Starting phenix.real_space_refine on Sat May 2 18:56:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymc_39394/05_2026/8ymc_39394.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymc_39394/05_2026/8ymc_39394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ymc_39394/05_2026/8ymc_39394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymc_39394/05_2026/8ymc_39394.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ymc_39394/05_2026/8ymc_39394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymc_39394/05_2026/8ymc_39394.map" } resolution = 2.7 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= -0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 34 5.16 5 C 5262 2.51 5 N 1430 2.21 5 O 1512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8246 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1727 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "B" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1727 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2321 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 291} Chain: "D" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2321 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 291} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'LPP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'LPP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.15, per 1000 atoms: 0.26 Number of scatterers: 8246 At special positions: 0 Unit cell: (67.938, 82.134, 155.142, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 8 15.00 O 1512 8.00 N 1430 7.00 C 5262 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 258.5 milliseconds 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1912 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 7 sheets defined 63.7% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 40 through 49 removed outlier: 3.538A pdb=" N ILE A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 95 through 108 Proline residue: A 103 - end of helix Processing helix chain 'A' and resid 110 through 126 removed outlier: 3.623A pdb=" N VAL A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.536A pdb=" N ALA A 131 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 139 through 151 removed outlier: 3.569A pdb=" N GLY A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 187 removed outlier: 3.592A pdb=" N VAL A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 202 removed outlier: 3.718A pdb=" N ARG A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 95 through 108 Proline residue: B 103 - end of helix Processing helix chain 'B' and resid 110 through 126 removed outlier: 3.640A pdb=" N VAL B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.653A pdb=" N ALA B 131 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 139 through 151 removed outlier: 3.565A pdb=" N GLY B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 187 removed outlier: 3.557A pdb=" N GLY B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 202 removed outlier: 3.505A pdb=" N ILE B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 70 removed outlier: 3.680A pdb=" N LEU C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS C 70 " --> pdb=" O ASP C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 106 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 120 through 133 Processing helix chain 'C' and resid 144 through 157 Processing helix chain 'C' and resid 158 through 165 removed outlier: 4.240A pdb=" N ALA C 161 " --> pdb=" O PHE C 158 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 162 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP C 163 " --> pdb=" O GLY C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 183 removed outlier: 3.696A pdb=" N GLN C 183 " --> pdb=" O LEU C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 183' Processing helix chain 'C' and resid 184 through 197 removed outlier: 3.674A pdb=" N GLN C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 250 Processing helix chain 'C' and resid 251 through 261 removed outlier: 3.711A pdb=" N ILE C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 310 Proline residue: C 271 - end of helix removed outlier: 3.609A pdb=" N ILE C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 350 removed outlier: 3.520A pdb=" N THR C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 70 removed outlier: 3.782A pdb=" N LEU D 67 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS D 70 " --> pdb=" O ASP D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 106 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 120 through 133 Processing helix chain 'D' and resid 144 through 157 Processing helix chain 'D' and resid 158 through 162 removed outlier: 4.005A pdb=" N ALA D 161 " --> pdb=" O PHE D 158 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 162 " --> pdb=" O GLY D 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 158 through 162' Processing helix chain 'D' and resid 184 through 198 Processing helix chain 'D' and resid 209 through 250 Processing helix chain 'D' and resid 251 through 261 removed outlier: 3.783A pdb=" N ILE D 255 " --> pdb=" O ARG D 251 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 310 removed outlier: 3.502A pdb=" N ARG D 270 " --> pdb=" O GLY D 266 " (cutoff:3.500A) Proline residue: D 271 - end of helix removed outlier: 3.585A pdb=" N ILE D 289 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA D 301 " --> pdb=" O ARG D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 349 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 21 removed outlier: 5.627A pdb=" N GLN A 19 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LYS A 9 " --> pdb=" O GLN A 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 21 removed outlier: 5.627A pdb=" N GLN A 19 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LYS A 9 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL A 7 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA A 56 " --> pdb=" O VAL A 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 84 removed outlier: 3.818A pdb=" N ARG A 206 " --> pdb=" O MET A 30 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 21 through 25 removed outlier: 5.115A pdb=" N VAL B 21 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL B 7 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA B 56 " --> pdb=" O VAL B 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 81 through 84 removed outlier: 7.490A pdb=" N MET B 30 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N LEU B 208 " --> pdb=" O MET B 30 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N PHE B 32 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU B 210 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR B 34 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 137 through 143 removed outlier: 3.835A pdb=" N LYS C 139 " --> pdb=" O ILE C 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 137 through 143 549 hydrogen bonds defined for protein. 1593 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: 1.30 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1340 1.31 - 1.43: 2143 1.43 - 1.56: 4841 1.56 - 1.68: 12 1.68 - 1.81: 60 Bond restraints: 8396 Sorted by residual: bond pdb=" O5 LPP D 401 " pdb=" P1 LPP D 401 " ideal model delta sigma weight residual 2.278 1.647 0.631 2.00e-02 2.50e+03 9.95e+02 bond pdb=" O5 LPP C 401 " pdb=" P1 LPP C 401 " ideal model delta sigma weight residual 2.278 1.650 0.628 2.00e-02 2.50e+03 9.87e+02 bond pdb=" O4 LPP C 401 " pdb=" P1 LPP C 401 " ideal model delta sigma weight residual 1.764 1.510 0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" O4 LPP D 401 " pdb=" P1 LPP D 401 " ideal model delta sigma weight residual 1.764 1.511 0.253 2.00e-02 2.50e+03 1.60e+02 bond pdb=" C6 LPP C 401 " pdb=" O5 LPP C 401 " ideal model delta sigma weight residual 1.243 1.399 -0.156 2.00e-02 2.50e+03 6.09e+01 ... (remaining 8391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.32: 11348 9.32 - 18.64: 10 18.64 - 27.95: 2 27.95 - 37.27: 4 37.27 - 46.59: 2 Bond angle restraints: 11366 Sorted by residual: angle pdb=" O4 LPP D 401 " pdb=" P1 LPP D 401 " pdb=" O5 LPP D 401 " ideal model delta sigma weight residual 62.99 109.58 -46.59 3.00e+00 1.11e-01 2.41e+02 angle pdb=" O4 LPP C 401 " pdb=" P1 LPP C 401 " pdb=" O5 LPP C 401 " ideal model delta sigma weight residual 62.99 109.43 -46.44 3.00e+00 1.11e-01 2.40e+02 angle pdb=" C6 LPP C 401 " pdb=" O5 LPP C 401 " pdb=" P1 LPP C 401 " ideal model delta sigma weight residual 82.33 118.78 -36.45 3.00e+00 1.11e-01 1.48e+02 angle pdb=" C6 LPP D 401 " pdb=" O5 LPP D 401 " pdb=" P1 LPP D 401 " ideal model delta sigma weight residual 82.33 118.33 -36.00 3.00e+00 1.11e-01 1.44e+02 angle pdb=" O2 LPP C 401 " pdb=" P1 LPP C 401 " pdb=" O3 LPP C 401 " ideal model delta sigma weight residual 142.11 109.37 32.74 3.00e+00 1.11e-01 1.19e+02 ... (remaining 11361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 4429 17.23 - 34.46: 419 34.46 - 51.68: 156 51.68 - 68.91: 43 68.91 - 86.14: 13 Dihedral angle restraints: 5060 sinusoidal: 2080 harmonic: 2980 Sorted by residual: dihedral pdb=" CA ASP A 170 " pdb=" CB ASP A 170 " pdb=" CG ASP A 170 " pdb=" OD1 ASP A 170 " ideal model delta sinusoidal sigma weight residual -30.00 -87.20 57.20 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA ASN A 71 " pdb=" CB ASN A 71 " pdb=" CG ASN A 71 " pdb=" OD1 ASN A 71 " ideal model delta sinusoidal sigma weight residual -90.00 -160.40 70.40 2 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CG ARG D 213 " pdb=" CD ARG D 213 " pdb=" NE ARG D 213 " pdb=" CZ ARG D 213 " ideal model delta sinusoidal sigma weight residual 180.00 135.64 44.36 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 5057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1006 0.038 - 0.077: 225 0.077 - 0.115: 61 0.115 - 0.154: 10 0.154 - 0.192: 2 Chirality restraints: 1304 Sorted by residual: chirality pdb=" C7 LPP C 401 " pdb=" C6 LPP C 401 " pdb=" C8 LPP C 401 " pdb=" O9 LPP C 401 " both_signs ideal model delta sigma weight residual False -2.69 -2.50 -0.19 2.00e-01 2.50e+01 9.25e-01 chirality pdb=" C7 LPP D 401 " pdb=" C6 LPP D 401 " pdb=" C8 LPP D 401 " pdb=" O9 LPP D 401 " both_signs ideal model delta sigma weight residual False -2.69 -2.53 -0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CA ILE B 102 " pdb=" N ILE B 102 " pdb=" C ILE B 102 " pdb=" CB ILE B 102 " both_signs ideal model delta sigma weight residual False 2.43 2.29 0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 1301 not shown) Planarity restraints: 1444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 74 " 0.018 5.00e-02 4.00e+02 2.66e-02 1.14e+00 pdb=" N PRO A 75 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 74 " -0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO B 75 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 75 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 75 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 106 " 0.016 5.00e-02 4.00e+02 2.47e-02 9.78e-01 pdb=" N PRO D 107 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO D 107 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 107 " 0.014 5.00e-02 4.00e+02 ... (remaining 1441 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1896 2.79 - 3.32: 7936 3.32 - 3.85: 12975 3.85 - 4.37: 15371 4.37 - 4.90: 26244 Nonbonded interactions: 64422 Sorted by model distance: nonbonded pdb=" OE2 GLU A 181 " pdb=" OH TYR A 205 " model vdw 2.264 3.040 nonbonded pdb=" OG SER A 42 " pdb=" O1B ATP A 301 " model vdw 2.279 3.040 nonbonded pdb=" OD1 ASP C 121 " pdb=" OH TYR C 142 " model vdw 2.282 3.040 nonbonded pdb=" O ASP C 66 " pdb=" OG SER C 69 " model vdw 2.324 3.040 nonbonded pdb=" O VAL C 221 " pdb=" OG SER C 225 " model vdw 2.325 3.040 ... (remaining 64417 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.410 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.820 Find NCS groups from input model: 0.200 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:7.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 : 0.011 0.631 8396 Z= 0.556 Angle : 1.110 46.591 11366 Z= 0.411 Chirality : 0.037 0.192 1304 Planarity : 0.003 0.027 1444 Dihedral : 16.725 86.141 3148 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.63 % Favored : 98.27 % Rotamer: Outliers : 0.47 % Allowed : 15.35 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.26), residues: 1042 helix: 1.61 (0.20), residues: 640 sheet: 0.66 (0.51), residues: 114 loop : 0.03 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 15 TYR 0.011 0.001 TYR D 105 PHE 0.006 0.001 PHE B 76 TRP 0.005 0.001 TRP D 335 HIS 0.003 0.000 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.01118 ( 8396) covalent geometry : angle 1.11040 (11366) hydrogen bonds : bond 0.25100 ( 547) hydrogen bonds : angle 6.53865 ( 1593) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.8681 (pt0) cc_final: 0.8288 (pt0) REVERT: A 94 ARG cc_start: 0.8644 (mmm-85) cc_final: 0.8368 (mmm-85) REVERT: A 182 GLU cc_start: 0.9149 (tt0) cc_final: 0.8870 (tm-30) REVERT: A 207 MET cc_start: 0.8305 (tmm) cc_final: 0.7970 (tmm) REVERT: A 209 THR cc_start: 0.9291 (m) cc_final: 0.9055 (m) REVERT: B 25 MET cc_start: 0.9620 (mtp) cc_final: 0.9264 (mtp) REVERT: B 29 GLU cc_start: 0.8460 (tt0) cc_final: 0.7575 (pt0) REVERT: B 52 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8754 (mm-30) REVERT: B 207 MET cc_start: 0.9010 (mmm) cc_final: 0.8567 (tpt) REVERT: C 206 MET cc_start: 0.8518 (mtm) cc_final: 0.7814 (mpp) outliers start: 4 outliers final: 3 residues processed: 115 average time/residue: 0.7847 time to fit residues: 94.2256 Evaluate side-chains 109 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 295 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 50.0000 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 30.0000 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 133 ASN A 144 GLN B 19 GLN B 154 ASN D 183 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.125595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.071569 restraints weight = 15138.390| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.83 r_work: 0.2746 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8396 Z= 0.147 Angle : 0.547 7.377 11366 Z= 0.290 Chirality : 0.039 0.165 1304 Planarity : 0.003 0.028 1444 Dihedral : 11.844 87.175 1300 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.02 % Favored : 97.89 % Rotamer: Outliers : 3.26 % Allowed : 14.42 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.26), residues: 1042 helix: 2.46 (0.20), residues: 650 sheet: 0.19 (0.49), residues: 108 loop : -0.04 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 223 TYR 0.015 0.002 TYR D 105 PHE 0.008 0.001 PHE B 32 TRP 0.012 0.001 TRP C 335 HIS 0.003 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8396) covalent geometry : angle 0.54655 (11366) hydrogen bonds : bond 0.06686 ( 547) hydrogen bonds : angle 4.45251 ( 1593) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8190 (mm-30) REVERT: A 25 MET cc_start: 0.9446 (ttm) cc_final: 0.9165 (mtp) REVERT: A 29 GLU cc_start: 0.8605 (pt0) cc_final: 0.8253 (pt0) REVERT: A 73 GLU cc_start: 0.9128 (tp30) cc_final: 0.8447 (mp0) REVERT: A 94 ARG cc_start: 0.8350 (mmm-85) cc_final: 0.8043 (mmm-85) REVERT: A 123 ASP cc_start: 0.9089 (t0) cc_final: 0.8887 (t0) REVERT: A 133 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8523 (m-40) REVERT: A 142 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8246 (mt-10) REVERT: A 163 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8326 (mt0) REVERT: A 182 GLU cc_start: 0.9282 (tt0) cc_final: 0.8990 (tm-30) REVERT: A 198 ASN cc_start: 0.9244 (t0) cc_final: 0.8866 (t0) REVERT: A 207 MET cc_start: 0.8346 (tmm) cc_final: 0.7976 (tmm) REVERT: B 5 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8520 (mt-10) REVERT: B 25 MET cc_start: 0.9418 (mtp) cc_final: 0.9155 (mtp) REVERT: B 29 GLU cc_start: 0.8318 (tt0) cc_final: 0.7814 (tt0) REVERT: B 52 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8785 (mm-30) REVERT: B 174 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7327 (tm-30) REVERT: B 207 MET cc_start: 0.9041 (mmm) cc_final: 0.8573 (tpt) REVERT: C 206 MET cc_start: 0.8644 (mtm) cc_final: 0.7880 (mpp) REVERT: C 238 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8615 (mt) outliers start: 28 outliers final: 12 residues processed: 129 average time/residue: 0.7012 time to fit residues: 94.9397 Evaluate side-chains 125 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 295 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 48 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 93 optimal weight: 2.9990 chunk 27 optimal weight: 0.0030 chunk 78 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.125197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.070614 restraints weight = 15276.163| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.79 r_work: 0.2732 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 8396 Z= 0.187 Angle : 0.533 7.923 11366 Z= 0.277 Chirality : 0.039 0.159 1304 Planarity : 0.003 0.029 1444 Dihedral : 11.328 89.657 1300 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.11 % Favored : 97.79 % Rotamer: Outliers : 3.02 % Allowed : 15.70 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.26), residues: 1042 helix: 2.69 (0.20), residues: 650 sheet: -0.16 (0.47), residues: 108 loop : -0.09 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 251 TYR 0.016 0.001 TYR D 95 PHE 0.010 0.001 PHE B 76 TRP 0.011 0.001 TRP C 335 HIS 0.004 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 8396) covalent geometry : angle 0.53294 (11366) hydrogen bonds : bond 0.06151 ( 547) hydrogen bonds : angle 4.23558 ( 1593) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8300 (mm-30) REVERT: A 29 GLU cc_start: 0.8698 (pt0) cc_final: 0.8457 (pt0) REVERT: A 73 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8491 (mp0) REVERT: A 94 ARG cc_start: 0.8475 (mmm-85) cc_final: 0.8118 (mmm-85) REVERT: A 123 ASP cc_start: 0.9146 (t0) cc_final: 0.8907 (t0) REVERT: A 142 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8434 (mt-10) REVERT: A 163 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8464 (mt0) REVERT: A 181 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8767 (mm-30) REVERT: A 182 GLU cc_start: 0.9324 (tt0) cc_final: 0.9041 (tm-30) REVERT: A 198 ASN cc_start: 0.9313 (t0) cc_final: 0.8943 (t0) REVERT: A 207 MET cc_start: 0.8414 (tmm) cc_final: 0.8032 (tmm) REVERT: B 26 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7796 (mp10) REVERT: B 29 GLU cc_start: 0.8392 (tt0) cc_final: 0.7719 (tt0) REVERT: B 52 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8801 (mm-30) REVERT: B 60 TRP cc_start: 0.8874 (m-90) cc_final: 0.8463 (m100) REVERT: B 70 LYS cc_start: 0.8927 (mmmt) cc_final: 0.8584 (mppt) REVERT: B 163 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8202 (mt0) REVERT: B 174 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7582 (tm-30) REVERT: B 207 MET cc_start: 0.9047 (mmm) cc_final: 0.8622 (tpt) REVERT: C 206 MET cc_start: 0.8748 (mtm) cc_final: 0.7980 (mpp) REVERT: D 206 MET cc_start: 0.7717 (ppp) cc_final: 0.7433 (ppp) REVERT: D 312 LYS cc_start: 0.9312 (tppp) cc_final: 0.9051 (tppp) outliers start: 26 outliers final: 12 residues processed: 122 average time/residue: 0.7050 time to fit residues: 90.2688 Evaluate side-chains 123 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 295 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 20 optimal weight: 3.9990 chunk 56 optimal weight: 40.0000 chunk 49 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 95 optimal weight: 0.0980 chunk 58 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 154 ASN D 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.122607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.068926 restraints weight = 15519.473| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.65 r_work: 0.2698 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 8396 Z= 0.231 Angle : 0.543 7.639 11366 Z= 0.283 Chirality : 0.040 0.159 1304 Planarity : 0.003 0.032 1444 Dihedral : 10.878 87.730 1298 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 3.72 % Allowed : 15.58 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.26), residues: 1042 helix: 2.70 (0.20), residues: 650 sheet: -0.45 (0.46), residues: 108 loop : -0.17 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 251 TYR 0.017 0.001 TYR D 105 PHE 0.013 0.001 PHE B 76 TRP 0.012 0.001 TRP C 335 HIS 0.005 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00563 ( 8396) covalent geometry : angle 0.54349 (11366) hydrogen bonds : bond 0.06011 ( 547) hydrogen bonds : angle 4.13749 ( 1593) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8364 (mm-30) REVERT: A 29 GLU cc_start: 0.8696 (pt0) cc_final: 0.8404 (pt0) REVERT: A 73 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8453 (mp0) REVERT: A 94 ARG cc_start: 0.8528 (mmm-85) cc_final: 0.8170 (mmm-85) REVERT: A 123 ASP cc_start: 0.9179 (t0) cc_final: 0.8941 (t0) REVERT: A 142 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8485 (mt-10) REVERT: A 163 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8427 (mt0) REVERT: A 181 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8863 (mm-30) REVERT: A 182 GLU cc_start: 0.9342 (tt0) cc_final: 0.9029 (tm-30) REVERT: A 198 ASN cc_start: 0.9327 (t0) cc_final: 0.8955 (t0) REVERT: B 29 GLU cc_start: 0.8363 (tt0) cc_final: 0.7808 (tt0) REVERT: B 52 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8852 (mm-30) REVERT: B 60 TRP cc_start: 0.8843 (m-90) cc_final: 0.8510 (m100) REVERT: B 70 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8541 (mppt) REVERT: B 163 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8200 (mt0) REVERT: B 174 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7897 (tm-30) REVERT: B 207 MET cc_start: 0.8975 (mmm) cc_final: 0.8660 (tpp) REVERT: C 206 MET cc_start: 0.8723 (mtm) cc_final: 0.7939 (mpp) REVERT: C 238 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8758 (mt) outliers start: 32 outliers final: 15 residues processed: 125 average time/residue: 0.7292 time to fit residues: 95.6388 Evaluate side-chains 125 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 295 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 154 ASN B 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.126620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.072625 restraints weight = 15365.096| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.79 r_work: 0.2752 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8396 Z= 0.125 Angle : 0.498 6.976 11366 Z= 0.259 Chirality : 0.038 0.152 1304 Planarity : 0.003 0.030 1444 Dihedral : 10.649 88.014 1298 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 2.91 % Allowed : 16.16 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.26), residues: 1042 helix: 2.98 (0.20), residues: 650 sheet: -0.54 (0.46), residues: 108 loop : -0.11 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 72 TYR 0.019 0.001 TYR D 95 PHE 0.007 0.001 PHE B 4 TRP 0.013 0.001 TRP C 335 HIS 0.003 0.000 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8396) covalent geometry : angle 0.49786 (11366) hydrogen bonds : bond 0.05025 ( 547) hydrogen bonds : angle 3.84204 ( 1593) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8354 (mm-30) REVERT: A 29 GLU cc_start: 0.8704 (pt0) cc_final: 0.8395 (pt0) REVERT: A 73 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8491 (mp0) REVERT: A 94 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8054 (mmm-85) REVERT: A 123 ASP cc_start: 0.9163 (t0) cc_final: 0.8951 (t0) REVERT: A 142 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8427 (mt-10) REVERT: A 163 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8416 (mt0) REVERT: A 181 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8874 (mt-10) REVERT: A 182 GLU cc_start: 0.9322 (tt0) cc_final: 0.9029 (tm-30) REVERT: A 198 ASN cc_start: 0.9319 (t0) cc_final: 0.8954 (t0) REVERT: A 207 MET cc_start: 0.9110 (tpt) cc_final: 0.8783 (tmm) REVERT: B 25 MET cc_start: 0.9218 (mtp) cc_final: 0.8637 (ttm) REVERT: B 29 GLU cc_start: 0.8299 (tt0) cc_final: 0.7750 (tm-30) REVERT: B 60 TRP cc_start: 0.8823 (m-90) cc_final: 0.8516 (m100) REVERT: B 70 LYS cc_start: 0.8833 (mmmt) cc_final: 0.8480 (mppt) REVERT: B 163 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8275 (mt0) REVERT: B 174 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7889 (tm-30) REVERT: B 207 MET cc_start: 0.9024 (mmm) cc_final: 0.8570 (tpt) REVERT: C 206 MET cc_start: 0.8753 (mtm) cc_final: 0.8003 (mpp) REVERT: D 206 MET cc_start: 0.7882 (ppp) cc_final: 0.7653 (ppp) REVERT: D 332 MET cc_start: 0.8821 (mtm) cc_final: 0.8453 (mmp) outliers start: 25 outliers final: 10 residues processed: 123 average time/residue: 0.7023 time to fit residues: 90.6210 Evaluate side-chains 123 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 253 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 56 optimal weight: 30.0000 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 19 GLN B 154 ASN B 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.123620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.069229 restraints weight = 15381.747| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.88 r_work: 0.2715 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 8396 Z= 0.234 Angle : 0.551 7.177 11366 Z= 0.285 Chirality : 0.039 0.159 1304 Planarity : 0.003 0.034 1444 Dihedral : 10.415 87.590 1297 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.30 % Favored : 97.60 % Rotamer: Outliers : 3.02 % Allowed : 16.51 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.26), residues: 1042 helix: 2.91 (0.20), residues: 650 sheet: -0.67 (0.46), residues: 108 loop : -0.18 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.018 0.001 TYR D 105 PHE 0.019 0.001 PHE D 211 TRP 0.011 0.001 TRP C 335 HIS 0.005 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00573 ( 8396) covalent geometry : angle 0.55067 (11366) hydrogen bonds : bond 0.05547 ( 547) hydrogen bonds : angle 3.94480 ( 1593) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8379 (mm-30) REVERT: A 29 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8372 (pt0) REVERT: A 73 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8425 (mp0) REVERT: A 94 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8127 (mmm-85) REVERT: A 142 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8478 (mt-10) REVERT: A 163 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8436 (mt0) REVERT: A 181 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8839 (mm-30) REVERT: A 182 GLU cc_start: 0.9326 (tt0) cc_final: 0.9041 (tm-30) REVERT: A 198 ASN cc_start: 0.9340 (t0) cc_final: 0.8966 (t0) REVERT: A 207 MET cc_start: 0.9077 (tpt) cc_final: 0.8802 (tmm) REVERT: B 19 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8410 (mm110) REVERT: B 29 GLU cc_start: 0.8292 (tt0) cc_final: 0.7726 (tt0) REVERT: B 60 TRP cc_start: 0.8777 (m-90) cc_final: 0.8101 (m100) REVERT: B 70 LYS cc_start: 0.8880 (mmmt) cc_final: 0.8540 (mppt) REVERT: B 163 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8345 (mt0) REVERT: B 174 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7895 (tm-30) REVERT: B 207 MET cc_start: 0.8984 (mmm) cc_final: 0.8634 (tpp) REVERT: C 206 MET cc_start: 0.8782 (mtm) cc_final: 0.8059 (mpp) REVERT: D 332 MET cc_start: 0.8833 (mtm) cc_final: 0.8470 (mmp) outliers start: 26 outliers final: 11 residues processed: 117 average time/residue: 0.7610 time to fit residues: 93.0365 Evaluate side-chains 123 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 253 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 99 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 50.0000 chunk 50 optimal weight: 40.0000 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 19 GLN B 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.122578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.069894 restraints weight = 15506.471| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.51 r_work: 0.2708 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 8396 Z= 0.231 Angle : 0.567 7.555 11366 Z= 0.291 Chirality : 0.039 0.158 1304 Planarity : 0.003 0.034 1444 Dihedral : 10.429 87.776 1297 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 3.72 % Allowed : 16.40 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.26), residues: 1042 helix: 2.88 (0.20), residues: 650 sheet: -0.78 (0.45), residues: 108 loop : -0.21 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.019 0.001 TYR D 95 PHE 0.020 0.001 PHE D 211 TRP 0.012 0.001 TRP C 335 HIS 0.004 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 8396) covalent geometry : angle 0.56748 (11366) hydrogen bonds : bond 0.05612 ( 547) hydrogen bonds : angle 3.94898 ( 1593) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8453 (mm-30) REVERT: A 29 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8373 (pt0) REVERT: A 30 MET cc_start: 0.9084 (ptm) cc_final: 0.8746 (ttt) REVERT: A 73 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8434 (mp0) REVERT: A 94 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8146 (mmm-85) REVERT: A 142 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8480 (mt-10) REVERT: A 163 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8437 (mt0) REVERT: A 181 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8765 (mm-30) REVERT: A 182 GLU cc_start: 0.9325 (tt0) cc_final: 0.9045 (tm-30) REVERT: A 198 ASN cc_start: 0.9343 (t0) cc_final: 0.8964 (t0) REVERT: A 207 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8858 (tpt) REVERT: B 19 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8484 (mm110) REVERT: B 29 GLU cc_start: 0.8395 (tt0) cc_final: 0.7996 (tt0) REVERT: B 60 TRP cc_start: 0.8771 (m-90) cc_final: 0.8112 (m100) REVERT: B 70 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8545 (mppt) REVERT: B 163 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8233 (mt0) REVERT: B 174 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7892 (tm-30) REVERT: B 207 MET cc_start: 0.8954 (mmm) cc_final: 0.8586 (tpp) REVERT: C 206 MET cc_start: 0.8719 (mtm) cc_final: 0.7966 (mpp) REVERT: D 312 LYS cc_start: 0.9307 (tppp) cc_final: 0.8886 (tppt) REVERT: D 332 MET cc_start: 0.8834 (mtm) cc_final: 0.8479 (mmp) outliers start: 32 outliers final: 18 residues processed: 122 average time/residue: 0.7429 time to fit residues: 94.8006 Evaluate side-chains 129 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 328 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 66 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 86 optimal weight: 30.0000 chunk 18 optimal weight: 0.6980 chunk 81 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 19 GLN B 154 ASN C 141 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.123149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.069807 restraints weight = 15384.040| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.63 r_work: 0.2725 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8396 Z= 0.162 Angle : 0.539 8.972 11366 Z= 0.277 Chirality : 0.038 0.154 1304 Planarity : 0.003 0.032 1444 Dihedral : 10.397 87.887 1297 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 3.49 % Allowed : 16.74 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.26), residues: 1042 helix: 2.99 (0.20), residues: 648 sheet: -0.75 (0.45), residues: 104 loop : -0.26 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 72 TYR 0.017 0.001 TYR D 105 PHE 0.022 0.001 PHE D 211 TRP 0.012 0.001 TRP C 335 HIS 0.003 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8396) covalent geometry : angle 0.53918 (11366) hydrogen bonds : bond 0.05273 ( 547) hydrogen bonds : angle 3.82828 ( 1593) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8455 (mm-30) REVERT: A 29 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8372 (pt0) REVERT: A 73 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8420 (mp0) REVERT: A 94 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8069 (mmm-85) REVERT: A 142 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8433 (mt-10) REVERT: A 163 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8419 (mt0) REVERT: A 182 GLU cc_start: 0.9319 (tt0) cc_final: 0.9041 (tm-30) REVERT: A 198 ASN cc_start: 0.9344 (t0) cc_final: 0.8954 (t0) REVERT: A 207 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8821 (tpt) REVERT: B 5 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8173 (mp0) REVERT: B 19 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8591 (mm110) REVERT: B 25 MET cc_start: 0.9358 (mtp) cc_final: 0.8524 (ttp) REVERT: B 29 GLU cc_start: 0.8366 (tt0) cc_final: 0.7903 (tm-30) REVERT: B 60 TRP cc_start: 0.8749 (m-90) cc_final: 0.8516 (m100) REVERT: B 70 LYS cc_start: 0.8863 (mmmt) cc_final: 0.8496 (mppt) REVERT: B 163 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8213 (mt0) REVERT: B 174 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7817 (tm-30) REVERT: B 207 MET cc_start: 0.8972 (mmm) cc_final: 0.8667 (tpp) REVERT: C 206 MET cc_start: 0.8724 (mtm) cc_final: 0.7963 (mpp) REVERT: D 206 MET cc_start: 0.7557 (ppp) cc_final: 0.7351 (ppp) REVERT: D 312 LYS cc_start: 0.9354 (tppp) cc_final: 0.8955 (tppt) REVERT: D 332 MET cc_start: 0.8836 (mtm) cc_final: 0.8473 (mmp) outliers start: 30 outliers final: 17 residues processed: 121 average time/residue: 0.7098 time to fit residues: 90.0720 Evaluate side-chains 131 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 253 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 53 optimal weight: 50.0000 chunk 20 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 19 GLN B 154 ASN B 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.122703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.068140 restraints weight = 15589.549| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.86 r_work: 0.2695 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 8396 Z= 0.283 Angle : 0.610 9.700 11366 Z= 0.311 Chirality : 0.041 0.161 1304 Planarity : 0.003 0.035 1444 Dihedral : 10.397 87.922 1297 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.50 % Favored : 97.41 % Rotamer: Outliers : 3.84 % Allowed : 16.51 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.26), residues: 1042 helix: 2.86 (0.20), residues: 648 sheet: -0.84 (0.44), residues: 104 loop : -0.35 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 251 TYR 0.020 0.002 TYR D 95 PHE 0.021 0.002 PHE D 211 TRP 0.012 0.001 TRP C 335 HIS 0.005 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00695 ( 8396) covalent geometry : angle 0.61029 (11366) hydrogen bonds : bond 0.05767 ( 547) hydrogen bonds : angle 3.97165 ( 1593) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8450 (mm-30) REVERT: A 29 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8416 (pt0) REVERT: A 73 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8446 (mp0) REVERT: A 94 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8162 (mmm-85) REVERT: A 163 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8461 (mt0) REVERT: A 181 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8814 (mm-30) REVERT: A 182 GLU cc_start: 0.9320 (tt0) cc_final: 0.9049 (tm-30) REVERT: A 198 ASN cc_start: 0.9353 (t0) cc_final: 0.8971 (t0) REVERT: A 207 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8830 (tpt) REVERT: B 5 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8233 (mp0) REVERT: B 19 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8559 (mm110) REVERT: B 29 GLU cc_start: 0.8361 (tt0) cc_final: 0.7890 (tt0) REVERT: B 60 TRP cc_start: 0.8757 (m-90) cc_final: 0.8083 (m100) REVERT: B 70 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8530 (mppt) REVERT: B 163 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8313 (mt0) REVERT: B 174 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7984 (tm-30) REVERT: B 207 MET cc_start: 0.8972 (mmm) cc_final: 0.8681 (tpp) REVERT: C 206 MET cc_start: 0.8751 (mtm) cc_final: 0.7980 (mpp) REVERT: C 311 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8806 (t) REVERT: D 206 MET cc_start: 0.7717 (ppp) cc_final: 0.7515 (ppp) REVERT: D 312 LYS cc_start: 0.9411 (tppp) cc_final: 0.9194 (tppp) REVERT: D 332 MET cc_start: 0.8871 (mtm) cc_final: 0.8498 (mmp) outliers start: 33 outliers final: 17 residues processed: 121 average time/residue: 0.7160 time to fit residues: 90.8929 Evaluate side-chains 127 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 302 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 19 GLN B 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.125211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.070833 restraints weight = 15347.642| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.80 r_work: 0.2736 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8396 Z= 0.141 Angle : 0.558 10.403 11366 Z= 0.285 Chirality : 0.038 0.151 1304 Planarity : 0.003 0.034 1444 Dihedral : 10.365 89.375 1297 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.40 % Favored : 97.50 % Rotamer: Outliers : 2.67 % Allowed : 17.67 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.26), residues: 1042 helix: 3.01 (0.20), residues: 648 sheet: -0.87 (0.44), residues: 114 loop : -0.27 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 72 TYR 0.013 0.001 TYR D 105 PHE 0.025 0.001 PHE D 211 TRP 0.012 0.001 TRP C 335 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8396) covalent geometry : angle 0.55848 (11366) hydrogen bonds : bond 0.05109 ( 547) hydrogen bonds : angle 3.81129 ( 1593) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8452 (mm-30) REVERT: A 25 MET cc_start: 0.9405 (ttm) cc_final: 0.8395 (mtp) REVERT: A 29 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8121 (pp20) REVERT: A 73 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: A 94 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8041 (mmm-85) REVERT: A 163 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8415 (mt0) REVERT: A 181 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8793 (mm-30) REVERT: A 182 GLU cc_start: 0.9313 (tt0) cc_final: 0.9035 (tm-30) REVERT: A 198 ASN cc_start: 0.9350 (t0) cc_final: 0.8960 (t0) REVERT: A 207 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8831 (tpt) REVERT: B 5 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8185 (mp0) REVERT: B 19 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8564 (mm110) REVERT: B 25 MET cc_start: 0.9295 (mtp) cc_final: 0.8527 (ttp) REVERT: B 29 GLU cc_start: 0.8313 (tt0) cc_final: 0.7891 (tm-30) REVERT: B 174 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7852 (tm-30) REVERT: B 207 MET cc_start: 0.8983 (mmm) cc_final: 0.8660 (tpp) REVERT: C 206 MET cc_start: 0.8797 (mtm) cc_final: 0.8038 (mpp) REVERT: C 311 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8811 (t) REVERT: D 206 MET cc_start: 0.7763 (ppp) cc_final: 0.7560 (ppp) REVERT: D 312 LYS cc_start: 0.9417 (tppp) cc_final: 0.9206 (tppp) REVERT: D 332 MET cc_start: 0.8843 (mtm) cc_final: 0.8454 (mmp) outliers start: 23 outliers final: 14 residues processed: 114 average time/residue: 0.7278 time to fit residues: 86.8557 Evaluate side-chains 123 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 253 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN B 154 ASN B 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.125065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.070684 restraints weight = 15457.626| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.88 r_work: 0.2729 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 8396 Z= 0.249 Angle : 1.177 59.200 11366 Z= 0.631 Chirality : 0.048 0.995 1304 Planarity : 0.004 0.108 1444 Dihedral : 10.385 89.379 1297 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.50 % Favored : 97.41 % Rotamer: Outliers : 2.56 % Allowed : 17.44 % Favored : 80.00 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.26), residues: 1042 helix: 2.99 (0.20), residues: 648 sheet: -0.87 (0.44), residues: 114 loop : -0.27 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 94 TYR 0.011 0.001 TYR D 105 PHE 0.023 0.001 PHE D 211 TRP 0.012 0.001 TRP C 335 HIS 0.005 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 8396) covalent geometry : angle 1.17664 (11366) hydrogen bonds : bond 0.05211 ( 547) hydrogen bonds : angle 3.82183 ( 1593) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3607.07 seconds wall clock time: 61 minutes 59.75 seconds (3719.75 seconds total)