Starting phenix.real_space_refine on Tue Mar 3 14:09:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n38_48848/03_2026/9n38_48848.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n38_48848/03_2026/9n38_48848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n38_48848/03_2026/9n38_48848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n38_48848/03_2026/9n38_48848.map" model { file = "/net/cci-nas-00/data/ceres_data/9n38_48848/03_2026/9n38_48848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n38_48848/03_2026/9n38_48848.cif" } resolution = 3.9 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= 0.014 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 12 5.16 5 C 3581 2.51 5 N 990 2.21 5 O 1094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5677 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 2004 Classifications: {'peptide': 245} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 236} Chain breaks: 1 Chain: "B" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1966 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Chain breaks: 2 Chain: "H" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 917 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 790 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Time building chain proxies: 1.14, per 1000 atoms: 0.20 Number of scatterers: 5677 At special positions: 0 Unit cell: (69.7345, 79.8573, 128.222, 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 12 16.00 O 1094 8.00 N 990 7.00 C 3581 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 300.3 milliseconds 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1318 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 13 sheets defined 3.1% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.919A pdb=" N ASN A 212 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 236 through 241 removed outlier: 3.612A pdb=" N ARG B 240 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 29 removed outlier: 3.513A pdb=" N ASP A 29 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 34 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 37 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN A 41 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 54 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP A 101 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 29 removed outlier: 3.513A pdb=" N ASP A 29 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 34 " --> pdb=" O ASP A 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 67 removed outlier: 3.517A pdb=" N ARG A 66 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N GLY A 82 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 172 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 86 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 67 removed outlier: 3.517A pdb=" N ARG A 66 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N THR A 77 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE A 260 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ARG A 79 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N PHE A 258 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP A 256 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER A 83 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 252 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 251 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG A 253 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N GLU A 257 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASP A 278 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS A 259 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS A 276 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER A 285 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 301 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 176 Processing sheet with id=AA6, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.741A pdb=" N ASP B 55 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE B 60 " --> pdb=" O ASP B 55 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN B 65 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 79 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B 247 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP B 127 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER B 252 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE B 125 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 176 through 179 removed outlier: 7.643A pdb=" N SER B 109 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LYS B 106 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU B 273 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ASP B 271 " --> pdb=" O PRO B 108 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 263 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 176 through 179 removed outlier: 7.643A pdb=" N SER B 109 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LYS B 106 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU B 273 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ASP B 271 " --> pdb=" O PRO B 108 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 263 " --> pdb=" O GLN B 116 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR B 260 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP B 291 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP B 312 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLU B 300 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL B 310 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 197 through 199 Processing sheet with id=AB1, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.619A pdb=" N MET H 83 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU H 20 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.668A pdb=" N THR H 115 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL H 97 " --> pdb=" O ASN H 35 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN H 35 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 20 through 22 removed outlier: 3.942A pdb=" N THR L 74 " --> pdb=" O SER L 63 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 45 through 46 150 hydrogen bonds defined for protein. 393 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: 0.67 Time building geometry restraints manager: 0.33 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: 1849 1.34 - 1.46: 1261 1.46 - 1.58: 2680 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 5810 Sorted by residual: bond pdb=" CA LYS H 76 " pdb=" CB LYS H 76 " ideal model delta sigma weight residual 1.522 1.555 -0.033 1.27e-02 6.20e+03 6.80e+00 bond pdb=" CA TYR L 91 " pdb=" CB TYR L 91 " ideal model delta sigma weight residual 1.527 1.546 -0.020 1.39e-02 5.18e+03 2.03e+00 bond pdb=" CB PRO L 40 " pdb=" CG PRO L 40 " ideal model delta sigma weight residual 1.492 1.558 -0.066 5.00e-02 4.00e+02 1.72e+00 bond pdb=" CB GLN A 31 " pdb=" CG GLN A 31 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.53e+00 bond pdb=" CA ILE H 70 " pdb=" CB ILE H 70 " ideal model delta sigma weight residual 1.531 1.544 -0.013 1.11e-02 8.12e+03 1.45e+00 ... (remaining 5805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 7662 2.18 - 4.35: 171 4.35 - 6.53: 24 6.53 - 8.71: 4 8.71 - 10.88: 1 Bond angle restraints: 7862 Sorted by residual: angle pdb=" N ALA L 84 " pdb=" CA ALA L 84 " pdb=" C ALA L 84 " ideal model delta sigma weight residual 108.45 113.91 -5.46 1.26e+00 6.30e-01 1.88e+01 angle pdb=" N TRP L 35 " pdb=" CA TRP L 35 " pdb=" C TRP L 35 " ideal model delta sigma weight residual 111.17 116.92 -5.75 1.41e+00 5.03e-01 1.66e+01 angle pdb=" C ILE L 75 " pdb=" N SER L 76 " pdb=" CA SER L 76 " ideal model delta sigma weight residual 121.54 129.26 -7.72 1.91e+00 2.74e-01 1.63e+01 angle pdb=" CA LYS H 76 " pdb=" CB LYS H 76 " pdb=" CG LYS H 76 " ideal model delta sigma weight residual 114.10 121.25 -7.15 2.00e+00 2.50e-01 1.28e+01 angle pdb=" C TRP A 292 " pdb=" N LYS A 293 " pdb=" CA LYS A 293 " ideal model delta sigma weight residual 125.02 131.23 -6.21 1.76e+00 3.23e-01 1.24e+01 ... (remaining 7857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 2803 17.06 - 34.12: 487 34.12 - 51.18: 133 51.18 - 68.24: 26 68.24 - 85.30: 12 Dihedral angle restraints: 3461 sinusoidal: 1414 harmonic: 2047 Sorted by residual: dihedral pdb=" CA ALA L 13 " pdb=" C ALA L 13 " pdb=" N SER L 14 " pdb=" CA SER L 14 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA SER L 56 " pdb=" C SER L 56 " pdb=" N GLY L 57 " pdb=" CA GLY L 57 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA VAL H 97 " pdb=" C VAL H 97 " pdb=" N LYS H 98 " pdb=" CA LYS H 98 " ideal model delta harmonic sigma weight residual 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 3458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 649 0.048 - 0.096: 145 0.096 - 0.144: 39 0.144 - 0.192: 3 0.192 - 0.240: 2 Chirality restraints: 838 Sorted by residual: chirality pdb=" CB ILE H 70 " pdb=" CA ILE H 70 " pdb=" CG1 ILE H 70 " pdb=" CG2 ILE H 70 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB THR B 265 " pdb=" CA THR B 265 " pdb=" OG1 THR B 265 " pdb=" CG2 THR B 265 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 835 not shown) Planarity restraints: 1014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 228 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO A 229 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 39 " -0.066 5.00e-02 4.00e+02 9.85e-02 1.55e+01 pdb=" N PRO L 40 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO L 40 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO L 40 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 191 " -0.015 2.00e-02 2.50e+03 1.63e-02 6.67e+00 pdb=" CG TRP B 191 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP B 191 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 191 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 191 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 191 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 191 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 191 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 191 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 191 " -0.003 2.00e-02 2.50e+03 ... (remaining 1011 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 122 2.65 - 3.21: 5394 3.21 - 3.77: 8607 3.77 - 4.34: 11843 4.34 - 4.90: 19596 Nonbonded interactions: 45562 Sorted by model distance: nonbonded pdb=" O ALA H 24 " pdb=" ND2 ASN H 77 " model vdw 2.086 3.120 nonbonded pdb=" O LYS H 76 " pdb=" OG1 THR H 78 " model vdw 2.142 3.040 nonbonded pdb=" O GLU B 98 " pdb=" OG SER B 102 " model vdw 2.148 3.040 nonbonded pdb=" OG SER A 63 " pdb=" O THR A 222 " model vdw 2.174 3.040 nonbonded pdb=" OE1 GLU B 110 " pdb=" ND2 ASN B 269 " model vdw 2.199 3.120 ... (remaining 45557 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.920 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 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 : 0.004 0.066 5812 Z= 0.171 Angle : 0.797 10.882 7866 Z= 0.437 Chirality : 0.045 0.240 838 Planarity : 0.007 0.104 1014 Dihedral : 18.862 85.296 2137 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.19 % Favored : 87.81 % Rotamer: Outliers : 0.47 % Allowed : 39.91 % Favored : 59.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -2.69 (0.31), residues: 689 helix: None (None), residues: 0 sheet: -0.91 (0.33), residues: 268 loop : -2.50 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.037 0.001 TYR L 91 PHE 0.011 0.002 PHE L 71 TRP 0.043 0.002 TRP B 191 HIS 0.014 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 5810) covalent geometry : angle 0.79679 ( 7862) SS BOND : bond 0.00060 ( 2) SS BOND : angle 1.09110 ( 4) hydrogen bonds : bond 0.32345 ( 131) hydrogen bonds : angle 12.70833 ( 393) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 182 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 PHE cc_start: 0.6337 (m-80) cc_final: 0.5602 (m-80) REVERT: A 276 HIS cc_start: 0.7995 (m-70) cc_final: 0.7631 (m-70) REVERT: B 51 GLU cc_start: 0.7017 (mp0) cc_final: 0.6713 (mp0) REVERT: B 103 ASN cc_start: 0.7860 (m110) cc_final: 0.7624 (m-40) REVERT: B 177 ASP cc_start: 0.7271 (m-30) cc_final: 0.7016 (m-30) REVERT: B 199 LYS cc_start: 0.7057 (ptmt) cc_final: 0.6814 (ptmt) REVERT: B 233 TYR cc_start: 0.6868 (m-80) cc_final: 0.6412 (m-80) REVERT: B 269 ASN cc_start: 0.6014 (t0) cc_final: 0.5705 (t0) REVERT: B 276 ARG cc_start: 0.6763 (tpp-160) cc_final: 0.6348 (tpp-160) REVERT: L 106 ILE cc_start: 0.7586 (pt) cc_final: 0.7340 (mm) outliers start: 3 outliers final: 1 residues processed: 183 average time/residue: 0.0982 time to fit residues: 22.1224 Evaluate side-chains 165 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.0070 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 ASN ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 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 = 0.4214 r_free = 0.4214 target = 0.171346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.150835 restraints weight = 9427.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.156385 restraints weight = 5395.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.160158 restraints weight = 3421.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.162808 restraints weight = 2323.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.164685 restraints weight = 1651.788| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6171 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5812 Z= 0.218 Angle : 0.793 10.462 7866 Z= 0.422 Chirality : 0.048 0.298 838 Planarity : 0.006 0.064 1014 Dihedral : 6.321 33.604 759 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 6.62 % Allowed : 32.97 % Favored : 60.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -2.80 (0.30), residues: 689 helix: -5.33 (0.39), residues: 6 sheet: -1.02 (0.31), residues: 268 loop : -2.49 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 207 TYR 0.014 0.002 TYR A 48 PHE 0.021 0.002 PHE L 98 TRP 0.029 0.003 TRP A 292 HIS 0.009 0.002 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 5810) covalent geometry : angle 0.79300 ( 7862) SS BOND : bond 0.00103 ( 2) SS BOND : angle 1.12426 ( 4) hydrogen bonds : bond 0.05449 ( 131) hydrogen bonds : angle 8.19218 ( 393) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 THR cc_start: 0.7550 (OUTLIER) cc_final: 0.7289 (p) REVERT: A 252 LYS cc_start: 0.7032 (pttm) cc_final: 0.6550 (pttm) REVERT: A 289 GLU cc_start: 0.5357 (OUTLIER) cc_final: 0.4744 (mt-10) REVERT: B 57 LYS cc_start: 0.6655 (ptpp) cc_final: 0.6260 (pttm) REVERT: B 64 LEU cc_start: 0.7643 (mp) cc_final: 0.7437 (tp) REVERT: B 82 LYS cc_start: 0.7920 (tttp) cc_final: 0.7473 (ttpp) REVERT: B 83 LYS cc_start: 0.7052 (mtmm) cc_final: 0.6825 (pttp) REVERT: B 102 SER cc_start: 0.8477 (m) cc_final: 0.8250 (m) REVERT: B 194 ILE cc_start: 0.7013 (mp) cc_final: 0.6700 (tt) REVERT: B 218 ARG cc_start: 0.8124 (mmp80) cc_final: 0.7799 (mmp80) REVERT: B 233 TYR cc_start: 0.7243 (m-80) cc_final: 0.7041 (m-80) REVERT: B 246 GLU cc_start: 0.6552 (pp20) cc_final: 0.6172 (pp20) REVERT: B 269 ASN cc_start: 0.6298 (t0) cc_final: 0.5801 (t0) REVERT: B 309 LYS cc_start: 0.7777 (mmtm) cc_final: 0.7506 (mmtm) REVERT: H 64 VAL cc_start: 0.8227 (OUTLIER) cc_final: 0.8026 (m) REVERT: H 65 LYS cc_start: 0.8452 (mmtt) cc_final: 0.8096 (tppt) REVERT: L 11 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7714 (pt) REVERT: L 90 LYS cc_start: 0.8627 (ptmt) cc_final: 0.7938 (ptmm) REVERT: L 106 ILE cc_start: 0.7919 (pt) cc_final: 0.7500 (mm) outliers start: 42 outliers final: 17 residues processed: 180 average time/residue: 0.0816 time to fit residues: 18.5896 Evaluate side-chains 174 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 71 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 33 optimal weight: 0.0970 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 HIS ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 ASN B 216 ASN ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 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 = 0.4222 r_free = 0.4222 target = 0.173199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.152037 restraints weight = 9197.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.157610 restraints weight = 5257.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.161565 restraints weight = 3335.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.164239 restraints weight = 2261.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.166217 restraints weight = 1615.299| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5812 Z= 0.203 Angle : 0.745 9.702 7866 Z= 0.397 Chirality : 0.048 0.350 838 Planarity : 0.005 0.048 1014 Dihedral : 6.287 34.754 759 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.06 % Favored : 86.94 % Rotamer: Outliers : 7.89 % Allowed : 31.07 % Favored : 61.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -2.90 (0.30), residues: 689 helix: -5.38 (0.37), residues: 6 sheet: -1.18 (0.31), residues: 273 loop : -2.50 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 38 TYR 0.016 0.002 TYR A 48 PHE 0.016 0.002 PHE L 98 TRP 0.024 0.003 TRP A 208 HIS 0.007 0.002 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 5810) covalent geometry : angle 0.74512 ( 7862) SS BOND : bond 0.00131 ( 2) SS BOND : angle 1.23673 ( 4) hydrogen bonds : bond 0.04973 ( 131) hydrogen bonds : angle 7.43889 ( 393) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 154 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 THR cc_start: 0.7530 (OUTLIER) cc_final: 0.7283 (p) REVERT: A 252 LYS cc_start: 0.7148 (pttm) cc_final: 0.6559 (pttm) REVERT: B 48 LYS cc_start: 0.6944 (pttp) cc_final: 0.6617 (pttp) REVERT: B 57 LYS cc_start: 0.6547 (ptpp) cc_final: 0.6184 (pttm) REVERT: B 82 LYS cc_start: 0.7868 (tttp) cc_final: 0.7477 (ttpp) REVERT: B 98 GLU cc_start: 0.5846 (OUTLIER) cc_final: 0.5587 (pm20) REVERT: B 194 ILE cc_start: 0.6919 (mp) cc_final: 0.6719 (tt) REVERT: B 218 ARG cc_start: 0.8114 (mmp80) cc_final: 0.7646 (mmp80) REVERT: B 246 GLU cc_start: 0.6505 (pp20) cc_final: 0.6259 (pp20) REVERT: B 269 ASN cc_start: 0.6186 (t0) cc_final: 0.5872 (t0) REVERT: B 300 GLU cc_start: 0.5697 (tm-30) cc_final: 0.5400 (mm-30) REVERT: H 65 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8092 (tppt) REVERT: L 90 LYS cc_start: 0.8582 (ptmt) cc_final: 0.8283 (ptmm) REVERT: L 106 ILE cc_start: 0.7917 (pt) cc_final: 0.7489 (mm) outliers start: 50 outliers final: 20 residues processed: 186 average time/residue: 0.0824 time to fit residues: 19.4173 Evaluate side-chains 169 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 71 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 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 = 0.4201 r_free = 0.4201 target = 0.170797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.149861 restraints weight = 9233.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.155330 restraints weight = 5289.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.159229 restraints weight = 3359.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.161825 restraints weight = 2273.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.163774 restraints weight = 1631.521| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5812 Z= 0.239 Angle : 0.767 9.463 7866 Z= 0.408 Chirality : 0.049 0.415 838 Planarity : 0.005 0.047 1014 Dihedral : 6.555 37.040 759 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % Rotamer: Outliers : 6.94 % Allowed : 32.02 % Favored : 61.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -3.10 (0.29), residues: 689 helix: -2.65 (1.88), residues: 6 sheet: -1.38 (0.31), residues: 269 loop : -2.63 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 184 TYR 0.019 0.002 TYR A 48 PHE 0.023 0.002 PHE L 98 TRP 0.024 0.003 TRP A 208 HIS 0.007 0.002 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 5810) covalent geometry : angle 0.76721 ( 7862) SS BOND : bond 0.00113 ( 2) SS BOND : angle 1.05053 ( 4) hydrogen bonds : bond 0.04958 ( 131) hydrogen bonds : angle 7.31584 ( 393) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 163 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 THR cc_start: 0.7525 (OUTLIER) cc_final: 0.7264 (p) REVERT: A 210 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8291 (ttmm) REVERT: A 252 LYS cc_start: 0.7055 (pttm) cc_final: 0.6773 (pttm) REVERT: A 289 GLU cc_start: 0.5305 (OUTLIER) cc_final: 0.5028 (mt-10) REVERT: B 57 LYS cc_start: 0.6608 (ptpp) cc_final: 0.6272 (pttm) REVERT: B 82 LYS cc_start: 0.8033 (tttp) cc_final: 0.7655 (ttpp) REVERT: B 246 GLU cc_start: 0.6424 (pp20) cc_final: 0.6176 (pp20) REVERT: B 269 ASN cc_start: 0.6115 (t0) cc_final: 0.5759 (t0) REVERT: B 300 GLU cc_start: 0.5647 (tm-30) cc_final: 0.5401 (mm-30) REVERT: B 309 LYS cc_start: 0.7820 (mmtp) cc_final: 0.7572 (mmtp) REVERT: H 65 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8119 (tppt) REVERT: L 11 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7679 (pp) REVERT: L 90 LYS cc_start: 0.8581 (ptmt) cc_final: 0.8358 (ptmm) REVERT: L 106 ILE cc_start: 0.8030 (pt) cc_final: 0.7583 (mm) outliers start: 44 outliers final: 28 residues processed: 186 average time/residue: 0.0849 time to fit residues: 19.8664 Evaluate side-chains 191 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 71 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 47 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 60 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.168475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.147432 restraints weight = 9389.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.152933 restraints weight = 5372.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.156707 restraints weight = 3417.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.159490 restraints weight = 2339.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.161403 restraints weight = 1668.460| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 5812 Z= 0.289 Angle : 0.806 8.873 7866 Z= 0.429 Chirality : 0.052 0.454 838 Planarity : 0.006 0.051 1014 Dihedral : 6.857 36.319 759 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 24.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.50 % Favored : 86.50 % Rotamer: Outliers : 8.52 % Allowed : 30.91 % Favored : 60.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -3.31 (0.29), residues: 689 helix: -3.64 (1.36), residues: 6 sheet: -1.68 (0.30), residues: 284 loop : -2.64 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 184 TYR 0.014 0.002 TYR L 91 PHE 0.039 0.003 PHE A 54 TRP 0.028 0.003 TRP A 208 HIS 0.007 0.002 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00621 ( 5810) covalent geometry : angle 0.80564 ( 7862) SS BOND : bond 0.00291 ( 2) SS BOND : angle 0.93561 ( 4) hydrogen bonds : bond 0.05210 ( 131) hydrogen bonds : angle 7.43434 ( 393) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 161 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 THR cc_start: 0.7528 (OUTLIER) cc_final: 0.7280 (p) REVERT: A 252 LYS cc_start: 0.7159 (pttm) cc_final: 0.6890 (pttm) REVERT: A 281 GLU cc_start: 0.6233 (pm20) cc_final: 0.5999 (pm20) REVERT: A 289 GLU cc_start: 0.5276 (OUTLIER) cc_final: 0.5034 (mt-10) REVERT: B 48 LYS cc_start: 0.7803 (pttp) cc_final: 0.7517 (pttp) REVERT: B 57 LYS cc_start: 0.6814 (ptpp) cc_final: 0.6480 (ptpp) REVERT: B 82 LYS cc_start: 0.8119 (tttp) cc_final: 0.7736 (ttpp) REVERT: B 92 LYS cc_start: 0.8233 (mttt) cc_final: 0.8005 (mmtt) REVERT: B 246 GLU cc_start: 0.6627 (pp20) cc_final: 0.6341 (pp20) REVERT: B 300 GLU cc_start: 0.5652 (tm-30) cc_final: 0.5427 (mm-30) REVERT: B 309 LYS cc_start: 0.7862 (mmtp) cc_final: 0.7557 (mmtp) REVERT: H 34 MET cc_start: 0.7910 (mmm) cc_final: 0.7297 (mmm) REVERT: H 65 LYS cc_start: 0.8466 (mmtt) cc_final: 0.8036 (tppt) REVERT: H 121 SER cc_start: 0.4646 (OUTLIER) cc_final: 0.4414 (t) REVERT: L 11 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7795 (pp) REVERT: L 90 LYS cc_start: 0.8581 (ptmt) cc_final: 0.8305 (ptmm) outliers start: 54 outliers final: 34 residues processed: 187 average time/residue: 0.0788 time to fit residues: 18.6428 Evaluate side-chains 196 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.6980 chunk 22 optimal weight: 0.1980 chunk 37 optimal weight: 0.0170 chunk 18 optimal weight: 0.1980 chunk 65 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.175185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.153694 restraints weight = 9156.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.159377 restraints weight = 5286.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.163357 restraints weight = 3367.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.166036 restraints weight = 2296.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.168121 restraints weight = 1652.995| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5812 Z= 0.146 Angle : 0.716 10.043 7866 Z= 0.375 Chirality : 0.047 0.335 838 Planarity : 0.005 0.044 1014 Dihedral : 6.164 36.569 759 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % Rotamer: Outliers : 6.62 % Allowed : 34.54 % Favored : 58.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -3.18 (0.30), residues: 689 helix: None (None), residues: 0 sheet: -1.62 (0.30), residues: 284 loop : -2.55 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 218 TYR 0.013 0.001 TYR L 91 PHE 0.022 0.002 PHE A 227 TRP 0.029 0.002 TRP A 208 HIS 0.006 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5810) covalent geometry : angle 0.71561 ( 7862) SS BOND : bond 0.00410 ( 2) SS BOND : angle 1.06469 ( 4) hydrogen bonds : bond 0.03886 ( 131) hydrogen bonds : angle 6.55372 ( 393) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 LYS cc_start: 0.7195 (pttm) cc_final: 0.6949 (pttm) REVERT: A 264 ARG cc_start: 0.6267 (ttp80) cc_final: 0.6040 (ttp80) REVERT: A 289 GLU cc_start: 0.4959 (OUTLIER) cc_final: 0.4717 (mt-10) REVERT: B 57 LYS cc_start: 0.6593 (ptpp) cc_final: 0.6320 (ptpp) REVERT: B 82 LYS cc_start: 0.8099 (tttp) cc_final: 0.7741 (ttpp) REVERT: B 87 ILE cc_start: 0.7905 (mm) cc_final: 0.7673 (mm) REVERT: B 246 GLU cc_start: 0.6472 (pp20) cc_final: 0.5900 (pp20) REVERT: B 293 GLN cc_start: 0.6550 (mp10) cc_final: 0.5831 (mp10) REVERT: B 309 LYS cc_start: 0.7834 (mmtp) cc_final: 0.7558 (mmtm) REVERT: H 34 MET cc_start: 0.8174 (mmm) cc_final: 0.7885 (mmm) REVERT: H 46 GLU cc_start: 0.7364 (tt0) cc_final: 0.7017 (tt0) REVERT: H 65 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8105 (tppt) REVERT: H 121 SER cc_start: 0.4519 (OUTLIER) cc_final: 0.4290 (t) REVERT: L 90 LYS cc_start: 0.8484 (ptmt) cc_final: 0.8199 (ptmm) REVERT: L 106 ILE cc_start: 0.7992 (pt) cc_final: 0.7519 (mm) outliers start: 42 outliers final: 26 residues processed: 185 average time/residue: 0.0770 time to fit residues: 18.3056 Evaluate side-chains 186 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.169853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.149097 restraints weight = 9233.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.154723 restraints weight = 5307.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.158606 restraints weight = 3359.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.161369 restraints weight = 2269.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.163248 restraints weight = 1606.655| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5812 Z= 0.215 Angle : 0.761 13.214 7866 Z= 0.399 Chirality : 0.049 0.331 838 Planarity : 0.005 0.045 1014 Dihedral : 6.447 34.933 759 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % Rotamer: Outliers : 8.04 % Allowed : 34.23 % Favored : 57.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -3.22 (0.30), residues: 689 helix: -2.94 (1.93), residues: 6 sheet: -1.60 (0.30), residues: 284 loop : -2.61 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 218 TYR 0.015 0.002 TYR A 48 PHE 0.033 0.003 PHE A 227 TRP 0.021 0.002 TRP A 292 HIS 0.006 0.002 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 5810) covalent geometry : angle 0.76088 ( 7862) SS BOND : bond 0.00171 ( 2) SS BOND : angle 1.12726 ( 4) hydrogen bonds : bond 0.04450 ( 131) hydrogen bonds : angle 6.93181 ( 393) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 158 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.6867 (mm-40) cc_final: 0.6506 (mm-40) REVERT: A 252 LYS cc_start: 0.7191 (pttm) cc_final: 0.6924 (pttm) REVERT: A 279 LYS cc_start: 0.7545 (mmmt) cc_final: 0.7141 (mmmt) REVERT: A 289 GLU cc_start: 0.4977 (OUTLIER) cc_final: 0.4756 (mt-10) REVERT: B 57 LYS cc_start: 0.6620 (ptpp) cc_final: 0.6304 (ptpp) REVERT: B 82 LYS cc_start: 0.8061 (tttp) cc_final: 0.7718 (ttpp) REVERT: B 232 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6867 (mtmm) REVERT: B 246 GLU cc_start: 0.6602 (pp20) cc_final: 0.5980 (pp20) REVERT: B 293 GLN cc_start: 0.6587 (mp10) cc_final: 0.5679 (mp10) REVERT: B 309 LYS cc_start: 0.7902 (mmtp) cc_final: 0.7601 (mmtm) REVERT: H 46 GLU cc_start: 0.7377 (tt0) cc_final: 0.7091 (tt0) REVERT: H 65 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8175 (tppt) REVERT: H 121 SER cc_start: 0.4524 (OUTLIER) cc_final: 0.4255 (t) REVERT: L 90 LYS cc_start: 0.8533 (ptmt) cc_final: 0.8274 (ptmm) REVERT: L 98 PHE cc_start: 0.8002 (m-10) cc_final: 0.7794 (m-10) outliers start: 51 outliers final: 37 residues processed: 182 average time/residue: 0.0742 time to fit residues: 17.1010 Evaluate side-chains 197 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.170179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.149261 restraints weight = 9145.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.154944 restraints weight = 5260.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.158901 restraints weight = 3338.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.161705 restraints weight = 2254.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.163571 restraints weight = 1595.017| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5812 Z= 0.201 Angle : 0.762 13.315 7866 Z= 0.396 Chirality : 0.048 0.228 838 Planarity : 0.006 0.047 1014 Dihedral : 6.385 35.620 759 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.06 % Favored : 86.94 % Rotamer: Outliers : 7.57 % Allowed : 34.23 % Favored : 58.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -3.32 (0.29), residues: 689 helix: -4.87 (0.99), residues: 6 sheet: -1.69 (0.30), residues: 278 loop : -2.62 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 218 TYR 0.013 0.002 TYR L 91 PHE 0.021 0.002 PHE A 54 TRP 0.032 0.002 TRP A 208 HIS 0.006 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 5810) covalent geometry : angle 0.76129 ( 7862) SS BOND : bond 0.00094 ( 2) SS BOND : angle 1.17497 ( 4) hydrogen bonds : bond 0.04303 ( 131) hydrogen bonds : angle 6.73152 ( 393) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 155 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8180 (p0) cc_final: 0.7719 (p0) REVERT: A 252 LYS cc_start: 0.7206 (pttm) cc_final: 0.6959 (pttm) REVERT: A 279 LYS cc_start: 0.7707 (mmmt) cc_final: 0.7272 (mmmt) REVERT: A 289 GLU cc_start: 0.4905 (OUTLIER) cc_final: 0.4462 (mp0) REVERT: B 57 LYS cc_start: 0.6624 (ptpp) cc_final: 0.6285 (ptpp) REVERT: B 82 LYS cc_start: 0.8071 (tttp) cc_final: 0.7738 (ttpp) REVERT: B 212 LEU cc_start: 0.5011 (OUTLIER) cc_final: 0.4625 (mt) REVERT: B 218 ARG cc_start: 0.8087 (mmp80) cc_final: 0.7828 (mmp80) REVERT: B 232 LYS cc_start: 0.7106 (OUTLIER) cc_final: 0.6899 (mtmm) REVERT: B 246 GLU cc_start: 0.6560 (pp20) cc_final: 0.5949 (pp20) REVERT: B 293 GLN cc_start: 0.6565 (mp10) cc_final: 0.5662 (mp10) REVERT: B 309 LYS cc_start: 0.8013 (mmtp) cc_final: 0.7699 (mmtp) REVERT: H 46 GLU cc_start: 0.7387 (tt0) cc_final: 0.7104 (tt0) REVERT: H 65 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8083 (tppt) REVERT: H 121 SER cc_start: 0.4511 (OUTLIER) cc_final: 0.4234 (t) REVERT: L 90 LYS cc_start: 0.8508 (ptmt) cc_final: 0.8244 (ptmm) REVERT: L 98 PHE cc_start: 0.8037 (m-10) cc_final: 0.7835 (m-10) outliers start: 48 outliers final: 33 residues processed: 185 average time/residue: 0.0748 time to fit residues: 17.6874 Evaluate side-chains 186 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 16 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.170207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.149122 restraints weight = 9146.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.154860 restraints weight = 5256.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.158833 restraints weight = 3337.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.161571 restraints weight = 2253.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.163611 restraints weight = 1604.162| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5812 Z= 0.206 Angle : 0.779 12.741 7866 Z= 0.406 Chirality : 0.048 0.169 838 Planarity : 0.005 0.045 1014 Dihedral : 6.458 35.410 759 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 8.04 % Allowed : 34.86 % Favored : 57.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -3.37 (0.29), residues: 689 helix: -3.72 (1.13), residues: 12 sheet: -1.66 (0.30), residues: 273 loop : -2.70 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 218 TYR 0.022 0.002 TYR A 48 PHE 0.023 0.002 PHE A 54 TRP 0.044 0.003 TRP A 208 HIS 0.006 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 5810) covalent geometry : angle 0.77920 ( 7862) SS BOND : bond 0.00131 ( 2) SS BOND : angle 1.11674 ( 4) hydrogen bonds : bond 0.04274 ( 131) hydrogen bonds : angle 6.77858 ( 393) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 159 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TRP cc_start: 0.7620 (m-10) cc_final: 0.7368 (m-10) REVERT: A 252 LYS cc_start: 0.7218 (pttm) cc_final: 0.6801 (pttm) REVERT: A 279 LYS cc_start: 0.7720 (mmmt) cc_final: 0.7250 (mmmt) REVERT: A 289 GLU cc_start: 0.4861 (OUTLIER) cc_final: 0.4426 (mp0) REVERT: B 57 LYS cc_start: 0.6621 (ptpp) cc_final: 0.6318 (ptpp) REVERT: B 82 LYS cc_start: 0.8032 (tttp) cc_final: 0.7673 (ttpp) REVERT: B 212 LEU cc_start: 0.5068 (OUTLIER) cc_final: 0.4804 (mt) REVERT: B 232 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6880 (mtmm) REVERT: B 246 GLU cc_start: 0.6560 (pp20) cc_final: 0.5960 (pp20) REVERT: B 309 LYS cc_start: 0.8106 (mmtp) cc_final: 0.7897 (mmtp) REVERT: H 34 MET cc_start: 0.7692 (mmm) cc_final: 0.7302 (mmm) REVERT: H 46 GLU cc_start: 0.7366 (tt0) cc_final: 0.7069 (tt0) REVERT: H 65 LYS cc_start: 0.8556 (mmtt) cc_final: 0.8064 (tppt) REVERT: H 121 SER cc_start: 0.4513 (OUTLIER) cc_final: 0.4213 (t) REVERT: L 11 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7703 (pp) REVERT: L 90 LYS cc_start: 0.8510 (ptmt) cc_final: 0.8277 (ptmm) outliers start: 51 outliers final: 38 residues processed: 185 average time/residue: 0.0791 time to fit residues: 18.6532 Evaluate side-chains 199 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 156 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.0770 chunk 60 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 53 optimal weight: 0.0070 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.174329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.153352 restraints weight = 9195.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.159150 restraints weight = 5239.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.163143 restraints weight = 3308.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.165849 restraints weight = 2228.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.167847 restraints weight = 1580.789| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5812 Z= 0.145 Angle : 0.773 13.263 7866 Z= 0.400 Chirality : 0.047 0.165 838 Planarity : 0.005 0.065 1014 Dihedral : 6.042 34.411 759 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 6.31 % Allowed : 36.91 % Favored : 56.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -3.27 (0.29), residues: 689 helix: -4.72 (1.13), residues: 6 sheet: -1.56 (0.30), residues: 278 loop : -2.67 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 218 TYR 0.014 0.001 TYR B 233 PHE 0.019 0.002 PHE A 54 TRP 0.035 0.002 TRP A 208 HIS 0.005 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5810) covalent geometry : angle 0.77286 ( 7862) SS BOND : bond 0.00040 ( 2) SS BOND : angle 0.92470 ( 4) hydrogen bonds : bond 0.03687 ( 131) hydrogen bonds : angle 6.29884 ( 393) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TRP cc_start: 0.7637 (m-10) cc_final: 0.7372 (m-10) REVERT: A 252 LYS cc_start: 0.7007 (pttm) cc_final: 0.6775 (pttm) REVERT: A 279 LYS cc_start: 0.7530 (mmmt) cc_final: 0.7137 (mmmt) REVERT: A 289 GLU cc_start: 0.4873 (OUTLIER) cc_final: 0.4526 (mp0) REVERT: B 57 LYS cc_start: 0.6616 (ptpp) cc_final: 0.6304 (ptpp) REVERT: B 82 LYS cc_start: 0.7991 (tttp) cc_final: 0.7693 (ttpp) REVERT: B 246 GLU cc_start: 0.6429 (pp20) cc_final: 0.5863 (pp20) REVERT: B 293 GLN cc_start: 0.6460 (mp10) cc_final: 0.5782 (mp10) REVERT: H 34 MET cc_start: 0.7468 (mmm) cc_final: 0.7255 (mmm) REVERT: H 46 GLU cc_start: 0.7297 (tt0) cc_final: 0.6974 (tt0) REVERT: L 90 LYS cc_start: 0.8510 (ptmt) cc_final: 0.8272 (ptmm) REVERT: L 106 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7551 (mm) outliers start: 40 outliers final: 32 residues processed: 170 average time/residue: 0.0757 time to fit residues: 16.3558 Evaluate side-chains 184 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 4 optimal weight: 0.0010 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 2 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 0.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN ** L 92 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 = 0.4272 r_free = 0.4272 target = 0.176381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.154889 restraints weight = 9179.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.160579 restraints weight = 5320.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.164584 restraints weight = 3417.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.167395 restraints weight = 2337.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.169409 restraints weight = 1668.197| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5812 Z= 0.144 Angle : 0.765 13.196 7866 Z= 0.395 Chirality : 0.047 0.166 838 Planarity : 0.005 0.060 1014 Dihedral : 5.917 33.681 759 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 5.68 % Allowed : 37.38 % Favored : 56.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -3.18 (0.29), residues: 689 helix: -4.57 (1.28), residues: 6 sheet: -1.45 (0.31), residues: 273 loop : -2.65 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 218 TYR 0.022 0.001 TYR A 251 PHE 0.020 0.002 PHE A 54 TRP 0.029 0.002 TRP A 208 HIS 0.006 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 5810) covalent geometry : angle 0.76472 ( 7862) SS BOND : bond 0.00074 ( 2) SS BOND : angle 0.93787 ( 4) hydrogen bonds : bond 0.03827 ( 131) hydrogen bonds : angle 6.29024 ( 393) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1055.66 seconds wall clock time: 19 minutes 1.47 seconds (1141.47 seconds total)