228 TYR cc_start: 0.8130 (m-80) cc_final: 0.7884 (m-80) REVERT: A 703 LYS cc_start: 0.8326 (pttm) cc_final: 0.8063 (pmtt) REVERT: A 746 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.5418 (tt0) REVERT: C 86 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7018 (pm20) REVERT: C 155 LYS cc_start: 0.8967 (ptmm) cc_final: 0.8635 (ttpp) REVERT: C 228 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7208 (mtpm) outliers start: 30 outliers final: 13 residues processed: 115 average time/residue: 0.6254 time to fit residues: 77.0373 Evaluate side-chains 102 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 228 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.092363 restraints weight = 11891.946| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.73 r_work: 0.3006 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9438 Z= 0.129 Angle : 0.809 30.150 12802 Z= 0.350 Chirality : 0.042 0.196 1445 Planarity : 0.005 0.091 1585 Dihedral : 10.218 130.279 1361 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.69 % Allowed : 24.23 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1109 helix: 1.38 (0.23), residues: 513 sheet: 0.84 (0.40), residues: 161 loop : -1.28 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.018 0.002 TYR A 771 PHE 0.016 0.001 PHE A 894 TRP 0.012 0.001 TRP A 323 HIS 0.002 0.001 HIS A1023 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9429) covalent geometry : angle 0.80513 (12782) SS BOND : bond 0.00577 ( 4) SS BOND : angle 1.20887 ( 8) hydrogen bonds : bond 0.04273 ( 412) hydrogen bonds : angle 4.19700 ( 1164) Misc. bond : bond 0.00035 ( 1) link_ALPHA1-4 : bond 0.01498 ( 1) link_ALPHA1-4 : angle 3.54922 ( 3) link_BETA1-4 : bond 0.00005 ( 1) link_BETA1-4 : angle 1.27802 ( 3) link_NAG-ASN : bond 0.00493 ( 2) link_NAG-ASN : angle 2.35002 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7752 (OUTLIER) cc_final: 0.7411 (p0) REVERT: A 49 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8130 (ptpt) REVERT: A 67 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8448 (mt) REVERT: A 210 GLU cc_start: 0.8210 (tp30) cc_final: 0.7845 (mt-10) REVERT: A 226 ASN cc_start: 0.8469 (t0) cc_final: 0.8034 (m110) REVERT: A 228 TYR cc_start: 0.8154 (m-80) cc_final: 0.7921 (m-80) REVERT: A 746 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.5431 (tt0) REVERT: C 86 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6996 (pm20) REVERT: C 155 LYS cc_start: 0.8981 (ptmm) cc_final: 0.8662 (ttpp) REVERT: C 228 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7307 (mtpm) outliers start: 27 outliers final: 15 residues processed: 103 average time/residue: 0.6095 time to fit residues: 67.3639 Evaluate side-chains 105 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 343 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.090523 restraints weight = 11968.792| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.73 r_work: 0.2979 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9438 Z= 0.163 Angle : 0.833 30.543 12802 Z= 0.365 Chirality : 0.043 0.203 1445 Planarity : 0.005 0.088 1585 Dihedral : 10.467 129.594 1361 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.89 % Allowed : 24.03 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1109 helix: 1.38 (0.23), residues: 507 sheet: 0.87 (0.40), residues: 159 loop : -1.24 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 789 TYR 0.017 0.002 TYR A 311 PHE 0.015 0.002 PHE A 894 TRP 0.012 0.002 TRP A 323 HIS 0.003 0.001 HIS A1023 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9429) covalent geometry : angle 0.82911 (12782) SS BOND : bond 0.00693 ( 4) SS BOND : angle 1.17142 ( 8) hydrogen bonds : bond 0.04753 ( 412) hydrogen bonds : angle 4.27265 ( 1164) Misc. bond : bond 0.00059 ( 1) link_ALPHA1-4 : bond 0.01421 ( 1) link_ALPHA1-4 : angle 3.60414 ( 3) link_BETA1-4 : bond 0.00156 ( 1) link_BETA1-4 : angle 1.56384 ( 3) link_NAG-ASN : bond 0.00657 ( 2) link_NAG-ASN : angle 2.47606 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7432 (p0) REVERT: A 49 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8108 (ptpt) REVERT: A 67 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8456 (mt) REVERT: A 210 GLU cc_start: 0.8248 (tp30) cc_final: 0.7849 (mt-10) REVERT: A 226 ASN cc_start: 0.8489 (t0) cc_final: 0.8156 (m110) REVERT: A 746 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.5477 (tt0) REVERT: C 86 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7066 (pm20) REVERT: C 115 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7232 (mm-30) REVERT: C 155 LYS cc_start: 0.8973 (ptmm) cc_final: 0.8649 (ttpp) REVERT: C 225 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7700 (mm-30) REVERT: C 338 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7244 (tt) outliers start: 29 outliers final: 16 residues processed: 108 average time/residue: 0.6550 time to fit residues: 75.5285 Evaluate side-chains 105 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 0.0970 chunk 106 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 716 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.091795 restraints weight = 12022.044| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.73 r_work: 0.2998 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9438 Z= 0.131 Angle : 0.817 30.318 12802 Z= 0.355 Chirality : 0.042 0.223 1445 Planarity : 0.005 0.088 1585 Dihedral : 10.309 129.013 1361 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.79 % Allowed : 24.33 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.25), residues: 1109 helix: 1.39 (0.23), residues: 513 sheet: 0.88 (0.40), residues: 159 loop : -1.23 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.016 0.002 TYR A 324 PHE 0.015 0.001 PHE A 894 TRP 0.014 0.001 TRP A 323 HIS 0.002 0.001 HIS A1023 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9429) covalent geometry : angle 0.81320 (12782) SS BOND : bond 0.00584 ( 4) SS BOND : angle 0.96362 ( 8) hydrogen bonds : bond 0.04379 ( 412) hydrogen bonds : angle 4.22198 ( 1164) Misc. bond : bond 0.00051 ( 1) link_ALPHA1-4 : bond 0.01542 ( 1) link_ALPHA1-4 : angle 3.54721 ( 3) link_BETA1-4 : bond 0.00093 ( 1) link_BETA1-4 : angle 1.25452 ( 3) link_NAG-ASN : bond 0.00479 ( 2) link_NAG-ASN : angle 2.32003 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7706 (OUTLIER) cc_final: 0.7267 (p0) REVERT: A 49 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8148 (ptpt) REVERT: A 67 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8442 (mt) REVERT: A 210 GLU cc_start: 0.8244 (tp30) cc_final: 0.7842 (mt-10) REVERT: A 226 ASN cc_start: 0.8443 (t0) cc_final: 0.8013 (m110) REVERT: A 746 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.5470 (tt0) REVERT: C 86 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7034 (pm20) REVERT: C 115 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7228 (mm-30) REVERT: C 155 LYS cc_start: 0.8959 (ptmm) cc_final: 0.8640 (ttpp) REVERT: C 166 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8399 (ttmm) REVERT: C 225 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7682 (mm-30) REVERT: C 309 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7662 (mtm180) REVERT: C 338 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7217 (tt) outliers start: 28 outliers final: 17 residues processed: 104 average time/residue: 0.6512 time to fit residues: 72.5971 Evaluate side-chains 109 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.091806 restraints weight = 11856.978| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.72 r_work: 0.2999 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9438 Z= 0.134 Angle : 0.818 30.341 12802 Z= 0.355 Chirality : 0.042 0.230 1445 Planarity : 0.004 0.088 1585 Dihedral : 10.254 128.203 1361 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.09 % Allowed : 24.13 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.25), residues: 1109 helix: 1.41 (0.23), residues: 513 sheet: 0.89 (0.40), residues: 159 loop : -1.22 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.016 0.002 TYR A 324 PHE 0.015 0.001 PHE A 894 TRP 0.013 0.001 TRP A 323 HIS 0.002 0.001 HIS A1023 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9429) covalent geometry : angle 0.81440 (12782) SS BOND : bond 0.00582 ( 4) SS BOND : angle 0.97038 ( 8) hydrogen bonds : bond 0.04387 ( 412) hydrogen bonds : angle 4.21017 ( 1164) Misc. bond : bond 0.00049 ( 1) link_ALPHA1-4 : bond 0.01441 ( 1) link_ALPHA1-4 : angle 3.52482 ( 3) link_BETA1-4 : bond 0.00016 ( 1) link_BETA1-4 : angle 1.29305 ( 3) link_NAG-ASN : bond 0.00503 ( 2) link_NAG-ASN : angle 2.32983 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3593.36 seconds wall clock time: 62 minutes 3.93 seconds (3723.93 seconds total)