Starting phenix.real_space_refine on Fri Jul 3 03:22:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tcg_41154/07_2026/8tcg_41154_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tcg_41154/07_2026/8tcg_41154.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/8tcg_41154/07_2026/8tcg_41154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tcg_41154/07_2026/8tcg_41154.map" model { file = "/net/cci-nas-00/data/ceres_data/8tcg_41154/07_2026/8tcg_41154_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tcg_41154/07_2026/8tcg_41154_trim.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= 0.021 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Mn 3 7.51 5 S 28 5.16 5 C 3763 2.51 5 N 985 2.21 5 O 1162 1.98 5 H 5652 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11597 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6564 Classifications: {'peptide': 440} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 418} Chain: "B" Number of atoms: 3761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3761 Classifications: {'peptide': 242} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 229} Chain: "C" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1187 Classifications: {'peptide': 72} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 28 Ad-hoc single atom residues: {' CA': 4} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' MN': 3} Chain breaks: 3 Time building chain proxies: 2.11, per 1000 atoms: 0.18 Number of scatterers: 11597 At special positions: 0 Unit cell: (75.174, 102.102, 84.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 3 24.99 Ca 4 19.99 S 28 16.00 O 1162 8.00 N 985 7.00 C 3763 6.00 H 5652 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 155 " distance=2.05 Simple disulfide: pdb=" SG CYS A 401 " - pdb=" SG CYS B 270 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 187 " distance=2.02 Simple disulfide: pdb=" SG CYS B 235 " - pdb=" SG CYS B 276 " distance=2.02 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 73 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA D 3 " - " MAN D 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A2005 " - " ASN A 44 " " NAG A2006 " - " ASN A 260 " " NAG D 1 " - " ASN A 266 " Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 216.4 milliseconds 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1372 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 13 sheets defined 22.1% alpha, 24.8% 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 175 through 180 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 131 through 147 removed outlier: 3.729A pdb=" N SER B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 202 through 212 removed outlier: 3.570A pdb=" N ASN B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 235 Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 261 through 267 removed outlier: 3.767A pdb=" N LEU B 265 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 305 Processing helix chain 'B' and resid 314 through 326 removed outlier: 4.500A pdb=" N HIS B 319 " --> pdb=" O GLN B 315 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 350 removed outlier: 3.590A pdb=" N LEU B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU B 346 " --> pdb=" O ASN B 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 29 Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 51 through 54 Processing helix chain 'C' and resid 55 through 64 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 12 removed outlier: 4.213A pdb=" N ARG A 437 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ASP A 6 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 10.919A pdb=" N LEU A 435 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 10.059A pdb=" N ALA A 433 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASP A 422 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 7.014A pdb=" N ASP A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.508A pdb=" N HIS A 113 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 101 removed outlier: 4.075A pdb=" N SER A 97 " --> pdb=" O CYS A 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.705A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.571A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE A 255 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 283 Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 348 removed outlier: 6.306A pdb=" N ILE A 344 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ALA A 361 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ALA A 359 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY A 348 " --> pdb=" O ASP A 357 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AB3, first strand: chain 'B' and resid 193 through 200 removed outlier: 5.380A pdb=" N HIS B 195 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER B 159 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU B 199 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU B 155 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 33 through 37 removed outlier: 3.536A pdb=" N ASN C 33 " --> pdb=" O ARG C 46 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 573 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 5652 1.13 - 1.31: 1052 1.31 - 1.49: 2547 1.49 - 1.67: 2431 1.67 - 1.84: 42 Bond restraints: 11724 Sorted by residual: bond pdb=" NE1 TRP B 241 " pdb=" HE1 TRP B 241 " ideal model delta sigma weight residual 0.860 1.034 -0.174 2.00e-02 2.50e+03 7.54e+01 bond pdb=" NE1 TRP A 395 " pdb=" HE1 TRP A 395 " ideal model delta sigma weight residual 0.860 1.030 -0.170 2.00e-02 2.50e+03 7.26e+01 bond pdb=" CE2 PHE A 1 " pdb=" HE2 PHE A 1 " ideal model delta sigma weight residual 0.930 1.096 -0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" NH2 ARG C 10 " pdb="HH22 ARG C 10 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.88e+01 bond pdb=" CD2 PHE A 177 " pdb=" HD2 PHE A 177 " ideal model delta sigma weight residual 0.930 1.096 -0.166 2.00e-02 2.50e+03 6.87e+01 ... (remaining 11719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.36: 21097 15.36 - 30.71: 2 30.71 - 46.07: 0 46.07 - 61.42: 0 61.42 - 76.78: 1 Bond angle restraints: 21100 Sorted by residual: angle pdb=" CB ASN C 39 " pdb=" CG ASN C 39 " pdb=" OD1 ASN C 39 " ideal model delta sigma weight residual 120.80 44.02 76.78 2.00e+00 2.50e-01 1.47e+03 angle pdb=" OD1 ASN C 39 " pdb=" CG ASN C 39 " pdb=" ND2 ASN C 39 " ideal model delta sigma weight residual 122.60 138.21 -15.61 1.00e+00 1.00e+00 2.44e+02 angle pdb=" CB ASN C 39 " pdb=" CG ASN C 39 " pdb=" ND2 ASN C 39 " ideal model delta sigma weight residual 116.40 94.20 22.20 1.50e+00 4.44e-01 2.19e+02 angle pdb=" C GLY A 173 " pdb=" N PRO A 174 " pdb=" CA PRO A 174 " ideal model delta sigma weight residual 119.56 127.93 -8.37 1.02e+00 9.61e-01 6.74e+01 angle pdb=" C ALA A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta sigma weight residual 119.56 127.79 -8.23 1.02e+00 9.61e-01 6.50e+01 ... (remaining 21095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 5408 21.69 - 43.38: 185 43.38 - 65.07: 55 65.07 - 86.76: 13 86.76 - 108.45: 5 Dihedral angle restraints: 5666 sinusoidal: 3087 harmonic: 2579 Sorted by residual: dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual 93.00 38.64 54.36 1 1.00e+01 1.00e-02 4.01e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.74 108.45 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" CA VAL A 243 " pdb=" C VAL A 243 " pdb=" N PRO A 244 " pdb=" CA PRO A 244 " ideal model delta harmonic sigma weight residual 180.00 -161.33 -18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 616 0.072 - 0.144: 215 0.144 - 0.217: 55 0.217 - 0.289: 8 0.289 - 0.361: 7 Chirality restraints: 901 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.80e+01 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 6.71e+00 chirality pdb=" C1 MAN D 4 " pdb=" O6 BMA D 3 " pdb=" C2 MAN D 4 " pdb=" O5 MAN D 4 " both_signs ideal model delta sigma weight residual False 2.40 2.45 -0.05 2.00e-02 2.50e+03 6.66e+00 ... (remaining 898 not shown) Planarity restraints: 1797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 395 " -0.068 2.00e-02 2.50e+03 2.51e-02 2.53e+01 pdb=" CG TRP A 395 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP A 395 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 395 " 0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP A 395 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TRP A 395 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP A 395 " 0.027 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 395 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 395 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 395 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 TRP A 395 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP A 395 " 0.018 2.00e-02 2.50e+03 pdb=" HE3 TRP A 395 " 0.035 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 395 " -0.015 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 395 " 0.004 2.00e-02 2.50e+03 pdb=" HH2 TRP A 395 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 114 " -0.062 2.00e-02 2.50e+03 2.35e-02 2.20e+01 pdb=" CG TRP A 114 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP A 114 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 114 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP A 114 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP A 114 " 0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP A 114 " 0.021 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 114 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 114 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 114 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 TRP A 114 " -0.019 2.00e-02 2.50e+03 pdb=" HE1 TRP A 114 " 0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP A 114 " 0.030 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 114 " -0.007 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 114 " -0.008 2.00e-02 2.50e+03 pdb=" HH2 TRP A 114 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 266 " 0.031 2.00e-02 2.50e+03 3.82e-02 2.19e+01 pdb=" CG ASN A 266 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN A 266 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 266 " -0.036 2.00e-02 2.50e+03 pdb="HD21 ASN A 266 " -0.042 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.067 2.00e-02 2.50e+03 ... (remaining 1794 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.75: 29 1.75 - 2.46: 5801 2.46 - 3.17: 37052 3.17 - 3.89: 48022 3.89 - 4.60: 76469 Nonbonded interactions: 167373 Sorted by model distance: nonbonded pdb=" OD1 ASN C 39 " pdb=" HB2 ASN C 39 " model vdw 1.037 2.096 nonbonded pdb=" O SER B 182 " pdb="HH22 ARG C 63 " model vdw 1.655 2.450 nonbonded pdb=" OD2 ASP A 73 " pdb=" HZ3 LYS A 89 " model vdw 1.658 2.450 nonbonded pdb="HD21 ASN A 266 " pdb=" O5 NAG D 1 " model vdw 1.663 1.960 nonbonded pdb="HD21 ASN A 260 " pdb=" O5 NAG A2006 " model vdw 1.663 1.960 ... (remaining 167368 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: 2.830 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: 0.090 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.500 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 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 : 0.014 0.074 6085 Z= 0.739 Angle : 1.690 76.776 8257 Z= 1.081 Chirality : 0.083 0.361 901 Planarity : 0.006 0.034 1078 Dihedral : 12.479 108.448 2300 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.16 % Allowed : 1.27 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.29), residues: 748 helix: -0.81 (0.41), residues: 117 sheet: 0.41 (0.34), residues: 206 loop : 0.29 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 245 TYR 0.031 0.005 TYR B 120 PHE 0.021 0.004 PHE B 311 TRP 0.044 0.009 TRP A 114 HIS 0.005 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.01353 / 0.73 ( 6072) covalent geometry : angle 1.68087 / 1.08 ( 8225) SS BOND : bond 0.01551 / 0.77 ( 7) SS BOND : angle 3.59193 / 2.14 ( 14) hydrogen bonds : bond 0.17491 / 12.16 ( 221) hydrogen bonds : angle 8.77155 / 6.28 ( 573) link_ALPHA1-6 : bond 0.06312 / 3.32 ( 1) link_ALPHA1-6 : angle 2.50149 / 1.33 ( 3) link_BETA1-4 : bond 0.06388 / 3.17 ( 2) link_BETA1-4 : angle 4.31029 / 2.58 ( 6) link_NAG-ASN : bond 0.06769 / 3.37 ( 3) link_NAG-ASN : angle 2.23795 / 1.47 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.322 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8953 (mp) cc_final: 0.8750 (mt) REVERT: A 75 THR cc_start: 0.6994 (p) cc_final: 0.6789 (t) REVERT: A 114 TRP cc_start: 0.7678 (t60) cc_final: 0.7292 (t60) REVERT: B 128 MET cc_start: 0.7740 (mmm) cc_final: 0.7186 (mmm) REVERT: C 39 ASN cc_start: 0.5563 (m110) cc_final: 0.4991 (m110) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.2023 time to fit residues: 43.8777 Evaluate side-chains 91 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.117231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.103906 restraints weight = 33968.457| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.04 r_work: 0.3482 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 6085 Z= 0.196 Angle : 0.895 35.190 8257 Z= 0.429 Chirality : 0.049 0.349 901 Planarity : 0.005 0.056 1078 Dihedral : 8.202 68.238 936 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.07 % Favored : 96.79 % Rotamer: Outliers : 1.11 % Allowed : 10.33 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.08 (0.30), residues: 748 helix: 0.36 (0.46), residues: 122 sheet: 0.20 (0.32), residues: 235 loop : -0.02 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 63 TYR 0.013 0.002 TYR B 351 PHE 0.018 0.002 PHE B 311 TRP 0.010 0.002 TRP A 114 HIS 0.003 0.001 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 ( 6072) covalent geometry : angle 0.69234 / 0.38 ( 8225) SS BOND : bond 0.01120 / 0.57 ( 7) SS BOND : angle 3.09274 / 1.79 ( 14) hydrogen bonds : bond 0.05748 / 3.99 ( 221) hydrogen bonds : angle 7.50188 / 5.35 ( 573) link_ALPHA1-6 : bond 0.00221 / 0.12 ( 1) link_ALPHA1-6 : angle 1.98130 / 1.61 ( 3) link_BETA1-4 : bond 0.00194 / 0.10 ( 2) link_BETA1-4 : angle 3.75138 / 2.69 ( 6) link_NAG-ASN : bond 0.00989 / 0.49 ( 3) link_NAG-ASN : angle 16.44896 / 9.37 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.311 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 THR cc_start: 0.7619 (p) cc_final: 0.7345 (t) REVERT: A 114 TRP cc_start: 0.7935 (t60) cc_final: 0.7373 (t60) REVERT: A 144 SER cc_start: 0.8827 (t) cc_final: 0.8525 (p) REVERT: A 301 MET cc_start: 0.7908 (mtm) cc_final: 0.7668 (mtm) REVERT: B 323 ASN cc_start: 0.9036 (m-40) cc_final: 0.8671 (m110) REVERT: C 12 ASP cc_start: 0.8155 (t0) cc_final: 0.7826 (t0) outliers start: 7 outliers final: 3 residues processed: 109 average time/residue: 0.1764 time to fit residues: 25.0738 Evaluate side-chains 91 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 4 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 1 optimal weight: 0.0770 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 GLN B 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.114058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.100780 restraints weight = 35056.768| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.06 r_work: 0.3420 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 6085 Z= 0.160 Angle : 0.822 37.525 8257 Z= 0.370 Chirality : 0.046 0.223 901 Planarity : 0.004 0.047 1078 Dihedral : 6.592 47.640 936 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.79 % Allowed : 9.86 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.17 (0.30), residues: 748 helix: 0.87 (0.47), residues: 120 sheet: -0.23 (0.31), residues: 246 loop : -0.23 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 55 TYR 0.018 0.001 TYR B 321 PHE 0.014 0.001 PHE A 376 TRP 0.009 0.001 TRP A 395 HIS 0.002 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 6072) covalent geometry : angle 0.57477 / 0.31 ( 8225) SS BOND : bond 0.00567 / 0.30 ( 7) SS BOND : angle 2.49783 / 1.43 ( 14) hydrogen bonds : bond 0.04384 / 3.00 ( 221) hydrogen bonds : angle 6.81173 / 4.85 ( 573) link_ALPHA1-6 : bond 0.00191 / 0.10 ( 1) link_ALPHA1-6 : angle 1.67356 / 1.12 ( 3) link_BETA1-4 : bond 0.00377 / 0.18 ( 2) link_BETA1-4 : angle 2.48460 / 1.72 ( 6) link_NAG-ASN : bond 0.00520 / 0.26 ( 3) link_NAG-ASN : angle 17.42413 / 9.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.323 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: symmetry clash REVERT: A 34 MET cc_start: 0.8061 (mmt) cc_final: 0.6752 (mmt) REVERT: A 75 THR cc_start: 0.7841 (p) cc_final: 0.7592 (t) REVERT: A 132 ASP cc_start: 0.8051 (t0) cc_final: 0.7558 (p0) REVERT: A 152 GLN cc_start: 0.8118 (mt0) cc_final: 0.7582 (mt0) REVERT: B 323 ASN cc_start: 0.9086 (m-40) cc_final: 0.8811 (m110) REVERT: C 12 ASP cc_start: 0.8226 (t0) cc_final: 0.7911 (t0) REVERT: C 49 HIS cc_start: 0.6166 (t70) cc_final: 0.5829 (t70) outliers start: 5 outliers final: 3 residues processed: 91 average time/residue: 0.1764 time to fit residues: 21.4862 Evaluate side-chains 77 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain C residue 4 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.0370 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.108074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.094511 restraints weight = 35838.495| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.09 r_work: 0.3315 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 6085 Z= 0.245 Angle : 0.848 36.305 8257 Z= 0.392 Chirality : 0.048 0.271 901 Planarity : 0.005 0.054 1078 Dihedral : 6.080 50.000 936 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.27 % Allowed : 10.65 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.67 (0.30), residues: 748 helix: 0.68 (0.47), residues: 120 sheet: -0.41 (0.32), residues: 244 loop : -0.76 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 55 TYR 0.016 0.002 TYR B 120 PHE 0.030 0.002 PHE A 376 TRP 0.011 0.002 TRP A 179 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.24 ( 6072) covalent geometry : angle 0.62583 / 0.34 ( 8225) SS BOND : bond 0.00916 / 0.45 ( 7) SS BOND : angle 2.27630 / 1.31 ( 14) hydrogen bonds : bond 0.04447 / 3.01 ( 221) hydrogen bonds : angle 6.56876 / 4.64 ( 573) link_ALPHA1-6 : bond 0.00012 / 0.01 ( 1) link_ALPHA1-6 : angle 1.70870 / 1.20 ( 3) link_BETA1-4 : bond 0.00350 / 0.18 ( 2) link_BETA1-4 : angle 2.91475 / 2.27 ( 6) link_NAG-ASN : bond 0.00343 / 0.17 ( 3) link_NAG-ASN : angle 16.92550 / 9.51 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.324 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.8077 (t0) cc_final: 0.7756 (p0) REVERT: B 323 ASN cc_start: 0.9210 (m-40) cc_final: 0.8930 (m110) outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 0.1515 time to fit residues: 16.7220 Evaluate side-chains 76 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 71 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 34 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.109156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.095889 restraints weight = 35322.914| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.03 r_work: 0.3335 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6085 Z= 0.155 Angle : 0.794 37.130 8257 Z= 0.353 Chirality : 0.045 0.226 901 Planarity : 0.004 0.049 1078 Dihedral : 5.597 49.592 936 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.27 % Allowed : 10.97 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.65 (0.30), residues: 748 helix: 0.77 (0.48), residues: 123 sheet: -0.37 (0.32), residues: 238 loop : -0.80 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 55 TYR 0.014 0.001 TYR A 139 PHE 0.017 0.001 PHE A 376 TRP 0.009 0.001 TRP A 114 HIS 0.001 0.001 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 6072) covalent geometry : angle 0.54281 / 0.29 ( 8225) SS BOND : bond 0.00643 / 0.34 ( 7) SS BOND : angle 1.92597 / 1.12 ( 14) hydrogen bonds : bond 0.03936 / 2.67 ( 221) hydrogen bonds : angle 6.35730 / 4.48 ( 573) link_ALPHA1-6 : bond 0.00434 / 0.23 ( 1) link_ALPHA1-6 : angle 1.47112 / 1.07 ( 3) link_BETA1-4 : bond 0.00225 / 0.12 ( 2) link_BETA1-4 : angle 1.82452 / 1.34 ( 6) link_NAG-ASN : bond 0.00106 / 0.05 ( 3) link_NAG-ASN : angle 17.35156 / 9.72 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.215 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: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.7979 (t0) cc_final: 0.7743 (p0) REVERT: B 323 ASN cc_start: 0.9248 (m-40) cc_final: 0.8991 (m110) outliers start: 8 outliers final: 7 residues processed: 79 average time/residue: 0.1609 time to fit residues: 17.3291 Evaluate side-chains 73 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 71 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.104793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.091967 restraints weight = 35991.272| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.99 r_work: 0.3284 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 6085 Z= 0.263 Angle : 0.842 36.398 8257 Z= 0.388 Chirality : 0.047 0.269 901 Planarity : 0.005 0.053 1078 Dihedral : 6.054 50.500 936 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 1.91 % Allowed : 11.92 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.05 (0.30), residues: 748 helix: 0.44 (0.46), residues: 124 sheet: -0.51 (0.32), residues: 246 loop : -1.17 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 55 TYR 0.014 0.002 TYR B 120 PHE 0.029 0.002 PHE A 376 TRP 0.009 0.002 TRP A 114 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.26 ( 6072) covalent geometry : angle 0.62020 / 0.34 ( 8225) SS BOND : bond 0.00717 / 0.37 ( 7) SS BOND : angle 1.94014 / 1.12 ( 14) hydrogen bonds : bond 0.04416 / 2.95 ( 221) hydrogen bonds : angle 6.42153 / 4.51 ( 573) link_ALPHA1-6 : bond 0.00027 / 0.01 ( 1) link_ALPHA1-6 : angle 1.52594 / 1.11 ( 3) link_BETA1-4 : bond 0.00252 / 0.13 ( 2) link_BETA1-4 : angle 2.86939 / 2.28 ( 6) link_NAG-ASN : bond 0.00333 / 0.17 ( 3) link_NAG-ASN : angle 16.93540 / 9.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.299 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.7945 (t0) cc_final: 0.7710 (p0) REVERT: B 199 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7384 (pp) REVERT: C 15 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7682 (mt-10) outliers start: 12 outliers final: 9 residues processed: 78 average time/residue: 0.1481 time to fit residues: 15.7158 Evaluate side-chains 76 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 71 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 319 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.106974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.093742 restraints weight = 35264.687| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.02 r_work: 0.3302 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6085 Z= 0.162 Angle : 0.798 36.989 8257 Z= 0.356 Chirality : 0.045 0.229 901 Planarity : 0.004 0.048 1078 Dihedral : 5.697 50.405 936 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.75 % Allowed : 13.04 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.98 (0.30), residues: 748 helix: 0.51 (0.46), residues: 124 sheet: -0.46 (0.32), residues: 246 loop : -1.13 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 55 TYR 0.012 0.001 TYR A 139 PHE 0.015 0.001 PHE A 376 TRP 0.013 0.001 TRP A 114 HIS 0.001 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 6072) covalent geometry : angle 0.55011 / 0.30 ( 8225) SS BOND : bond 0.00582 / 0.31 ( 7) SS BOND : angle 1.73841 / 1.01 ( 14) hydrogen bonds : bond 0.03956 / 2.67 ( 221) hydrogen bonds : angle 6.26485 / 4.40 ( 573) link_ALPHA1-6 : bond 0.00418 / 0.22 ( 1) link_ALPHA1-6 : angle 1.55435 / 1.15 ( 3) link_BETA1-4 : bond 0.00107 / 0.05 ( 2) link_BETA1-4 : angle 1.98475 / 1.52 ( 6) link_NAG-ASN : bond 0.00097 / 0.05 ( 3) link_NAG-ASN : angle 17.29839 / 9.70 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.351 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: symmetry clash revert: symmetry clash REVERT: A 289 ASP cc_start: 0.8213 (t0) cc_final: 0.7967 (t0) REVERT: C 15 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7734 (mt-10) outliers start: 11 outliers final: 9 residues processed: 78 average time/residue: 0.1683 time to fit residues: 17.8288 Evaluate side-chains 75 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 71 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 0.0470 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 65 optimal weight: 0.2980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.106974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094948 restraints weight = 33901.176| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.78 r_work: 0.3334 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6085 Z= 0.125 Angle : 0.795 37.405 8257 Z= 0.348 Chirality : 0.045 0.210 901 Planarity : 0.004 0.047 1078 Dihedral : 5.358 47.642 936 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.11 % Allowed : 13.83 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.87 (0.30), residues: 748 helix: 0.73 (0.47), residues: 125 sheet: -0.39 (0.32), residues: 246 loop : -1.11 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 55 TYR 0.011 0.001 TYR A 139 PHE 0.012 0.001 PHE A 376 TRP 0.011 0.001 TRP A 114 HIS 0.001 0.000 HIS C 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 6072) covalent geometry : angle 0.53814 / 0.29 ( 8225) SS BOND : bond 0.00529 / 0.28 ( 7) SS BOND : angle 1.63451 / 0.95 ( 14) hydrogen bonds : bond 0.03735 / 2.55 ( 221) hydrogen bonds : angle 6.08522 / 4.28 ( 573) link_ALPHA1-6 : bond 0.00489 / 0.26 ( 1) link_ALPHA1-6 : angle 1.52485 / 1.15 ( 3) link_BETA1-4 : bond 0.00168 / 0.08 ( 2) link_BETA1-4 : angle 1.79585 / 1.36 ( 6) link_NAG-ASN : bond 0.00108 / 0.05 ( 3) link_NAG-ASN : angle 17.54047 / 9.82 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.328 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: symmetry clash REVERT: A 289 ASP cc_start: 0.8205 (t0) cc_final: 0.7966 (t0) REVERT: A 349 ASP cc_start: 0.7630 (t0) cc_final: 0.6968 (p0) REVERT: C 15 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7752 (mt-10) outliers start: 7 outliers final: 6 residues processed: 75 average time/residue: 0.1595 time to fit residues: 16.1687 Evaluate side-chains 75 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 0.1980 chunk 72 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.106638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.093341 restraints weight = 35231.376| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.03 r_work: 0.3303 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6085 Z= 0.167 Angle : 0.802 37.150 8257 Z= 0.355 Chirality : 0.045 0.224 901 Planarity : 0.004 0.040 1078 Dihedral : 5.346 45.109 936 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.27 % Allowed : 14.47 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.89 (0.30), residues: 748 helix: 0.79 (0.48), residues: 122 sheet: -0.39 (0.33), residues: 246 loop : -1.15 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 55 TYR 0.011 0.001 TYR A 139 PHE 0.018 0.001 PHE A 376 TRP 0.012 0.001 TRP A 114 HIS 0.002 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 6072) covalent geometry : angle 0.55341 / 0.30 ( 8225) SS BOND : bond 0.00525 / 0.28 ( 7) SS BOND : angle 1.60662 / 0.93 ( 14) hydrogen bonds : bond 0.03805 / 2.57 ( 221) hydrogen bonds : angle 6.06958 / 4.26 ( 573) link_ALPHA1-6 : bond 0.00507 / 0.27 ( 1) link_ALPHA1-6 : angle 1.64616 / 1.24 ( 3) link_BETA1-4 : bond 0.00179 / 0.09 ( 2) link_BETA1-4 : angle 2.14610 / 1.68 ( 6) link_NAG-ASN : bond 0.00163 / 0.08 ( 3) link_NAG-ASN : angle 17.40546 / 9.75 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.325 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: symmetry clash revert: symmetry clash REVERT: A 289 ASP cc_start: 0.8267 (t0) cc_final: 0.8028 (t0) REVERT: A 349 ASP cc_start: 0.7672 (t0) cc_final: 0.7009 (p0) outliers start: 8 outliers final: 8 residues processed: 77 average time/residue: 0.1600 time to fit residues: 16.7631 Evaluate side-chains 76 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.107392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.094010 restraints weight = 35306.818| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.05 r_work: 0.3314 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.6347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6085 Z= 0.145 Angle : 0.794 37.344 8257 Z= 0.349 Chirality : 0.044 0.210 901 Planarity : 0.004 0.043 1078 Dihedral : 5.210 43.451 936 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.95 % Allowed : 14.63 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.88 (0.30), residues: 748 helix: 0.82 (0.48), residues: 122 sheet: -0.40 (0.33), residues: 248 loop : -1.15 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 55 TYR 0.011 0.001 TYR A 139 PHE 0.015 0.001 PHE A 376 TRP 0.012 0.001 TRP A 114 HIS 0.001 0.000 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 6072) covalent geometry : angle 0.53965 / 0.29 ( 8225) SS BOND : bond 0.00524 / 0.28 ( 7) SS BOND : angle 1.53122 / 0.89 ( 14) hydrogen bonds : bond 0.03669 / 2.47 ( 221) hydrogen bonds : angle 6.00078 / 4.20 ( 573) link_ALPHA1-6 : bond 0.00414 / 0.22 ( 1) link_ALPHA1-6 : angle 1.52647 / 1.15 ( 3) link_BETA1-4 : bond 0.00130 / 0.06 ( 2) link_BETA1-4 : angle 1.83802 / 1.41 ( 6) link_NAG-ASN : bond 0.00082 / 0.04 ( 3) link_NAG-ASN : angle 17.50027 / 9.80 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.349 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: symmetry clash REVERT: A 289 ASP cc_start: 0.8257 (t0) cc_final: 0.8043 (t0) REVERT: A 349 ASP cc_start: 0.7688 (t0) cc_final: 0.7019 (p0) REVERT: C 15 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7721 (mt-10) outliers start: 6 outliers final: 6 residues processed: 73 average time/residue: 0.1742 time to fit residues: 17.2113 Evaluate side-chains 74 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 29 optimal weight: 0.0870 chunk 44 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.108196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.094776 restraints weight = 35195.067| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.07 r_work: 0.3326 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.6405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6085 Z= 0.120 Angle : 0.789 37.629 8257 Z= 0.342 Chirality : 0.044 0.204 901 Planarity : 0.004 0.042 1078 Dihedral : 4.980 40.923 936 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.27 % Allowed : 13.83 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.81 (0.30), residues: 748 helix: 0.88 (0.48), residues: 122 sheet: -0.38 (0.33), residues: 249 loop : -1.08 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 55 TYR 0.011 0.001 TYR B 321 PHE 0.012 0.001 PHE A 376 TRP 0.011 0.001 TRP A 114 HIS 0.001 0.000 HIS B 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 6072) covalent geometry : angle 0.52596 / 0.28 ( 8225) SS BOND : bond 0.00556 / 0.30 ( 7) SS BOND : angle 1.42508 / 0.83 ( 14) hydrogen bonds : bond 0.03464 / 2.34 ( 221) hydrogen bonds : angle 5.91258 / 4.13 ( 573) link_ALPHA1-6 : bond 0.00505 / 0.27 ( 1) link_ALPHA1-6 : angle 1.54585 / 1.19 ( 3) link_BETA1-4 : bond 0.00169 / 0.08 ( 2) link_BETA1-4 : angle 1.68576 / 1.29 ( 6) link_NAG-ASN : bond 0.00091 / 0.05 ( 3) link_NAG-ASN : angle 17.66654 / 9.88 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2771.95 seconds wall clock time: 47 minutes 44.98 seconds (2864.98 seconds total)