Starting phenix.real_space_refine on Tue Aug 4 18:28:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zxc_74919/08_2026/9zxc_74919.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zxc_74919/08_2026/9zxc_74919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zxc_74919/08_2026/9zxc_74919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zxc_74919/08_2026/9zxc_74919.map" model { file = "/net/cci-nas-00/data/ceres_data/9zxc_74919/08_2026/9zxc_74919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zxc_74919/08_2026/9zxc_74919.cif" } resolution = 3.4 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= 0.024 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: 5 Type Number sf(0) Gaussians S 27 5.16 5 Cl 1 4.86 5 C 3776 2.51 5 N 936 2.21 5 O 1038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5778 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3923 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 944 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "D" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 100 Unusual residues: {'LSN': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.53, per 1000 atoms: 0.26 Number of scatterers: 5778 At special positions: 0 Unit cell: (65.175, 98.175, 140.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 27 16.00 O 1038 8.00 N 936 7.00 C 3776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A-113 " - pdb=" SG CYS A -40 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 89 " 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: 0.50 Conformation dependent library (CDL) restraints added in 211.8 milliseconds 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1350 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 11 sheets defined 48.5% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid -110 through -103 removed outlier: 3.507A pdb=" N ARG A-105 " --> pdb=" O GLY A-109 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A-103 " --> pdb=" O ILE A-107 " (cutoff:3.500A) Processing helix chain 'A' and resid -49 through -45 removed outlier: 3.519A pdb=" N ASP A -46 " --> pdb=" O LYS A -49 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR A -45 " --> pdb=" O PRO A -48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid -49 through -45' Processing helix chain 'A' and resid 25 through 56 Proline residue: A 32 - end of helix removed outlier: 3.576A pdb=" N PHE A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 80 removed outlier: 3.577A pdb=" N VAL A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 90 removed outlier: 4.453A pdb=" N TRP A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 132 removed outlier: 3.786A pdb=" N SER A 105 " --> pdb=" O CYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 160 removed outlier: 4.407A pdb=" N LEU A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 157 " --> pdb=" O TRP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 166 removed outlier: 3.568A pdb=" N ILE A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 Processing helix chain 'A' and resid 204 through 245 removed outlier: 3.979A pdb=" N LEU A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 210 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 removed outlier: 3.681A pdb=" N LYS A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 306 removed outlier: 3.647A pdb=" N ASP A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 292 " --> pdb=" O HIS A 288 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 317 Processing helix chain 'A' and resid 318 through 327 removed outlier: 3.783A pdb=" N ALA A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 340 removed outlier: 3.724A pdb=" N ARG A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1268 removed outlier: 3.622A pdb=" N LYS A1240 " --> pdb=" O ASP A1236 " (cutoff:3.500A) Proline residue: A1255 - end of helix Processing helix chain 'A' and resid 1274 through 1292 removed outlier: 3.747A pdb=" N ILE A1279 " --> pdb=" O ARG A1275 " (cutoff:3.500A) Proline residue: A1285 - end of helix Processing helix chain 'A' and resid 1293 through 1298 removed outlier: 3.507A pdb=" N LEU A1297 " --> pdb=" O PHE A1293 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1306 removed outlier: 4.103A pdb=" N GLY A1303 " --> pdb=" O PRO A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1311 Processing sheet with id=AA1, first strand: chain 'A' and resid -115 through -112 removed outlier: 3.649A pdb=" N LEU A-115 " --> pdb=" O LEU A -55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid -90 through -84 removed outlier: 6.598A pdb=" N TRP A -99 " --> pdb=" O VAL A -87 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLY A -85 " --> pdb=" O MET A-101 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N MET A-101 " --> pdb=" O GLY A -85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid -30 through -29 Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 172 removed outlier: 4.317A pdb=" N ILE A 177 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 6 through 10 removed outlier: 3.582A pdb=" N LEU C 23 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA C 82 " --> pdb=" O CYS C 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.687A pdb=" N TRP C 39 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TYR C 53 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER C 55 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N PHE C 35 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER C 36 " --> pdb=" O TRP C 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP C 102 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA C 100 " --> pdb=" O HIS C 38 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 101 " --> pdb=" O TYR C 116 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TYR C 116 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.687A pdb=" N TRP C 39 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TYR C 53 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER C 55 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N PHE C 35 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 95 " --> pdb=" O VAL C 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.610A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 90 through 91 removed outlier: 3.522A pdb=" N THR D 99 " --> pdb=" O GLN D 91 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 909 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: 0.99 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1022 1.33 - 1.45: 1603 1.45 - 1.57: 3260 1.57 - 1.69: 0 1.69 - 1.82: 41 Bond restraints: 5926 Sorted by residual: bond pdb=" C ASN A1298 " pdb=" N PRO A1299 " ideal model delta sigma weight residual 1.337 1.373 -0.035 1.24e-02 6.50e+03 8.16e+00 bond pdb=" N1 LSN A1502 " pdb=" N2 LSN A1502 " ideal model delta sigma weight residual 1.290 1.326 -0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" C1 LSN A1502 " pdb=" N4 LSN A1502 " ideal model delta sigma weight residual 1.320 1.349 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C PHE A 206 " pdb=" N PRO A 207 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.20e-02 6.94e+03 1.54e+00 bond pdb=" CA ASN A1298 " pdb=" C ASN A1298 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.26e-02 6.30e+03 9.80e-01 ... (remaining 5921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 7890 1.57 - 3.15: 133 3.15 - 4.72: 23 4.72 - 6.30: 11 6.30 - 7.87: 4 Bond angle restraints: 8061 Sorted by residual: angle pdb=" C SER D 51 " pdb=" N ALA D 52 " pdb=" CA ALA D 52 " ideal model delta sigma weight residual 121.54 127.27 -5.73 1.91e+00 2.74e-01 8.98e+00 angle pdb=" N TYR C 53 " pdb=" CA TYR C 53 " pdb=" C TYR C 53 " ideal model delta sigma weight residual 108.46 112.46 -4.00 1.51e+00 4.39e-01 7.03e+00 angle pdb=" N2 LSN A1502 " pdb=" N3 LSN A1502 " pdb=" N4 LSN A1502 " ideal model delta sigma weight residual 114.47 106.60 7.87 3.00e+00 1.11e-01 6.88e+00 angle pdb=" N1 LSN A1502 " pdb=" N2 LSN A1502 " pdb=" N3 LSN A1502 " ideal model delta sigma weight residual 106.24 114.06 -7.82 3.00e+00 1.11e-01 6.80e+00 angle pdb=" N ASN A1298 " pdb=" CA ASN A1298 " pdb=" C ASN A1298 " ideal model delta sigma weight residual 109.81 115.37 -5.56 2.21e+00 2.05e-01 6.34e+00 ... (remaining 8056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 3262 17.67 - 35.34: 245 35.34 - 53.02: 47 53.02 - 70.69: 11 70.69 - 88.36: 7 Dihedral angle restraints: 3572 sinusoidal: 1464 harmonic: 2108 Sorted by residual: dihedral pdb=" CA TRP C 102 " pdb=" C TRP C 102 " pdb=" N GLY C 103 " pdb=" CA GLY C 103 " ideal model delta harmonic sigma weight residual 180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLN D 90 " pdb=" C GLN D 90 " pdb=" N GLN D 91 " pdb=" CA GLN D 91 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA GLN D 7 " pdb=" C GLN D 7 " pdb=" N SER D 8 " pdb=" CA SER D 8 " ideal model delta harmonic sigma weight residual -180.00 -162.95 -17.05 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 3569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 740 0.047 - 0.095: 141 0.095 - 0.142: 24 0.142 - 0.189: 0 0.189 - 0.237: 1 Chirality restraints: 906 Sorted by residual: chirality pdb=" CA ASN A1298 " pdb=" N ASN A1298 " pdb=" C ASN A1298 " pdb=" CB ASN A1298 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA VAL D 59 " pdb=" N VAL D 59 " pdb=" C VAL D 59 " pdb=" CB VAL D 59 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE A -84 " pdb=" N ILE A -84 " pdb=" C ILE A -84 " pdb=" CB ILE A -84 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 903 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 LSN A1502 " 0.012 2.00e-02 2.50e+03 3.09e-02 1.91e+01 pdb=" C11 LSN A1502 " 0.006 2.00e-02 2.50e+03 pdb=" C12 LSN A1502 " -0.044 2.00e-02 2.50e+03 pdb=" C13 LSN A1502 " 0.012 2.00e-02 2.50e+03 pdb=" C14 LSN A1502 " 0.023 2.00e-02 2.50e+03 pdb=" C7 LSN A1502 " -0.060 2.00e-02 2.50e+03 pdb=" C8 LSN A1502 " 0.027 2.00e-02 2.50e+03 pdb=" C9 LSN A1502 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 102 " 0.017 2.00e-02 2.50e+03 1.32e-02 4.37e+00 pdb=" CG TRP C 102 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP C 102 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP C 102 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 102 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 102 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 102 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 102 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 102 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 102 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 206 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 207 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " -0.029 5.00e-02 4.00e+02 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1161 2.78 - 3.31: 5615 3.31 - 3.84: 9426 3.84 - 4.37: 11263 4.37 - 4.90: 19608 Nonbonded interactions: 47073 Sorted by model distance: nonbonded pdb=" OG SER D 64 " pdb=" OG1 THR D 75 " model vdw 2.249 3.040 nonbonded pdb=" OG SER D 15 " pdb=" OD2 ASP D 18 " model vdw 2.265 3.040 nonbonded pdb=" OE1 GLN D 7 " pdb=" OG1 THR D 104 " model vdw 2.292 3.040 nonbonded pdb=" NH1 ARG A-102 " pdb=" OE2 GLU A 173 " model vdw 2.320 3.120 nonbonded pdb=" NE ARG D 62 " pdb=" OD2 ASP D 83 " model vdw 2.349 3.120 ... (remaining 47068 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.730 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.560 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 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 : 0.002 0.036 5930 Z= 0.120 Angle : 0.558 7.869 8069 Z= 0.284 Chirality : 0.038 0.237 906 Planarity : 0.004 0.052 990 Dihedral : 13.336 88.359 2210 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.33), residues: 711 helix: 0.87 (0.30), residues: 307 sheet: -0.74 (0.46), residues: 147 loop : -1.32 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A -97 TYR 0.010 0.001 TYR D 92 PHE 0.014 0.001 PHE A 204 TRP 0.036 0.001 TRP C 102 HIS 0.002 0.000 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 ( 5926) covalent geometry : angle 0.55754 / 0.28 ( 8061) SS BOND : bond 0.00122 / 0.08 ( 4) SS BOND : angle 0.64805 / 0.38 ( 8) hydrogen bonds : bond 0.22551 / 15.17 ( 311) hydrogen bonds : angle 7.76352 / 5.23 ( 909) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 283 MET cc_start: 0.7370 (tpp) cc_final: 0.7159 (tpp) REVERT: A 1309 PHE cc_start: 0.8172 (m-80) cc_final: 0.7838 (m-80) REVERT: A 1311 ARG cc_start: 0.7422 (mtt180) cc_final: 0.6645 (mmt180) REVERT: C 9 GLU cc_start: 0.8665 (mp0) cc_final: 0.8419 (mp0) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.0843 time to fit residues: 11.8401 Evaluate side-chains 90 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A -59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 ASN ** D 38 GLN ** 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 = 0.3645 r_free = 0.3645 target = 0.153282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.119296 restraints weight = 6960.883| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.98 r_work: 0.3041 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5930 Z= 0.235 Angle : 0.650 6.820 8069 Z= 0.344 Chirality : 0.044 0.210 906 Planarity : 0.005 0.044 990 Dihedral : 6.724 78.779 943 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.16 % Allowed : 7.44 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.52 (0.32), residues: 711 helix: 0.78 (0.28), residues: 324 sheet: -1.12 (0.42), residues: 167 loop : -1.23 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 167 TYR 0.025 0.002 TYR C 53 PHE 0.021 0.002 PHE A -88 TRP 0.054 0.002 TRP C 102 HIS 0.004 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.23 ( 5926) covalent geometry : angle 0.64810 / 0.34 ( 8061) SS BOND : bond 0.00584 / 0.30 ( 4) SS BOND : angle 1.67087 / 0.92 ( 8) hydrogen bonds : bond 0.05509 / 3.71 ( 311) hydrogen bonds : angle 5.54244 / 3.75 ( 909) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.210 Fit side-chains REVERT: A 283 MET cc_start: 0.7245 (tpp) cc_final: 0.6985 (tpp) REVERT: A 1284 MET cc_start: 0.7376 (mmm) cc_final: 0.7118 (mmm) REVERT: C 80 ASN cc_start: 0.8037 (t0) cc_final: 0.7510 (t0) outliers start: 7 outliers final: 5 residues processed: 108 average time/residue: 0.0831 time to fit residues: 11.7584 Evaluate side-chains 90 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -67 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 1298 ASN Chi-restraints excluded: chain D residue 59 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 66 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 2 optimal weight: 0.0470 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A -59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** 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 = 0.3710 r_free = 0.3710 target = 0.158142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.122117 restraints weight = 6964.195| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.99 r_work: 0.3077 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5930 Z= 0.156 Angle : 0.583 6.781 8069 Z= 0.307 Chirality : 0.041 0.175 906 Planarity : 0.004 0.047 990 Dihedral : 6.594 81.199 943 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.32 % Allowed : 10.74 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.32), residues: 711 helix: 1.07 (0.29), residues: 320 sheet: -1.05 (0.42), residues: 163 loop : -1.35 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.015 0.001 TYR C 53 PHE 0.015 0.001 PHE A -88 TRP 0.032 0.002 TRP C 102 HIS 0.003 0.001 HIS A1256 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 5926) covalent geometry : angle 0.58212 / 0.31 ( 8061) SS BOND : bond 0.00512 / 0.27 ( 4) SS BOND : angle 1.21418 / 0.66 ( 8) hydrogen bonds : bond 0.04663 / 3.16 ( 311) hydrogen bonds : angle 5.14609 / 3.49 ( 909) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.208 Fit side-chains REVERT: A -33 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6779 (mtt-85) REVERT: A 90 MET cc_start: 0.8641 (ptm) cc_final: 0.8418 (ptm) REVERT: A 1284 MET cc_start: 0.7276 (mmm) cc_final: 0.6969 (mmm) REVERT: C 9 GLU cc_start: 0.8589 (mp0) cc_final: 0.8367 (mp0) outliers start: 8 outliers final: 5 residues processed: 101 average time/residue: 0.0825 time to fit residues: 11.0100 Evaluate side-chains 93 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -33 ARG Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 1296 CYS Chi-restraints excluded: chain A residue 1298 ASN Chi-restraints excluded: chain D residue 59 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 56 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.0470 chunk 8 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 44 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A -59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** 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 = 0.3839 r_free = 0.3839 target = 0.168973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.137535 restraints weight = 6693.083| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.79 r_work: 0.3149 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5930 Z= 0.121 Angle : 0.556 6.656 8069 Z= 0.289 Chirality : 0.040 0.171 906 Planarity : 0.004 0.042 990 Dihedral : 6.454 85.371 943 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.83 % Allowed : 12.56 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.33), residues: 711 helix: 1.33 (0.29), residues: 319 sheet: -0.92 (0.44), residues: 156 loop : -1.45 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 167 TYR 0.016 0.001 TYR A-106 PHE 0.013 0.001 PHE A -88 TRP 0.025 0.001 TRP C 102 HIS 0.003 0.001 HIS A1256 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 5926) covalent geometry : angle 0.55562 / 0.29 ( 8061) SS BOND : bond 0.00242 / 0.14 ( 4) SS BOND : angle 0.97367 / 0.52 ( 8) hydrogen bonds : bond 0.04100 / 2.78 ( 311) hydrogen bonds : angle 4.82822 / 3.27 ( 909) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.217 Fit side-chains REVERT: A -88 PHE cc_start: 0.8561 (t80) cc_final: 0.8299 (t80) REVERT: A -33 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6715 (mtt-85) REVERT: A 93 ARG cc_start: 0.8220 (mtm110) cc_final: 0.7896 (mtp180) REVERT: A 285 ASP cc_start: 0.7611 (t0) cc_final: 0.7379 (t0) REVERT: A 1284 MET cc_start: 0.7294 (mmm) cc_final: 0.6991 (mmm) REVERT: D 43 LYS cc_start: 0.8149 (mtmm) cc_final: 0.7947 (mtmm) outliers start: 5 outliers final: 3 residues processed: 98 average time/residue: 0.0876 time to fit residues: 11.2519 Evaluate side-chains 90 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -33 ARG Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 1296 CYS Chi-restraints excluded: chain A residue 1298 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 15 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 34 optimal weight: 0.0000 chunk 62 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** 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 = 0.3693 r_free = 0.3693 target = 0.157209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.121677 restraints weight = 7104.032| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.23 r_work: 0.3065 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5930 Z= 0.146 Angle : 0.563 6.702 8069 Z= 0.293 Chirality : 0.041 0.178 906 Planarity : 0.004 0.039 990 Dihedral : 6.522 88.284 943 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.49 % Allowed : 13.55 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.33), residues: 711 helix: 1.34 (0.29), residues: 319 sheet: -0.71 (0.43), residues: 162 loop : -1.51 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 62 TYR 0.016 0.001 TYR A-106 PHE 0.015 0.001 PHE A -88 TRP 0.027 0.001 TRP C 102 HIS 0.002 0.001 HIS A1256 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 5926) covalent geometry : angle 0.56197 / 0.29 ( 8061) SS BOND : bond 0.00335 / 0.17 ( 4) SS BOND : angle 1.12845 / 0.61 ( 8) hydrogen bonds : bond 0.04139 / 2.81 ( 311) hydrogen bonds : angle 4.77901 / 3.25 ( 909) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.234 Fit side-chains REVERT: A -33 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6738 (mtt-85) REVERT: A 93 ARG cc_start: 0.8145 (mtm110) cc_final: 0.7781 (mtp180) REVERT: A 1284 MET cc_start: 0.7313 (mmm) cc_final: 0.6952 (mmm) outliers start: 9 outliers final: 6 residues processed: 102 average time/residue: 0.0892 time to fit residues: 11.7573 Evaluate side-chains 95 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -33 ARG Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 1296 CYS Chi-restraints excluded: chain A residue 1298 ASN Chi-restraints excluded: chain C residue 102 TRP Chi-restraints excluded: chain D residue 59 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 69 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 0.0370 chunk 63 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** 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 = 0.3719 r_free = 0.3719 target = 0.159402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.124497 restraints weight = 6965.815| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.93 r_work: 0.3114 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5930 Z= 0.124 Angle : 0.546 6.821 8069 Z= 0.283 Chirality : 0.040 0.171 906 Planarity : 0.004 0.038 990 Dihedral : 6.350 83.394 943 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.65 % Allowed : 15.37 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.33), residues: 711 helix: 1.46 (0.29), residues: 319 sheet: -0.76 (0.42), residues: 171 loop : -1.40 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 167 TYR 0.018 0.001 TYR A-106 PHE 0.012 0.001 PHE A -88 TRP 0.022 0.001 TRP C 102 HIS 0.002 0.001 HIS A1256 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 5926) covalent geometry : angle 0.54551 / 0.28 ( 8061) SS BOND : bond 0.00257 / 0.14 ( 4) SS BOND : angle 1.00956 / 0.54 ( 8) hydrogen bonds : bond 0.03942 / 2.68 ( 311) hydrogen bonds : angle 4.64781 / 3.16 ( 909) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.207 Fit side-chains REVERT: A -33 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6723 (mtt-85) REVERT: A 93 ARG cc_start: 0.8228 (mtm110) cc_final: 0.7892 (mtp180) REVERT: A 1284 MET cc_start: 0.7235 (mmm) cc_final: 0.6888 (mmm) outliers start: 10 outliers final: 6 residues processed: 100 average time/residue: 0.0884 time to fit residues: 11.4677 Evaluate side-chains 93 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -33 ARG Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 1296 CYS Chi-restraints excluded: chain A residue 1298 ASN Chi-restraints excluded: chain C residue 102 TRP Chi-restraints excluded: chain D residue 59 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** 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 = 0.3678 r_free = 0.3678 target = 0.155689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.121195 restraints weight = 7000.598| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.88 r_work: 0.3081 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5930 Z= 0.157 Angle : 0.573 6.723 8069 Z= 0.297 Chirality : 0.041 0.176 906 Planarity : 0.004 0.039 990 Dihedral : 6.438 81.964 943 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.32 % Allowed : 15.87 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.04 (0.33), residues: 711 helix: 1.39 (0.29), residues: 319 sheet: -0.78 (0.42), residues: 171 loop : -1.40 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A-102 TYR 0.029 0.001 TYR A 184 PHE 0.015 0.001 PHE A1304 TRP 0.028 0.001 TRP C 102 HIS 0.002 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 5926) covalent geometry : angle 0.57247 / 0.30 ( 8061) SS BOND : bond 0.00353 / 0.18 ( 4) SS BOND : angle 1.22048 / 0.66 ( 8) hydrogen bonds : bond 0.04085 / 2.77 ( 311) hydrogen bonds : angle 4.68758 / 3.19 ( 909) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.207 Fit side-chains REVERT: A -33 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6861 (mtt-85) REVERT: A 93 ARG cc_start: 0.8270 (mtm110) cc_final: 0.8000 (mtp180) outliers start: 8 outliers final: 6 residues processed: 92 average time/residue: 0.0822 time to fit residues: 9.9975 Evaluate side-chains 91 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -33 ARG Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 1296 CYS Chi-restraints excluded: chain A residue 1298 ASN Chi-restraints excluded: chain C residue 102 TRP Chi-restraints excluded: chain D residue 59 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 7 GLN ** D 38 GLN ** 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 = 0.3707 r_free = 0.3707 target = 0.158064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.123052 restraints weight = 6933.653| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.90 r_work: 0.3085 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5930 Z= 0.152 Angle : 0.571 6.720 8069 Z= 0.296 Chirality : 0.041 0.174 906 Planarity : 0.004 0.053 990 Dihedral : 6.399 79.020 943 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.65 % Allowed : 16.03 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.33), residues: 711 helix: 1.40 (0.29), residues: 319 sheet: -0.81 (0.42), residues: 171 loop : -1.38 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 62 TYR 0.017 0.001 TYR A-106 PHE 0.017 0.001 PHE A1304 TRP 0.027 0.001 TRP C 102 HIS 0.002 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 5926) covalent geometry : angle 0.57025 / 0.30 ( 8061) SS BOND : bond 0.00335 / 0.17 ( 4) SS BOND : angle 1.19732 / 0.65 ( 8) hydrogen bonds : bond 0.04064 / 2.76 ( 311) hydrogen bonds : angle 4.68173 / 3.19 ( 909) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.213 Fit side-chains REVERT: A -33 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6894 (mtt-85) REVERT: A 1284 MET cc_start: 0.7414 (mmm) cc_final: 0.7196 (mmm) REVERT: D 62 ARG cc_start: 0.7816 (ptt-90) cc_final: 0.7610 (ptt-90) outliers start: 10 outliers final: 7 residues processed: 94 average time/residue: 0.0795 time to fit residues: 9.9530 Evaluate side-chains 94 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -89 GLU Chi-restraints excluded: chain A residue -33 ARG Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 1296 CYS Chi-restraints excluded: chain A residue 1298 ASN Chi-restraints excluded: chain C residue 102 TRP Chi-restraints excluded: chain D residue 59 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 67 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.0070 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 38 GLN ** 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 = 0.3681 r_free = 0.3681 target = 0.156110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.121479 restraints weight = 7015.433| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.88 r_work: 0.3085 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5930 Z= 0.147 Angle : 0.571 6.780 8069 Z= 0.296 Chirality : 0.041 0.174 906 Planarity : 0.004 0.052 990 Dihedral : 6.367 77.036 943 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.65 % Allowed : 16.20 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.33), residues: 711 helix: 1.40 (0.29), residues: 319 sheet: -0.95 (0.41), residues: 178 loop : -1.40 (0.45), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 93 TYR 0.028 0.001 TYR A 184 PHE 0.017 0.001 PHE A1304 TRP 0.026 0.001 TRP C 102 HIS 0.002 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 5926) covalent geometry : angle 0.56981 / 0.30 ( 8061) SS BOND : bond 0.00323 / 0.16 ( 4) SS BOND : angle 1.16700 / 0.63 ( 8) hydrogen bonds : bond 0.04023 / 2.73 ( 311) hydrogen bonds : angle 4.67127 / 3.18 ( 909) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.227 Fit side-chains REVERT: A -33 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6984 (mtt-85) REVERT: A 1284 MET cc_start: 0.7331 (mmm) cc_final: 0.7083 (mmm) outliers start: 10 outliers final: 7 residues processed: 93 average time/residue: 0.0812 time to fit residues: 10.0294 Evaluate side-chains 93 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -89 GLU Chi-restraints excluded: chain A residue -33 ARG Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 1296 CYS Chi-restraints excluded: chain A residue 1298 ASN Chi-restraints excluded: chain C residue 102 TRP Chi-restraints excluded: chain D residue 59 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.0060 chunk 2 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 38 GLN ** 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 = 0.3706 r_free = 0.3706 target = 0.158052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.123981 restraints weight = 7075.497| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.98 r_work: 0.3087 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5930 Z= 0.137 Angle : 0.565 6.798 8069 Z= 0.293 Chirality : 0.041 0.169 906 Planarity : 0.004 0.052 990 Dihedral : 6.293 75.965 943 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.49 % Allowed : 16.69 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.33), residues: 711 helix: 1.45 (0.29), residues: 319 sheet: -0.93 (0.41), residues: 178 loop : -1.39 (0.45), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 93 TYR 0.019 0.001 TYR A 184 PHE 0.012 0.001 PHE A1250 TRP 0.025 0.001 TRP C 102 HIS 0.002 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 5926) covalent geometry : angle 0.56455 / 0.29 ( 8061) SS BOND : bond 0.00295 / 0.15 ( 4) SS BOND : angle 1.10293 / 0.59 ( 8) hydrogen bonds : bond 0.03933 / 2.67 ( 311) hydrogen bonds : angle 4.64220 / 3.16 ( 909) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.212 Fit side-chains REVERT: A -33 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6916 (mtt-85) REVERT: A 235 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7670 (tt) REVERT: A 1284 MET cc_start: 0.7300 (mmm) cc_final: 0.7069 (mmm) REVERT: D 62 ARG cc_start: 0.7785 (ptt-90) cc_final: 0.7482 (ptt-90) outliers start: 9 outliers final: 7 residues processed: 95 average time/residue: 0.0770 time to fit residues: 9.8479 Evaluate side-chains 96 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -89 GLU Chi-restraints excluded: chain A residue -33 ARG Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 1296 CYS Chi-restraints excluded: chain A residue 1298 ASN Chi-restraints excluded: chain C residue 102 TRP Chi-restraints excluded: chain D residue 59 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 0.0970 chunk 10 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.0570 chunk 60 optimal weight: 0.0980 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 38 GLN ** 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 = 0.3712 r_free = 0.3712 target = 0.158864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.125535 restraints weight = 6896.956| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.84 r_work: 0.3131 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5930 Z= 0.118 Angle : 0.553 6.864 8069 Z= 0.286 Chirality : 0.040 0.167 906 Planarity : 0.004 0.050 990 Dihedral : 6.194 73.642 943 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.16 % Allowed : 17.02 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.33), residues: 711 helix: 1.53 (0.29), residues: 319 sheet: -0.92 (0.43), residues: 159 loop : -1.28 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 93 TYR 0.016 0.001 TYR A-106 PHE 0.011 0.001 PHE A -88 TRP 0.022 0.001 TRP C 102 HIS 0.002 0.000 HIS A1256 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 5926) covalent geometry : angle 0.55281 / 0.29 ( 8061) SS BOND : bond 0.00223 / 0.12 ( 4) SS BOND : angle 0.92064 / 0.50 ( 8) hydrogen bonds : bond 0.03790 / 2.57 ( 311) hydrogen bonds : angle 4.58919 / 3.13 ( 909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1885.93 seconds wall clock time: 33 minutes 13.84 seconds (1993.84 seconds total)