Starting phenix.real_space_refine on Mon Dec 30 01:15:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tcg_41154/12_2024/8tcg_41154_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tcg_41154/12_2024/8tcg_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_41154/12_2024/8tcg_41154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tcg_41154/12_2024/8tcg_41154.map" model { file = "/net/cci-nas-00/data/ceres_data/8tcg_41154/12_2024/8tcg_41154_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tcg_41154/12_2024/8tcg_41154_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 6.79, per 1000 atoms: 0.59 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: 3.98 Conformation dependent library (CDL) restraints added in 999.1 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: 1.16 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: 4.44 Time building geometry restraints manager: 4.26 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: 3.000 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: 0.180 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.690 Find NCS groups from input model: 0.080 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.640 ------------------------------------------------------------------------------- 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 6072 Z= 0.884 Angle : 1.681 76.776 8225 Z= 1.080 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.044 0.009 TRP A 114 HIS 0.005 0.001 HIS B 195 PHE 0.021 0.004 PHE B 311 TYR 0.031 0.005 TYR B 120 ARG 0.004 0.001 ARG A 245 *********************** 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 : 0.977 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: 0.5463 time to fit residues: 117.7341 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 : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 6072 Z= 0.285 Angle : 0.696 11.511 8225 Z= 0.381 Chirality : 0.049 0.303 901 Planarity : 0.005 0.056 1078 Dihedral : 8.325 68.657 936 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.48 % Favored : 96.39 % Rotamer: Outliers : 1.27 % Allowed : 10.33 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.30), residues: 748 helix: 0.35 (0.46), residues: 122 sheet: 0.20 (0.32), residues: 238 loop : 0.20 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 395 HIS 0.003 0.001 HIS C 49 PHE 0.017 0.002 PHE C 64 TYR 0.013 0.002 TYR B 351 ARG 0.006 0.001 ARG C 63 *********************** 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 : 1.049 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: A 114 TRP cc_start: 0.7711 (t60) cc_final: 0.7253 (t60) REVERT: A 301 MET cc_start: 0.7556 (mtm) cc_final: 0.7346 (mtm) REVERT: B 175 GLU cc_start: 0.6696 (tt0) cc_final: 0.6495 (mt-10) REVERT: B 323 ASN cc_start: 0.8910 (m-40) cc_final: 0.8602 (m110) outliers start: 8 outliers final: 4 residues processed: 111 average time/residue: 0.4279 time to fit residues: 61.1776 Evaluate side-chains 90 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 37 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 6072 Z= 0.282 Angle : 0.596 11.878 8225 Z= 0.324 Chirality : 0.046 0.228 901 Planarity : 0.004 0.050 1078 Dihedral : 6.629 46.594 936 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.79 % Allowed : 10.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.30), residues: 748 helix: 0.87 (0.47), residues: 120 sheet: -0.29 (0.32), residues: 244 loop : -0.10 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 395 HIS 0.002 0.001 HIS C 31 PHE 0.017 0.001 PHE A 376 TYR 0.022 0.002 TYR B 321 ARG 0.003 0.000 ARG C 63 *********************** 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 86 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 1.078 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: B 323 ASN cc_start: 0.8973 (m-40) cc_final: 0.8765 (m110) REVERT: C 49 HIS cc_start: 0.5883 (t70) cc_final: 0.5676 (t70) outliers start: 5 outliers final: 4 residues processed: 83 average time/residue: 0.4242 time to fit residues: 46.1785 Evaluate side-chains 73 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6072 Z= 0.284 Angle : 0.582 10.489 8225 Z= 0.316 Chirality : 0.046 0.236 901 Planarity : 0.004 0.051 1078 Dihedral : 5.776 48.824 936 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.95 % Allowed : 11.13 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.30), residues: 748 helix: 0.96 (0.49), residues: 120 sheet: -0.44 (0.33), residues: 237 loop : -0.49 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 114 HIS 0.004 0.001 HIS C 31 PHE 0.018 0.002 PHE A 376 TYR 0.015 0.002 TYR B 120 ARG 0.006 0.000 ARG C 55 *********************** 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 78 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 1.014 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: B 128 MET cc_start: 0.8227 (mmm) cc_final: 0.7961 (mmm) REVERT: B 323 ASN cc_start: 0.9098 (m-40) cc_final: 0.8845 (m110) outliers start: 6 outliers final: 5 residues processed: 75 average time/residue: 0.3735 time to fit residues: 38.0856 Evaluate side-chains 71 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 325 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6072 Z= 0.245 Angle : 0.541 10.573 8225 Z= 0.293 Chirality : 0.045 0.220 901 Planarity : 0.004 0.047 1078 Dihedral : 5.437 48.322 936 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.59 % Allowed : 11.76 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.30), residues: 748 helix: 0.83 (0.48), residues: 123 sheet: -0.42 (0.33), residues: 238 loop : -0.62 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 114 HIS 0.002 0.001 HIS C 31 PHE 0.015 0.001 PHE A 376 TYR 0.012 0.001 TYR B 321 ARG 0.006 0.000 ARG C 55 *********************** 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: 10 poor density : 72 time to evaluate : 0.977 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: B 300 ASP cc_start: 0.8448 (t70) cc_final: 0.8224 (t0) REVERT: B 323 ASN cc_start: 0.9141 (m-40) cc_final: 0.8904 (m110) outliers start: 10 outliers final: 8 residues processed: 79 average time/residue: 0.3976 time to fit residues: 42.1777 Evaluate side-chains 77 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 113 ASP 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 65 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6072 Z= 0.273 Angle : 0.551 9.915 8225 Z= 0.299 Chirality : 0.045 0.224 901 Planarity : 0.004 0.047 1078 Dihedral : 5.431 48.036 936 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.75 % Allowed : 12.24 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.31), residues: 748 helix: 0.83 (0.49), residues: 123 sheet: -0.45 (0.33), residues: 238 loop : -0.74 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 114 HIS 0.003 0.001 HIS C 31 PHE 0.018 0.001 PHE A 376 TYR 0.012 0.001 TYR B 351 ARG 0.008 0.000 ARG C 55 *********************** 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 85 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 1.121 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: B 300 ASP cc_start: 0.8469 (t70) cc_final: 0.8249 (t0) outliers start: 11 outliers final: 8 residues processed: 82 average time/residue: 0.3926 time to fit residues: 43.4574 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 : 1.416 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 0.1980 chunk 52 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 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 319 HIS B 323 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6072 Z= 0.221 Angle : 0.526 9.852 8225 Z= 0.283 Chirality : 0.045 0.211 901 Planarity : 0.004 0.042 1078 Dihedral : 5.279 46.982 936 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.43 % Allowed : 12.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.31), residues: 748 helix: 0.82 (0.48), residues: 124 sheet: -0.40 (0.32), residues: 246 loop : -0.77 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 114 HIS 0.001 0.001 HIS A 113 PHE 0.013 0.001 PHE A 376 TYR 0.010 0.001 TYR B 321 ARG 0.007 0.000 ARG C 55 *********************** 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: 9 poor density : 72 time to evaluate : 0.968 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: 0.7275 (t0) cc_final: 0.6718 (p0) REVERT: B 300 ASP cc_start: 0.8471 (t70) cc_final: 0.8248 (t0) outliers start: 9 outliers final: 8 residues processed: 78 average time/residue: 0.3858 time to fit residues: 40.6188 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 : 1.037 ------------------------------------------------------------------------------- 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 150 THR 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 21 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 0.0060 chunk 69 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6072 Z= 0.206 Angle : 0.517 9.674 8225 Z= 0.278 Chirality : 0.045 0.205 901 Planarity : 0.004 0.040 1078 Dihedral : 5.147 45.102 936 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.27 % Allowed : 13.20 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.31), residues: 748 helix: 0.90 (0.48), residues: 124 sheet: -0.36 (0.33), residues: 246 loop : -0.81 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 114 HIS 0.002 0.001 HIS B 319 PHE 0.012 0.001 PHE A 376 TYR 0.010 0.001 TYR B 321 ARG 0.007 0.000 ARG C 55 *********************** 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 82 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 1.007 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 349 ASP cc_start: 0.7313 (t0) cc_final: 0.6741 (p0) REVERT: B 300 ASP cc_start: 0.8491 (t70) cc_final: 0.8268 (t0) outliers start: 8 outliers final: 8 residues processed: 79 average time/residue: 0.3795 time to fit residues: 40.2781 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 : 1.045 ------------------------------------------------------------------------------- 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 150 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6072 Z= 0.264 Angle : 0.542 9.413 8225 Z= 0.292 Chirality : 0.045 0.219 901 Planarity : 0.004 0.040 1078 Dihedral : 5.258 44.112 936 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 4.89 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.31), residues: 748 helix: 0.69 (0.48), residues: 125 sheet: -0.38 (0.33), residues: 246 loop : -0.89 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 114 HIS 0.002 0.001 HIS A 113 PHE 0.017 0.001 PHE A 376 TYR 0.017 0.001 TYR A 139 ARG 0.008 0.000 ARG C 55 *********************** 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 78 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 1.158 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: 0.7364 (t0) cc_final: 0.6797 (p0) REVERT: B 300 ASP cc_start: 0.8518 (t70) cc_final: 0.8299 (t0) outliers start: 7 outliers final: 7 residues processed: 76 average time/residue: 0.3906 time to fit residues: 39.8665 Evaluate side-chains 76 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 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 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 74 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.6170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6072 Z= 0.206 Angle : 0.523 9.496 8225 Z= 0.280 Chirality : 0.044 0.201 901 Planarity : 0.004 0.043 1078 Dihedral : 5.099 42.394 936 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.95 % Allowed : 13.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.31), residues: 748 helix: 0.83 (0.48), residues: 122 sheet: -0.32 (0.33), residues: 245 loop : -0.82 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 114 HIS 0.002 0.001 HIS B 319 PHE 0.012 0.001 PHE A 376 TYR 0.016 0.001 TYR A 139 ARG 0.010 0.000 ARG C 55 ********************** 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 78 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.906 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 34 MET cc_start: 0.7859 (mmt) cc_final: 0.6995 (mmt) REVERT: A 349 ASP cc_start: 0.7318 (t0) cc_final: 0.6736 (p0) REVERT: B 300 ASP cc_start: 0.8514 (t70) cc_final: 0.8303 (t0) outliers start: 6 outliers final: 6 residues processed: 76 average time/residue: 0.4117 time to fit residues: 42.2022 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 : 1.120 ------------------------------------------------------------------------------- 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 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 54 optimal weight: 0.9980 chunk 8 optimal weight: 0.0070 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.106102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.092852 restraints weight = 34811.398| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.07 r_work: 0.3317 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6072 Z= 0.231 Angle : 0.535 9.437 8225 Z= 0.287 Chirality : 0.045 0.210 901 Planarity : 0.004 0.042 1078 Dihedral : 5.094 41.076 936 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.11 % Allowed : 14.15 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.31), residues: 748 helix: 0.78 (0.47), residues: 122 sheet: -0.32 (0.33), residues: 244 loop : -0.88 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 114 HIS 0.001 0.001 HIS B 319 PHE 0.016 0.001 PHE A 376 TYR 0.015 0.001 TYR A 139 ARG 0.010 0.000 ARG C 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3482.68 seconds wall clock time: 63 minutes 2.48 seconds (3782.48 seconds total)