Starting phenix.real_space_refine on Wed Feb 4 07:47:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n5i_48922/02_2026/9n5i_48922.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n5i_48922/02_2026/9n5i_48922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n5i_48922/02_2026/9n5i_48922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n5i_48922/02_2026/9n5i_48922.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n5i_48922/02_2026/9n5i_48922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n5i_48922/02_2026/9n5i_48922.map" } resolution = 3.39 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= -0.000 sd= 0.019 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 5887 2.51 5 N 1520 2.21 5 O 1778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 9224 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2367 Classifications: {'peptide': 288} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 274} Chain: "D" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3213 Classifications: {'peptide': 397} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 16, 'TRANS': 377} Chain: "E" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 966 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain: "H" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 996 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 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 Time building chain proxies: 2.33, per 1000 atoms: 0.25 Number of scatterers: 9224 At special positions: 0 Unit cell: (102.3, 76.26, 162.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1778 8.00 N 1520 7.00 C 5887 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A2835 " - pdb=" SG CYS A2846 " distance=2.03 Simple disulfide: pdb=" SG CYS A2986 " - pdb=" SG CYS A3010 " distance=2.03 Simple disulfide: pdb=" SG CYS A3024 " - pdb=" SG CYS A3090 " distance=2.03 Simple disulfide: pdb=" SG CYS A3035 " - pdb=" SG CYS A3088 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 71 " distance=2.03 Simple disulfide: pdb=" SG CYS D 102 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 227 " - pdb=" SG CYS D 275 " distance=2.03 Simple disulfide: pdb=" SG CYS D 234 " - pdb=" SG CYS D 273 " distance=2.03 Simple disulfide: pdb=" SG CYS D 298 " - pdb=" SG CYS D 327 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 412 " distance=2.02 Simple disulfide: pdb=" SG CYS D 352 " - pdb=" SG CYS D 410 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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=0, symmetry=0 Links applied BETA1-6 " NAG B 1 " - " FUC B 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG B 1 " - " ASN F 54 " Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 332.6 milliseconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 24 sheets defined 4.7% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 2911 through 2915 Processing helix chain 'A' and resid 3051 through 3055 Processing helix chain 'D' and resid 33 through 38 removed outlier: 3.953A pdb=" N ASN D 38 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 204 through 208 removed outlier: 3.539A pdb=" N ASN D 207 " --> pdb=" O ASN D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 280 Processing helix chain 'D' and resid 372 through 377 Processing helix chain 'F' and resid 83 through 87 removed outlier: 4.183A pdb=" N THR F 87 " --> pdb=" O ALA F 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.245A pdb=" N ASP H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR H 32 " --> pdb=" O LEU H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.550A pdb=" N THR H 87 " --> pdb=" O ILE H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2836 through 2838 removed outlier: 3.662A pdb=" N LYS A2878 " --> pdb=" O CYS A2846 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2862 through 2869 removed outlier: 4.067A pdb=" N VAL A2863 " --> pdb=" O VAL A2969 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A2971 " --> pdb=" O VAL A2863 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR A2865 " --> pdb=" O LYS A2971 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2900 through 2904 removed outlier: 3.596A pdb=" N TYR A2903 " --> pdb=" O LYS A2907 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS A2907 " --> pdb=" O TYR A2903 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2957 through 2960 Processing sheet with id=AA5, first strand: chain 'A' and resid 2986 through 2987 removed outlier: 3.554A pdb=" N ALA A3023 " --> pdb=" O CYS A2986 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 3009 through 3014 removed outlier: 6.132A pdb=" N CYS A3010 " --> pdb=" O ARG A3100 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR A3102 " --> pdb=" O CYS A3010 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A3012 " --> pdb=" O THR A3102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 3009 through 3014 removed outlier: 6.132A pdb=" N CYS A3010 " --> pdb=" O ARG A3100 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR A3102 " --> pdb=" O CYS A3010 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A3012 " --> pdb=" O THR A3102 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR A3089 " --> pdb=" O SER A3038 " (cutoff:3.500A) removed outlier: 11.006A pdb=" N SER A3038 " --> pdb=" O THR A3089 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A3047 " --> pdb=" O ASP A3041 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 3117 through 3119 removed outlier: 6.552A pdb=" N ILE D 69 " --> pdb=" O MET D 174 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N HIS D 176 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N CYS D 71 " --> pdb=" O HIS D 176 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ARG D 178 " --> pdb=" O CYS D 71 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE D 73 " --> pdb=" O ARG D 178 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 47 through 50 removed outlier: 3.572A pdb=" N ARG D 140 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ASP H 100A" --> pdb=" O PRO H 100E" (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 105 through 107 Processing sheet with id=AB2, first strand: chain 'D' and resid 187 through 190 removed outlier: 6.652A pdb=" N LEU D 187 " --> pdb=" O VAL D 224 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA D 226 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR D 189 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 212 through 217 removed outlier: 6.042A pdb=" N LEU D 213 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LYS D 287 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL D 215 " --> pdb=" O LYS D 287 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 298 through 299 removed outlier: 6.574A pdb=" N CYS D 298 " --> pdb=" O ASN D 343 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 347 through 349 removed outlier: 6.884A pdb=" N ILE D 325 " --> pdb=" O TYR D 420 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N THR D 422 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N CYS D 327 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N THR D 424 " --> pdb=" O CYS D 327 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL D 329 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 355 through 356 Processing sheet with id=AB7, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.039A pdb=" N GLU E 105 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA E 13 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.039A pdb=" N GLU E 105 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA E 13 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 46 through 51 removed outlier: 4.559A pdb=" N SER F 50 " --> pdb=" O TRP F 35A" (cutoff:3.500A) removed outlier: 6.176A pdb=" N TRP F 35A" --> pdb=" O SER F 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.690A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.678A pdb=" N GLN L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.521A pdb=" N VAL L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 741 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: 1.83 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2907 1.34 - 1.46: 2283 1.46 - 1.58: 4215 1.58 - 1.70: 0 1.70 - 1.82: 46 Bond restraints: 9451 Sorted by residual: bond pdb=" CA ILE F 51 " pdb=" CB ILE F 51 " ideal model delta sigma weight residual 1.544 1.566 -0.022 1.42e-02 4.96e+03 2.31e+00 bond pdb=" C ASP A3104 " pdb=" O ASP A3104 " ideal model delta sigma weight residual 1.249 1.237 0.011 8.50e-03 1.38e+04 1.80e+00 bond pdb=" CA TYR E 91 " pdb=" CB TYR E 91 " ideal model delta sigma weight residual 1.524 1.542 -0.019 1.51e-02 4.39e+03 1.52e+00 bond pdb=" CB GLN E 100 " pdb=" CG GLN E 100 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CA ASP D 380 " pdb=" CB ASP D 380 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.69e-02 3.50e+03 1.29e+00 ... (remaining 9446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 12527 1.68 - 3.36: 252 3.36 - 5.03: 31 5.03 - 6.71: 4 6.71 - 8.39: 2 Bond angle restraints: 12816 Sorted by residual: angle pdb=" C GLY D 379 " pdb=" N ASP D 380 " pdb=" CA ASP D 380 " ideal model delta sigma weight residual 121.54 127.35 -5.81 1.91e+00 2.74e-01 9.26e+00 angle pdb=" N PRO F 33 " pdb=" CA PRO F 33 " pdb=" C PRO F 33 " ideal model delta sigma weight residual 114.92 111.31 3.61 1.19e+00 7.06e-01 9.19e+00 angle pdb=" CA ILE F 51 " pdb=" CB ILE F 51 " pdb=" CG1 ILE F 51 " ideal model delta sigma weight residual 110.40 115.37 -4.97 1.70e+00 3.46e-01 8.53e+00 angle pdb=" C SER L 30 " pdb=" CA SER L 30 " pdb=" CB SER L 30 " ideal model delta sigma weight residual 110.42 116.03 -5.61 1.99e+00 2.53e-01 7.93e+00 angle pdb=" N ILE E 29 " pdb=" CA ILE E 29 " pdb=" C ILE E 29 " ideal model delta sigma weight residual 111.77 108.85 2.92 1.04e+00 9.25e-01 7.89e+00 ... (remaining 12811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4881 17.95 - 35.90: 625 35.90 - 53.86: 162 53.86 - 71.81: 24 71.81 - 89.76: 13 Dihedral angle restraints: 5705 sinusoidal: 2316 harmonic: 3389 Sorted by residual: dihedral pdb=" CB CYS D 227 " pdb=" SG CYS D 227 " pdb=" SG CYS D 275 " pdb=" CB CYS D 275 " ideal model delta sinusoidal sigma weight residual -86.00 -169.16 83.16 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS D 298 " pdb=" SG CYS D 298 " pdb=" SG CYS D 327 " pdb=" CB CYS D 327 " ideal model delta sinusoidal sigma weight residual 93.00 138.23 -45.23 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" CB CYS D 352 " pdb=" SG CYS D 352 " pdb=" SG CYS D 410 " pdb=" CB CYS D 410 " ideal model delta sinusoidal sigma weight residual -86.00 -121.83 35.83 1 1.00e+01 1.00e-02 1.82e+01 ... (remaining 5702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1037 0.044 - 0.087: 247 0.087 - 0.131: 124 0.131 - 0.174: 8 0.174 - 0.218: 2 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CB ILE D 45 " pdb=" CA ILE D 45 " pdb=" CG1 ILE D 45 " pdb=" CG2 ILE D 45 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASP D 380 " pdb=" N ASP D 380 " pdb=" C ASP D 380 " pdb=" CB ASP D 380 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.64e-01 chirality pdb=" CB ILE F 51 " pdb=" CA ILE F 51 " pdb=" CG1 ILE F 51 " pdb=" CG2 ILE F 51 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 1415 not shown) Planarity restraints: 1628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A2907 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A2908 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A2908 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A2908 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 287 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO D 288 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 288 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 288 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 100H" 0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO F 100I" -0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 100I" 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 100I" 0.025 5.00e-02 4.00e+02 ... (remaining 1625 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 554 2.73 - 3.27: 8721 3.27 - 3.82: 14791 3.82 - 4.36: 17854 4.36 - 4.90: 31598 Nonbonded interactions: 73518 Sorted by model distance: nonbonded pdb=" OG SER D 246 " pdb=" O LYS D 259 " model vdw 2.189 3.040 nonbonded pdb=" O TYR D 203 " pdb=" ND2 ASN D 204 " model vdw 2.196 3.120 nonbonded pdb=" OG1 THR H 35 " pdb=" OG1 THR H 93 " model vdw 2.212 3.040 nonbonded pdb=" OE2 GLU A2912 " pdb=" OH TYR A2992 " model vdw 2.223 3.040 nonbonded pdb=" O CYS A3035 " pdb=" OG SER A3073 " model vdw 2.269 3.040 ... (remaining 73513 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: 10.540 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: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.310 Find NCS groups from input model: 0.050 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9468 Z= 0.134 Angle : 0.586 8.391 12852 Z= 0.327 Chirality : 0.046 0.218 1418 Planarity : 0.004 0.048 1627 Dihedral : 16.933 89.762 3486 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.76 % Allowed : 24.76 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.18 % Twisted Proline : 0.00 % 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: -0.90 (0.25), residues: 1144 helix: -2.57 (0.73), residues: 37 sheet: -0.18 (0.25), residues: 432 loop : -0.72 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 94 TYR 0.020 0.001 TYR E 91 PHE 0.016 0.001 PHE F 78 TRP 0.010 0.001 TRP H 99 HIS 0.006 0.001 HIS D 324 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9451) covalent geometry : angle 0.58474 (12816) SS BOND : bond 0.00379 ( 15) SS BOND : angle 0.57091 ( 30) hydrogen bonds : bond 0.12602 ( 296) hydrogen bonds : angle 7.66407 ( 741) link_BETA1-6 : bond 0.00359 ( 1) link_BETA1-6 : angle 1.27828 ( 3) link_NAG-ASN : bond 0.00093 ( 1) link_NAG-ASN : angle 1.89049 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2972 ILE cc_start: 0.7352 (mm) cc_final: 0.7085 (tp) REVERT: A 3057 LYS cc_start: 0.7505 (mttt) cc_final: 0.7144 (tptm) REVERT: A 3106 ASN cc_start: 0.8203 (m-40) cc_final: 0.7978 (t0) REVERT: D 150 LYS cc_start: 0.8478 (mttt) cc_final: 0.8209 (tmmt) REVERT: D 214 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6873 (pm20) REVERT: D 229 LEU cc_start: 0.7180 (mm) cc_final: 0.6469 (pt) REVERT: D 240 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8466 (pm20) REVERT: D 287 LYS cc_start: 0.7594 (pttt) cc_final: 0.7296 (ptpt) REVERT: E 42 GLU cc_start: 0.7980 (mp0) cc_final: 0.7310 (mp0) REVERT: E 82 ASP cc_start: 0.7683 (t0) cc_final: 0.7177 (t0) REVERT: E 90 GLN cc_start: 0.8342 (pp30) cc_final: 0.7737 (pp30) REVERT: F 16 GLU cc_start: 0.7700 (tt0) cc_final: 0.7462 (tt0) REVERT: H 52 LYS cc_start: 0.8782 (tptp) cc_final: 0.7841 (ttmm) REVERT: H 59 TYR cc_start: 0.7856 (m-80) cc_final: 0.7439 (m-80) REVERT: H 85 GLU cc_start: 0.7565 (pp20) cc_final: 0.7219 (mm-30) outliers start: 8 outliers final: 7 residues processed: 133 average time/residue: 0.0914 time to fit residues: 17.4097 Evaluate side-chains 131 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 156 CYS Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.0870 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2984 HIS D 279 ASN L 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.160041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.123616 restraints weight = 12173.668| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.22 r_work: 0.3491 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9468 Z= 0.151 Angle : 0.546 7.701 12852 Z= 0.288 Chirality : 0.046 0.162 1418 Planarity : 0.004 0.046 1627 Dihedral : 5.019 42.171 1297 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.10 % Allowed : 23.80 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.18 % Twisted Proline : 0.00 % 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: -0.80 (0.25), residues: 1144 helix: -1.67 (0.98), residues: 25 sheet: -0.30 (0.24), residues: 436 loop : -0.59 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3100 TYR 0.012 0.001 TYR D 47 PHE 0.015 0.001 PHE F 78 TRP 0.012 0.001 TRP H 99 HIS 0.006 0.001 HIS D 176 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9451) covalent geometry : angle 0.54391 (12816) SS BOND : bond 0.00531 ( 15) SS BOND : angle 0.67542 ( 30) hydrogen bonds : bond 0.03329 ( 296) hydrogen bonds : angle 6.26744 ( 741) link_BETA1-6 : bond 0.00253 ( 1) link_BETA1-6 : angle 1.35735 ( 3) link_NAG-ASN : bond 0.00201 ( 1) link_NAG-ASN : angle 2.14524 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2912 GLU cc_start: 0.7936 (tp30) cc_final: 0.7537 (tp30) REVERT: A 2972 ILE cc_start: 0.7511 (mm) cc_final: 0.7218 (tp) REVERT: A 3057 LYS cc_start: 0.7485 (mttt) cc_final: 0.7097 (tptm) REVERT: A 3106 ASN cc_start: 0.8209 (m-40) cc_final: 0.7963 (t0) REVERT: D 150 LYS cc_start: 0.8623 (mttt) cc_final: 0.8295 (tmmt) REVERT: D 214 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6864 (pm20) REVERT: D 229 LEU cc_start: 0.7169 (mm) cc_final: 0.6355 (pt) REVERT: D 287 LYS cc_start: 0.7607 (pttt) cc_final: 0.7242 (ptpt) REVERT: E 42 GLU cc_start: 0.8057 (mp0) cc_final: 0.7654 (mp0) REVERT: E 82 ASP cc_start: 0.7727 (t0) cc_final: 0.7298 (t0) REVERT: E 90 GLN cc_start: 0.8440 (pp30) cc_final: 0.7536 (pp30) REVERT: F 50 SER cc_start: 0.8521 (p) cc_final: 0.8298 (p) REVERT: H 52 LYS cc_start: 0.8691 (tptp) cc_final: 0.7816 (ttmm) REVERT: H 85 GLU cc_start: 0.7623 (pp20) cc_final: 0.7262 (mm-30) REVERT: L 100 ARG cc_start: 0.8371 (mmm160) cc_final: 0.8013 (tpp-160) outliers start: 22 outliers final: 12 residues processed: 146 average time/residue: 0.0895 time to fit residues: 18.6157 Evaluate side-chains 136 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2984 HIS D 254 ASN D 279 ASN ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 ASN L 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.156561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.120749 restraints weight = 12521.941| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.16 r_work: 0.3468 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9468 Z= 0.246 Angle : 0.617 7.782 12852 Z= 0.329 Chirality : 0.048 0.170 1418 Planarity : 0.005 0.050 1627 Dihedral : 5.114 36.728 1293 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.86 % Favored : 93.97 % Rotamer: Outliers : 3.44 % Allowed : 23.90 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.18 % Twisted Proline : 0.00 % 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: -1.12 (0.24), residues: 1144 helix: -1.76 (0.95), residues: 25 sheet: -0.55 (0.24), residues: 442 loop : -0.78 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 94 TYR 0.036 0.002 TYR E 91 PHE 0.018 0.002 PHE L 62 TRP 0.015 0.002 TRP H 99 HIS 0.008 0.001 HIS D 338 Details of bonding type rmsd covalent geometry : bond 0.00594 ( 9451) covalent geometry : angle 0.61435 (12816) SS BOND : bond 0.00854 ( 15) SS BOND : angle 0.94097 ( 30) hydrogen bonds : bond 0.03770 ( 296) hydrogen bonds : angle 6.48255 ( 741) link_BETA1-6 : bond 0.00014 ( 1) link_BETA1-6 : angle 1.41237 ( 3) link_NAG-ASN : bond 0.00143 ( 1) link_NAG-ASN : angle 2.59621 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 3057 LYS cc_start: 0.7539 (mttt) cc_final: 0.7066 (tptm) REVERT: A 3106 ASN cc_start: 0.8234 (m-40) cc_final: 0.7991 (t0) REVERT: D 150 LYS cc_start: 0.8642 (mttt) cc_final: 0.8351 (tmmt) REVERT: D 214 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7006 (pm20) REVERT: D 237 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7500 (pm20) REVERT: E 37 GLN cc_start: 0.7150 (pt0) cc_final: 0.6716 (tt0) REVERT: E 42 GLU cc_start: 0.8091 (mp0) cc_final: 0.7753 (mp0) REVERT: E 82 ASP cc_start: 0.7799 (t0) cc_final: 0.7344 (t0) REVERT: E 90 GLN cc_start: 0.8505 (pp30) cc_final: 0.8282 (pp30) REVERT: H 38 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7138 (ptp90) REVERT: H 85 GLU cc_start: 0.7669 (pp20) cc_final: 0.7404 (mm-30) REVERT: L 100 ARG cc_start: 0.8283 (mmm160) cc_final: 0.7878 (tpp-160) outliers start: 36 outliers final: 19 residues processed: 146 average time/residue: 0.0880 time to fit residues: 18.3793 Evaluate side-chains 133 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2840 THR Chi-restraints excluded: chain D residue 156 CYS Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2984 HIS D 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.158302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.122104 restraints weight = 12705.211| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.24 r_work: 0.3489 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9468 Z= 0.156 Angle : 0.554 8.436 12852 Z= 0.294 Chirality : 0.047 0.158 1418 Planarity : 0.004 0.045 1627 Dihedral : 4.869 37.192 1292 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.72 % Favored : 95.10 % Rotamer: Outliers : 3.15 % Allowed : 24.67 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.18 % Twisted Proline : 0.00 % 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: -1.02 (0.24), residues: 1144 helix: -1.82 (0.91), residues: 25 sheet: -0.56 (0.24), residues: 441 loop : -0.64 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3100 TYR 0.021 0.001 TYR E 91 PHE 0.016 0.001 PHE F 78 TRP 0.014 0.002 TRP H 99 HIS 0.006 0.001 HIS D 338 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 9451) covalent geometry : angle 0.55191 (12816) SS BOND : bond 0.00596 ( 15) SS BOND : angle 0.70493 ( 30) hydrogen bonds : bond 0.03153 ( 296) hydrogen bonds : angle 6.13655 ( 741) link_BETA1-6 : bond 0.00344 ( 1) link_BETA1-6 : angle 1.41614 ( 3) link_NAG-ASN : bond 0.00036 ( 1) link_NAG-ASN : angle 2.37327 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 3057 LYS cc_start: 0.7549 (mttt) cc_final: 0.7066 (tptm) REVERT: A 3106 ASN cc_start: 0.8235 (m-40) cc_final: 0.8033 (t0) REVERT: D 101 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6713 (mtmm) REVERT: D 150 LYS cc_start: 0.8609 (mttt) cc_final: 0.8260 (tmmt) REVERT: D 214 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6908 (pm20) REVERT: D 229 LEU cc_start: 0.7169 (mm) cc_final: 0.6345 (pt) REVERT: E 37 GLN cc_start: 0.6986 (pt0) cc_final: 0.6614 (tt0) REVERT: E 42 GLU cc_start: 0.8084 (mp0) cc_final: 0.7731 (mp0) REVERT: E 82 ASP cc_start: 0.7811 (t0) cc_final: 0.7351 (t0) REVERT: E 90 GLN cc_start: 0.8499 (pp30) cc_final: 0.8288 (pp30) REVERT: H 85 GLU cc_start: 0.7641 (pp20) cc_final: 0.7382 (mm-30) REVERT: L 100 ARG cc_start: 0.8353 (mmm160) cc_final: 0.7969 (tpp-160) outliers start: 33 outliers final: 20 residues processed: 144 average time/residue: 0.0918 time to fit residues: 19.0021 Evaluate side-chains 130 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3111 GLU Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 chunk 53 optimal weight: 0.0000 chunk 84 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2984 HIS D 279 ASN L 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.159811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.124501 restraints weight = 12543.212| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 3.15 r_work: 0.3513 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9468 Z= 0.128 Angle : 0.532 8.212 12852 Z= 0.281 Chirality : 0.046 0.161 1418 Planarity : 0.004 0.045 1627 Dihedral : 4.671 36.071 1292 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.72 % Favored : 95.10 % Rotamer: Outliers : 3.73 % Allowed : 24.67 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.18 % Twisted Proline : 0.00 % 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: -0.92 (0.25), residues: 1144 helix: -1.90 (0.91), residues: 25 sheet: -0.48 (0.24), residues: 442 loop : -0.57 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A3100 TYR 0.019 0.001 TYR H 32 PHE 0.015 0.001 PHE F 78 TRP 0.014 0.001 TRP H 99 HIS 0.005 0.001 HIS D 338 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9451) covalent geometry : angle 0.53038 (12816) SS BOND : bond 0.00501 ( 15) SS BOND : angle 0.56180 ( 30) hydrogen bonds : bond 0.02945 ( 296) hydrogen bonds : angle 5.89160 ( 741) link_BETA1-6 : bond 0.00289 ( 1) link_BETA1-6 : angle 1.29963 ( 3) link_NAG-ASN : bond 0.00104 ( 1) link_NAG-ASN : angle 2.14485 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 3057 LYS cc_start: 0.7592 (mttt) cc_final: 0.7199 (tptp) REVERT: D 94 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8127 (mt-10) REVERT: D 101 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6722 (mtmm) REVERT: D 150 LYS cc_start: 0.8593 (mttt) cc_final: 0.8274 (tmmt) REVERT: D 214 GLU cc_start: 0.7459 (mt-10) cc_final: 0.6894 (pm20) REVERT: D 229 LEU cc_start: 0.7154 (mm) cc_final: 0.6359 (pt) REVERT: D 237 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7484 (pm20) REVERT: E 37 GLN cc_start: 0.6973 (pt0) cc_final: 0.6645 (tt0) REVERT: E 42 GLU cc_start: 0.8068 (mp0) cc_final: 0.7731 (mp0) REVERT: E 82 ASP cc_start: 0.7804 (t0) cc_final: 0.7359 (t0) REVERT: F 66 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7642 (ptt180) REVERT: F 105 GLN cc_start: 0.8219 (pt0) cc_final: 0.7976 (pt0) REVERT: H 44 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8378 (pm20) REVERT: H 85 GLU cc_start: 0.7633 (pp20) cc_final: 0.7329 (mm-30) REVERT: L 100 ARG cc_start: 0.8358 (mmm160) cc_final: 0.7776 (tpp-160) outliers start: 39 outliers final: 20 residues processed: 152 average time/residue: 0.0936 time to fit residues: 20.0741 Evaluate side-chains 139 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2843 VAL Chi-restraints excluded: chain A residue 3051 LEU Chi-restraints excluded: chain A residue 3099 ILE Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 156 CYS Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2984 HIS A3113 GLN ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN L 42 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.155154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.118848 restraints weight = 12604.990| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.22 r_work: 0.3454 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9468 Z= 0.249 Angle : 0.621 8.366 12852 Z= 0.331 Chirality : 0.049 0.166 1418 Planarity : 0.005 0.051 1627 Dihedral : 5.007 35.081 1291 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.94 % Favored : 93.88 % Rotamer: Outliers : 3.63 % Allowed : 25.05 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.18 % Twisted Proline : 0.00 % 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: -1.10 (0.24), residues: 1144 helix: -2.04 (0.87), residues: 25 sheet: -0.58 (0.24), residues: 444 loop : -0.72 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A3100 TYR 0.018 0.002 TYR H 32 PHE 0.018 0.002 PHE A2947 TRP 0.013 0.002 TRP H 99 HIS 0.007 0.001 HIS D 338 Details of bonding type rmsd covalent geometry : bond 0.00599 ( 9451) covalent geometry : angle 0.61928 (12816) SS BOND : bond 0.00849 ( 15) SS BOND : angle 0.85233 ( 30) hydrogen bonds : bond 0.03636 ( 296) hydrogen bonds : angle 6.31957 ( 741) link_BETA1-6 : bond 0.00215 ( 1) link_BETA1-6 : angle 1.37433 ( 3) link_NAG-ASN : bond 0.00062 ( 1) link_NAG-ASN : angle 2.54076 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 3057 LYS cc_start: 0.7503 (mttt) cc_final: 0.7104 (tptm) REVERT: D 94 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: D 101 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6837 (mtmm) REVERT: D 150 LYS cc_start: 0.8627 (mttt) cc_final: 0.8291 (tmmt) REVERT: D 214 GLU cc_start: 0.7574 (mt-10) cc_final: 0.6977 (pm20) REVERT: D 237 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7534 (pm20) REVERT: E 37 GLN cc_start: 0.7085 (pt0) cc_final: 0.6644 (tt0) REVERT: E 42 GLU cc_start: 0.8088 (mp0) cc_final: 0.7289 (mp0) REVERT: E 82 ASP cc_start: 0.7815 (t0) cc_final: 0.7318 (t0) REVERT: F 66 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7562 (ptt180) REVERT: H 38 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7276 (ptp90) REVERT: H 44 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8332 (pm20) REVERT: H 52 LYS cc_start: 0.8657 (tptp) cc_final: 0.7685 (ttmm) REVERT: H 85 GLU cc_start: 0.7666 (pp20) cc_final: 0.7379 (mm-30) REVERT: L 100 ARG cc_start: 0.8295 (mmm160) cc_final: 0.7669 (tpp-160) outliers start: 38 outliers final: 21 residues processed: 142 average time/residue: 0.0911 time to fit residues: 18.4083 Evaluate side-chains 135 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2843 VAL Chi-restraints excluded: chain A residue 3099 ILE Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 156 CYS Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 107 optimal weight: 0.0670 chunk 50 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2984 HIS ** D 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 92 HIS L 42 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.156789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.120801 restraints weight = 12343.128| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.25 r_work: 0.3466 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9468 Z= 0.135 Angle : 0.549 8.412 12852 Z= 0.291 Chirality : 0.047 0.161 1418 Planarity : 0.004 0.044 1627 Dihedral : 4.786 36.066 1291 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.63 % Favored : 95.19 % Rotamer: Outliers : 3.44 % Allowed : 25.62 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.18 % Twisted Proline : 0.00 % 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: -0.99 (0.24), residues: 1144 helix: -2.18 (0.82), residues: 25 sheet: -0.49 (0.24), residues: 437 loop : -0.65 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 94 TYR 0.018 0.002 TYR H 32 PHE 0.017 0.001 PHE F 78 TRP 0.014 0.001 TRP H 99 HIS 0.005 0.001 HIS D 338 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9451) covalent geometry : angle 0.54771 (12816) SS BOND : bond 0.00462 ( 15) SS BOND : angle 0.62362 ( 30) hydrogen bonds : bond 0.03014 ( 296) hydrogen bonds : angle 5.96104 ( 741) link_BETA1-6 : bond 0.00343 ( 1) link_BETA1-6 : angle 1.28953 ( 3) link_NAG-ASN : bond 0.00050 ( 1) link_NAG-ASN : angle 2.19717 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 3057 LYS cc_start: 0.7477 (mttt) cc_final: 0.7082 (tptm) REVERT: D 32 CYS cc_start: 0.7575 (m) cc_final: 0.7301 (m) REVERT: D 94 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8191 (mt-10) REVERT: D 101 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6630 (mtmm) REVERT: D 150 LYS cc_start: 0.8541 (mttt) cc_final: 0.8181 (tmmt) REVERT: D 214 GLU cc_start: 0.7546 (mt-10) cc_final: 0.6868 (pm20) REVERT: D 237 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7475 (pm20) REVERT: E 37 GLN cc_start: 0.6978 (pt0) cc_final: 0.6562 (tt0) REVERT: E 42 GLU cc_start: 0.8021 (mp0) cc_final: 0.7204 (mp0) REVERT: E 82 ASP cc_start: 0.7643 (t0) cc_final: 0.7070 (t0) REVERT: E 90 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7473 (pp30) REVERT: F 66 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7576 (ptt180) REVERT: H 38 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7165 (ptp90) REVERT: H 44 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8337 (pm20) REVERT: H 52 LYS cc_start: 0.8614 (tptp) cc_final: 0.7660 (ttmm) REVERT: H 85 GLU cc_start: 0.7611 (pp20) cc_final: 0.7114 (mm-30) REVERT: L 100 ARG cc_start: 0.8251 (mmm160) cc_final: 0.7655 (tpp-160) outliers start: 36 outliers final: 19 residues processed: 142 average time/residue: 0.0927 time to fit residues: 18.7613 Evaluate side-chains 135 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2843 VAL Chi-restraints excluded: chain A residue 3051 LEU Chi-restraints excluded: chain A residue 3099 ILE Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 156 CYS Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 39 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2984 HIS ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN L 42 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.157194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.121539 restraints weight = 12273.322| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.18 r_work: 0.3475 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9468 Z= 0.136 Angle : 0.549 8.150 12852 Z= 0.290 Chirality : 0.047 0.162 1418 Planarity : 0.004 0.042 1627 Dihedral : 4.716 35.236 1291 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.63 % Favored : 95.19 % Rotamer: Outliers : 2.96 % Allowed : 26.29 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.18 % Twisted Proline : 0.00 % 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: -0.96 (0.24), residues: 1144 helix: -2.13 (0.82), residues: 25 sheet: -0.45 (0.24), residues: 437 loop : -0.64 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A3100 TYR 0.018 0.001 TYR H 32 PHE 0.018 0.001 PHE A2891 TRP 0.014 0.001 TRP H 99 HIS 0.006 0.001 HIS D 338 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9451) covalent geometry : angle 0.54747 (12816) SS BOND : bond 0.00490 ( 15) SS BOND : angle 0.60947 ( 30) hydrogen bonds : bond 0.03025 ( 296) hydrogen bonds : angle 5.87171 ( 741) link_BETA1-6 : bond 0.00365 ( 1) link_BETA1-6 : angle 1.29869 ( 3) link_NAG-ASN : bond 0.00081 ( 1) link_NAG-ASN : angle 2.03656 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 3057 LYS cc_start: 0.7516 (mttt) cc_final: 0.7165 (tptm) REVERT: D 32 CYS cc_start: 0.7574 (m) cc_final: 0.7290 (m) REVERT: D 94 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: D 101 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6651 (mtmm) REVERT: D 150 LYS cc_start: 0.8558 (mttt) cc_final: 0.8200 (tmmt) REVERT: D 214 GLU cc_start: 0.7513 (mt-10) cc_final: 0.6841 (pm20) REVERT: D 229 LEU cc_start: 0.7037 (mm) cc_final: 0.6251 (pt) REVERT: D 237 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7476 (pm20) REVERT: E 37 GLN cc_start: 0.6970 (pt0) cc_final: 0.6560 (tt0) REVERT: E 82 ASP cc_start: 0.7633 (t0) cc_final: 0.7062 (t0) REVERT: E 90 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7556 (pp30) REVERT: F 66 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7601 (ptt180) REVERT: H 38 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7566 (ptp90) REVERT: H 44 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: H 52 LYS cc_start: 0.8639 (tptp) cc_final: 0.7655 (ttmm) REVERT: H 85 GLU cc_start: 0.7603 (pp20) cc_final: 0.7128 (mm-30) outliers start: 31 outliers final: 20 residues processed: 137 average time/residue: 0.0901 time to fit residues: 17.3134 Evaluate side-chains 136 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2843 VAL Chi-restraints excluded: chain A residue 3099 ILE Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 156 CYS Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 0.0030 chunk 101 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2984 HIS E 90 GLN L 42 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.157646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.121998 restraints weight = 12204.284| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.17 r_work: 0.3479 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9468 Z= 0.132 Angle : 0.551 8.034 12852 Z= 0.290 Chirality : 0.046 0.163 1418 Planarity : 0.004 0.041 1627 Dihedral : 4.667 35.087 1291 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 3.15 % Allowed : 26.00 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.18 % Twisted Proline : 0.00 % 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: -0.92 (0.24), residues: 1144 helix: -2.06 (0.83), residues: 25 sheet: -0.42 (0.24), residues: 437 loop : -0.63 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A3100 TYR 0.018 0.002 TYR H 32 PHE 0.016 0.001 PHE F 78 TRP 0.013 0.001 TRP H 99 HIS 0.006 0.001 HIS D 338 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9451) covalent geometry : angle 0.54979 (12816) SS BOND : bond 0.00464 ( 15) SS BOND : angle 0.59433 ( 30) hydrogen bonds : bond 0.02976 ( 296) hydrogen bonds : angle 5.81142 ( 741) link_BETA1-6 : bond 0.00355 ( 1) link_BETA1-6 : angle 1.26843 ( 3) link_NAG-ASN : bond 0.00075 ( 1) link_NAG-ASN : angle 1.98215 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 3057 LYS cc_start: 0.7557 (mttt) cc_final: 0.7241 (tptm) REVERT: D 32 CYS cc_start: 0.7532 (m) cc_final: 0.7256 (m) REVERT: D 94 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8207 (mt-10) REVERT: D 101 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6653 (mtmm) REVERT: D 150 LYS cc_start: 0.8544 (mttt) cc_final: 0.8198 (tmmt) REVERT: D 214 GLU cc_start: 0.7499 (mt-10) cc_final: 0.6811 (pm20) REVERT: D 229 LEU cc_start: 0.7023 (mm) cc_final: 0.6248 (pt) REVERT: D 237 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7471 (pm20) REVERT: E 37 GLN cc_start: 0.6952 (pt0) cc_final: 0.6566 (tt0) REVERT: E 42 GLU cc_start: 0.7927 (mp0) cc_final: 0.7647 (mp0) REVERT: E 82 ASP cc_start: 0.7632 (t0) cc_final: 0.7057 (t0) REVERT: E 90 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7516 (pp30) REVERT: F 66 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7553 (ptt180) REVERT: H 38 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7216 (ptp90) REVERT: H 44 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8380 (pm20) REVERT: H 52 LYS cc_start: 0.8629 (tptp) cc_final: 0.7654 (ttmm) REVERT: H 85 GLU cc_start: 0.7573 (pp20) cc_final: 0.7056 (mm-30) outliers start: 33 outliers final: 21 residues processed: 141 average time/residue: 0.0934 time to fit residues: 18.5966 Evaluate side-chains 137 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2843 VAL Chi-restraints excluded: chain A residue 3099 ILE Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 156 CYS Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 58 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2984 HIS ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN F 105 GLN L 42 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.157557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.121323 restraints weight = 12296.717| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.27 r_work: 0.3467 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9468 Z= 0.143 Angle : 0.559 7.956 12852 Z= 0.294 Chirality : 0.047 0.165 1418 Planarity : 0.004 0.042 1627 Dihedral : 4.662 34.900 1291 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 3.44 % Allowed : 25.72 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.18 % Twisted Proline : 0.00 % 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: -0.91 (0.24), residues: 1144 helix: -2.06 (0.84), residues: 25 sheet: -0.39 (0.24), residues: 437 loop : -0.63 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A3100 TYR 0.018 0.002 TYR H 32 PHE 0.017 0.001 PHE A2890 TRP 0.013 0.001 TRP H 99 HIS 0.006 0.001 HIS D 338 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9451) covalent geometry : angle 0.55746 (12816) SS BOND : bond 0.00496 ( 15) SS BOND : angle 0.61074 ( 30) hydrogen bonds : bond 0.03027 ( 296) hydrogen bonds : angle 5.81286 ( 741) link_BETA1-6 : bond 0.00270 ( 1) link_BETA1-6 : angle 1.32138 ( 3) link_NAG-ASN : bond 0.00057 ( 1) link_NAG-ASN : angle 1.96886 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 3057 LYS cc_start: 0.7540 (mttt) cc_final: 0.7253 (tptm) REVERT: D 32 CYS cc_start: 0.7558 (m) cc_final: 0.7274 (m) REVERT: D 94 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8225 (mt-10) REVERT: D 101 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6673 (mtmm) REVERT: D 150 LYS cc_start: 0.8549 (mttt) cc_final: 0.8198 (tmmt) REVERT: D 214 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6830 (pm20) REVERT: D 229 LEU cc_start: 0.7034 (mm) cc_final: 0.6260 (pt) REVERT: D 237 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7503 (pm20) REVERT: E 37 GLN cc_start: 0.6966 (pt0) cc_final: 0.6571 (tt0) REVERT: E 42 GLU cc_start: 0.7959 (mp0) cc_final: 0.7678 (mp0) REVERT: E 82 ASP cc_start: 0.7627 (t0) cc_final: 0.7036 (t0) REVERT: E 90 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7531 (pp30) REVERT: F 66 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7557 (ptt180) REVERT: H 38 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7247 (ptp90) REVERT: H 52 LYS cc_start: 0.8615 (tptp) cc_final: 0.7661 (ttmm) REVERT: H 85 GLU cc_start: 0.7582 (pp20) cc_final: 0.7056 (mm-30) REVERT: L 81 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7742 (pm20) REVERT: L 100 ARG cc_start: 0.8153 (mmm160) cc_final: 0.7726 (tpp-160) outliers start: 36 outliers final: 23 residues processed: 140 average time/residue: 0.0968 time to fit residues: 18.9812 Evaluate side-chains 139 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2843 VAL Chi-restraints excluded: chain A residue 3099 ILE Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 156 CYS Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 0.0170 chunk 8 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 29 optimal weight: 0.0980 chunk 33 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 27 optimal weight: 0.0570 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2984 HIS ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.157650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.121877 restraints weight = 12213.285| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.18 r_work: 0.3479 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 9468 Z= 0.237 Angle : 0.910 59.200 12852 Z= 0.549 Chirality : 0.052 0.824 1418 Planarity : 0.006 0.146 1627 Dihedral : 4.722 35.107 1291 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.63 % Favored : 95.19 % Rotamer: Outliers : 2.96 % Allowed : 26.10 % Favored : 70.94 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.18 % Twisted Proline : 0.00 % 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: -0.94 (0.24), residues: 1144 helix: -2.03 (0.84), residues: 25 sheet: -0.40 (0.24), residues: 437 loop : -0.67 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 100 TYR 0.029 0.002 TYR D 198 PHE 0.016 0.001 PHE A2947 TRP 0.013 0.001 TRP H 99 HIS 0.005 0.001 HIS D 338 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 9451) covalent geometry : angle 0.91022 (12816) SS BOND : bond 0.00459 ( 15) SS BOND : angle 0.61028 ( 30) hydrogen bonds : bond 0.03019 ( 296) hydrogen bonds : angle 5.81406 ( 741) link_BETA1-6 : bond 0.00551 ( 1) link_BETA1-6 : angle 1.08094 ( 3) link_NAG-ASN : bond 0.00046 ( 1) link_NAG-ASN : angle 1.96473 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2044.32 seconds wall clock time: 36 minutes 0.95 seconds (2160.95 seconds total)