Starting phenix.real_space_refine on Sat Aug 23 11:45:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tcg_41154/08_2025/8tcg_41154_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tcg_41154/08_2025/8tcg_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_41154/08_2025/8tcg_41154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tcg_41154/08_2025/8tcg_41154.map" model { file = "/net/cci-nas-00/data/ceres_data/8tcg_41154/08_2025/8tcg_41154_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tcg_41154/08_2025/8tcg_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-2.0-5787/lib/python3.9/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, 32 Unusual residues: {' CA': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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, 3 Unusual residues: {' MN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.44, per 1000 atoms: 0.21 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: 1.20 Conformation dependent library (CDL) restraints added in 408.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.35 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: 3.08 Time building geometry restraints manager: 1.62 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: 4.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.070 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.850 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 aren 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 covalent geometry : bond 0.01353 ( 6072) covalent geometry : angle 1.68087 ( 8225) SS BOND : bond 0.01551 ( 7) SS BOND : angle 3.59193 ( 14) hydrogen bonds : bond 0.17491 ( 221) hydrogen bonds : angle 8.77155 ( 573) link_ALPHA1-6 : bond 0.06312 ( 1) link_ALPHA1-6 : angle 2.50149 ( 3) link_BETA1-4 : bond 0.06388 ( 2) link_BETA1-4 : angle 4.31029 ( 6) link_NAG-ASN : bond 0.06769 ( 3) link_NAG-ASN : angle 2.23795 ( 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 : 0.337 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: 0.2674 time to fit residues: 57.2853 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 : 0.314 ------------------------------------------------------------------------------- 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: 0.6980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.117136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.103989 restraints weight = 33662.178| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.99 r_work: 0.3479 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 6085 Z= 0.198 Angle : 0.900 35.745 8257 Z= 0.428 Chirality : 0.050 0.357 901 Planarity : 0.005 0.055 1078 Dihedral : 8.413 70.438 936 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.27 % Allowed : 10.49 % Favored : 88.24 % 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 aren not related in a simple way. whole: 0.25 (0.30), residues: 748 helix: 0.37 (0.46), residues: 122 sheet: 0.26 (0.32), residues: 228 loop : 0.19 (0.31), residues: 398 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 C 64 TRP 0.010 0.002 TRP A 114 HIS 0.003 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 6072) covalent geometry : angle 0.69375 ( 8225) SS BOND : bond 0.00685 ( 7) SS BOND : angle 2.44093 ( 14) hydrogen bonds : bond 0.05665 ( 221) hydrogen bonds : angle 7.51884 ( 573) link_ALPHA1-6 : bond 0.00228 ( 1) link_ALPHA1-6 : angle 1.96233 ( 3) link_BETA1-4 : bond 0.00064 ( 2) link_BETA1-4 : angle 3.86315 ( 6) link_NAG-ASN : bond 0.01345 ( 3) link_NAG-ASN : angle 16.82782 ( 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 114 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 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: 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 60 ASP cc_start: 0.8198 (t0) cc_final: 0.7986 (t0) REVERT: A 75 THR cc_start: 0.7598 (p) cc_final: 0.7327 (t) REVERT: A 114 TRP cc_start: 0.7956 (t60) cc_final: 0.7337 (t60) REVERT: A 301 MET cc_start: 0.7879 (mtm) cc_final: 0.7619 (mtm) REVERT: B 323 ASN cc_start: 0.9016 (m-40) cc_final: 0.8657 (m110) outliers start: 8 outliers final: 4 residues processed: 111 average time/residue: 0.2107 time to fit residues: 30.0836 Evaluate side-chains 91 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 334 PHE 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: 1.9990 chunk 5 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 64 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.113845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.100424 restraints weight = 34946.186| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.08 r_work: 0.3407 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 0.077 6085 Z= 0.160 Angle : 0.826 37.462 8257 Z= 0.371 Chirality : 0.046 0.213 901 Planarity : 0.005 0.069 1078 Dihedral : 6.453 46.674 936 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.48 % Allowed : 9.54 % Favored : 89.98 % 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 aren not related in a simple way. whole: -0.15 (0.30), residues: 748 helix: 0.87 (0.47), residues: 120 sheet: -0.31 (0.32), residues: 238 loop : -0.15 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 55 TYR 0.023 0.001 TYR B 321 PHE 0.015 0.001 PHE A 376 TRP 0.008 0.001 TRP A 395 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 6072) covalent geometry : angle 0.57794 ( 8225) SS BOND : bond 0.00612 ( 7) SS BOND : angle 2.59787 ( 14) hydrogen bonds : bond 0.04206 ( 221) hydrogen bonds : angle 6.76010 ( 573) link_ALPHA1-6 : bond 0.00580 ( 1) link_ALPHA1-6 : angle 1.67305 ( 3) link_BETA1-4 : bond 0.00322 ( 2) link_BETA1-4 : angle 2.40055 ( 6) link_NAG-ASN : bond 0.00547 ( 3) link_NAG-ASN : angle 17.48682 ( 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 91 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.188 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 75 THR cc_start: 0.7831 (p) cc_final: 0.7606 (t) REVERT: A 132 ASP cc_start: 0.8051 (t0) cc_final: 0.7655 (p0) REVERT: B 323 ASN cc_start: 0.9086 (m-40) cc_final: 0.8817 (m110) REVERT: C 49 HIS cc_start: 0.6045 (t70) cc_final: 0.5747 (t70) outliers start: 3 outliers final: 3 residues processed: 88 average time/residue: 0.1986 time to fit residues: 22.5596 Evaluate side-chains 79 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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: 0.8980 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.110451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.097266 restraints weight = 35246.565| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.04 r_work: 0.3361 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 6085 Z= 0.180 Angle : 0.810 37.060 8257 Z= 0.363 Chirality : 0.046 0.238 901 Planarity : 0.004 0.050 1078 Dihedral : 5.683 48.259 936 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.48 % Allowed : 10.65 % Favored : 88.87 % 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 aren not related in a simple way. whole: -0.30 (0.30), residues: 748 helix: 1.07 (0.49), residues: 120 sheet: -0.37 (0.33), residues: 237 loop : -0.39 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.016 0.001 TYR B 351 PHE 0.019 0.002 PHE B 153 TRP 0.009 0.002 TRP A 114 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 6072) covalent geometry : angle 0.56382 ( 8225) SS BOND : bond 0.00542 ( 7) SS BOND : angle 2.15932 ( 14) hydrogen bonds : bond 0.03987 ( 221) hydrogen bonds : angle 6.46819 ( 573) link_ALPHA1-6 : bond 0.00057 ( 1) link_ALPHA1-6 : angle 1.58151 ( 3) link_BETA1-4 : bond 0.00031 ( 2) link_BETA1-4 : angle 2.49764 ( 6) link_NAG-ASN : bond 0.00055 ( 3) link_NAG-ASN : angle 17.27892 ( 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 80 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 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 132 ASP cc_start: 0.8015 (t0) cc_final: 0.7710 (p0) REVERT: B 323 ASN cc_start: 0.9166 (m-40) cc_final: 0.8939 (m110) outliers start: 3 outliers final: 2 residues processed: 78 average time/residue: 0.1774 time to fit residues: 18.5891 Evaluate side-chains 71 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.109660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.096436 restraints weight = 35134.906| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.03 r_work: 0.3351 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6085 Z= 0.149 Angle : 0.789 37.310 8257 Z= 0.348 Chirality : 0.045 0.212 901 Planarity : 0.004 0.055 1078 Dihedral : 5.328 48.023 936 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.43 % Allowed : 10.97 % Favored : 87.60 % 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 aren not related in a simple way. whole: -0.41 (0.30), residues: 748 helix: 0.93 (0.48), residues: 123 sheet: -0.36 (0.33), residues: 238 loop : -0.52 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 55 TYR 0.012 0.001 TYR B 321 PHE 0.015 0.001 PHE B 311 TRP 0.008 0.001 TRP A 114 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 6072) covalent geometry : angle 0.53143 ( 8225) SS BOND : bond 0.00598 ( 7) SS BOND : angle 1.91551 ( 14) hydrogen bonds : bond 0.03752 ( 221) hydrogen bonds : angle 6.29851 ( 573) link_ALPHA1-6 : bond 0.00373 ( 1) link_ALPHA1-6 : angle 1.39034 ( 3) link_BETA1-4 : bond 0.00188 ( 2) link_BETA1-4 : angle 1.79775 ( 6) link_NAG-ASN : bond 0.00159 ( 3) link_NAG-ASN : angle 17.46198 ( 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 82 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.327 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: 0.7928 (t0) cc_final: 0.7714 (p0) REVERT: B 323 ASN cc_start: 0.9258 (m-40) cc_final: 0.8975 (m110) outliers start: 9 outliers final: 5 residues processed: 79 average time/residue: 0.1785 time to fit residues: 18.8213 Evaluate side-chains 74 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.0570 chunk 25 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 1.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.107131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.093967 restraints weight = 35565.936| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.04 r_work: 0.3310 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6085 Z= 0.214 Angle : 0.810 36.963 8257 Z= 0.364 Chirality : 0.046 0.239 901 Planarity : 0.004 0.049 1078 Dihedral : 5.533 48.891 936 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.59 % Allowed : 12.24 % 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 aren not related in a simple way. whole: -0.64 (0.30), residues: 748 helix: 0.76 (0.48), residues: 123 sheet: -0.43 (0.33), residues: 238 loop : -0.73 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 55 TYR 0.012 0.001 TYR B 120 PHE 0.020 0.002 PHE A 376 TRP 0.008 0.002 TRP A 114 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 6072) covalent geometry : angle 0.56800 ( 8225) SS BOND : bond 0.00708 ( 7) SS BOND : angle 1.87204 ( 14) hydrogen bonds : bond 0.04003 ( 221) hydrogen bonds : angle 6.28843 ( 573) link_ALPHA1-6 : bond 0.00370 ( 1) link_ALPHA1-6 : angle 1.64530 ( 3) link_BETA1-4 : bond 0.00143 ( 2) link_BETA1-4 : angle 2.31362 ( 6) link_NAG-ASN : bond 0.00200 ( 3) link_NAG-ASN : angle 17.23069 ( 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 79 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.336 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: 0.7955 (t0) cc_final: 0.7751 (p0) REVERT: B 323 ASN cc_start: 0.9301 (m-40) cc_final: 0.9074 (m110) outliers start: 10 outliers final: 9 residues processed: 75 average time/residue: 0.1814 time to fit residues: 18.1843 Evaluate side-chains 76 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE 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 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: 0.7980 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.108322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.095254 restraints weight = 35148.347| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.01 r_work: 0.3327 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5708 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= 0.155 Angle : 0.791 37.299 8257 Z= 0.348 Chirality : 0.045 0.213 901 Planarity : 0.004 0.046 1078 Dihedral : 5.339 47.957 936 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.59 % Allowed : 12.56 % Favored : 85.85 % 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 aren not related in a simple way. whole: -0.60 (0.31), residues: 748 helix: 0.88 (0.49), residues: 123 sheet: -0.43 (0.33), residues: 238 loop : -0.73 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 55 TYR 0.010 0.001 TYR B 120 PHE 0.014 0.001 PHE A 376 TRP 0.014 0.001 TRP A 114 HIS 0.002 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6072) covalent geometry : angle 0.53516 ( 8225) SS BOND : bond 0.00565 ( 7) SS BOND : angle 1.72567 ( 14) hydrogen bonds : bond 0.03692 ( 221) hydrogen bonds : angle 6.12415 ( 573) link_ALPHA1-6 : bond 0.00498 ( 1) link_ALPHA1-6 : angle 1.57523 ( 3) link_BETA1-4 : bond 0.00225 ( 2) link_BETA1-4 : angle 1.86162 ( 6) link_NAG-ASN : bond 0.00045 ( 3) link_NAG-ASN : angle 17.43546 ( 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 84 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.308 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 349 ASP cc_start: 0.7551 (t0) cc_final: 0.7076 (p0) REVERT: B 323 ASN cc_start: 0.9328 (m-40) cc_final: 0.9125 (m110) outliers start: 10 outliers final: 8 residues processed: 82 average time/residue: 0.1823 time to fit residues: 20.1759 Evaluate side-chains 82 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 0.0670 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.106092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.093724 restraints weight = 33940.121| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.85 r_work: 0.3348 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6085 Z= 0.142 Angle : 0.789 37.389 8257 Z= 0.347 Chirality : 0.045 0.213 901 Planarity : 0.004 0.039 1078 Dihedral : 5.229 46.526 936 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.43 % Allowed : 13.35 % 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 aren not related in a simple way. whole: -0.62 (0.31), residues: 748 helix: 0.79 (0.48), residues: 124 sheet: -0.39 (0.32), residues: 246 loop : -0.76 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 55 TYR 0.020 0.001 TYR A 139 PHE 0.016 0.001 PHE A 376 TRP 0.011 0.001 TRP A 114 HIS 0.002 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6072) covalent geometry : angle 0.53115 ( 8225) SS BOND : bond 0.00446 ( 7) SS BOND : angle 1.63851 ( 14) hydrogen bonds : bond 0.03617 ( 221) hydrogen bonds : angle 6.07164 ( 573) link_ALPHA1-6 : bond 0.00471 ( 1) link_ALPHA1-6 : angle 1.57414 ( 3) link_BETA1-4 : bond 0.00134 ( 2) link_BETA1-4 : angle 1.87188 ( 6) link_NAG-ASN : bond 0.00069 ( 3) link_NAG-ASN : angle 17.48938 ( 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 80 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ASP cc_start: 0.7539 (t0) cc_final: 0.7050 (p0) outliers start: 9 outliers final: 7 residues processed: 77 average time/residue: 0.1745 time to fit residues: 18.0460 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 : 0.285 ------------------------------------------------------------------------------- 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 C residue 69 THR Chi-restraints excluded: chain C residue 71 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: 0.6980 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 chunk 72 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.108662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.095462 restraints weight = 34918.469| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.04 r_work: 0.3326 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6085 Z= 0.140 Angle : 0.785 37.541 8257 Z= 0.342 Chirality : 0.045 0.209 901 Planarity : 0.004 0.045 1078 Dihedral : 5.069 43.185 936 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.27 % Allowed : 13.51 % 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 aren not related in a simple way. whole: -0.59 (0.30), residues: 748 helix: 0.99 (0.48), residues: 121 sheet: -0.39 (0.32), residues: 246 loop : -0.78 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 55 TYR 0.013 0.001 TYR A 139 PHE 0.016 0.001 PHE A 376 TRP 0.014 0.001 TRP A 114 HIS 0.002 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6072) covalent geometry : angle 0.52233 ( 8225) SS BOND : bond 0.00502 ( 7) SS BOND : angle 1.52585 ( 14) hydrogen bonds : bond 0.03482 ( 221) hydrogen bonds : angle 5.95628 ( 573) link_ALPHA1-6 : bond 0.00401 ( 1) link_ALPHA1-6 : angle 1.51504 ( 3) link_BETA1-4 : bond 0.00150 ( 2) link_BETA1-4 : angle 1.80507 ( 6) link_NAG-ASN : bond 0.00073 ( 3) link_NAG-ASN : angle 17.58241 ( 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 81 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.361 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 349 ASP cc_start: 0.7596 (t0) cc_final: 0.7080 (p0) outliers start: 8 outliers final: 8 residues processed: 79 average time/residue: 0.1659 time to fit residues: 17.6581 Evaluate side-chains 78 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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: 0.5980 chunk 72 optimal weight: 0.0870 chunk 67 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.108704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.095575 restraints weight = 35159.913| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.04 r_work: 0.3333 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.6105 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= 0.124 Angle : 0.789 37.679 8257 Z= 0.343 Chirality : 0.044 0.207 901 Planarity : 0.004 0.042 1078 Dihedral : 4.957 41.804 936 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % 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 aren not related in a simple way. whole: -0.51 (0.31), residues: 748 helix: 1.01 (0.48), residues: 121 sheet: -0.30 (0.33), residues: 245 loop : -0.74 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 55 TYR 0.015 0.001 TYR A 139 PHE 0.013 0.001 PHE A 376 TRP 0.011 0.001 TRP A 114 HIS 0.001 0.000 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6072) covalent geometry : angle 0.52732 ( 8225) SS BOND : bond 0.00452 ( 7) SS BOND : angle 1.44293 ( 14) hydrogen bonds : bond 0.03402 ( 221) hydrogen bonds : angle 5.90516 ( 573) link_ALPHA1-6 : bond 0.00457 ( 1) link_ALPHA1-6 : angle 1.51372 ( 3) link_BETA1-4 : bond 0.00174 ( 2) link_BETA1-4 : angle 1.72089 ( 6) link_NAG-ASN : bond 0.00082 ( 3) link_NAG-ASN : angle 17.63843 ( 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 80 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.326 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 349 ASP cc_start: 0.7591 (t0) cc_final: 0.7049 (p0) REVERT: B 261 MET cc_start: 0.9012 (mpp) cc_final: 0.8727 (mpp) outliers start: 8 outliers final: 8 residues processed: 77 average time/residue: 0.1779 time to fit residues: 18.2424 Evaluate side-chains 78 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 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 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.0020 chunk 29 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.105900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.093487 restraints weight = 34350.414| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.87 r_work: 0.3335 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.6207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6085 Z= 0.140 Angle : 0.789 37.561 8257 Z= 0.344 Chirality : 0.044 0.203 901 Planarity : 0.004 0.043 1078 Dihedral : 4.946 39.928 936 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.46 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 aren not related in a simple way. whole: -0.58 (0.31), residues: 748 helix: 0.97 (0.48), residues: 121 sheet: -0.31 (0.33), residues: 246 loop : -0.83 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 55 TYR 0.013 0.001 TYR A 139 PHE 0.016 0.001 PHE A 376 TRP 0.012 0.001 TRP A 114 HIS 0.001 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6072) covalent geometry : angle 0.52905 ( 8225) SS BOND : bond 0.00460 ( 7) SS BOND : angle 1.45138 ( 14) hydrogen bonds : bond 0.03432 ( 221) hydrogen bonds : angle 5.89880 ( 573) link_ALPHA1-6 : bond 0.00387 ( 1) link_ALPHA1-6 : angle 1.52040 ( 3) link_BETA1-4 : bond 0.00120 ( 2) link_BETA1-4 : angle 1.83028 ( 6) link_NAG-ASN : bond 0.00061 ( 3) link_NAG-ASN : angle 17.56856 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2800.60 seconds wall clock time: 48 minutes 18.14 seconds (2898.14 seconds total)