Starting phenix.real_space_refine on Thu Jul 2 09:34:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9enb_19830/07_2026/9enb_19830.cif Found real_map, /net/cci-nas-00/data/ceres_data/9enb_19830/07_2026/9enb_19830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9enb_19830/07_2026/9enb_19830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9enb_19830/07_2026/9enb_19830.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9enb_19830/07_2026/9enb_19830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9enb_19830/07_2026/9enb_19830.map" } resolution = 2.66 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= 0.036 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: 6 Type Number sf(0) Gaussians P 142 5.49 5 Mg 6 5.21 5 S 34 5.16 5 C 4700 2.51 5 N 1440 2.21 5 O 1942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8264 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2602 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 3 Chain: "B" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2602 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 3 Chain: "C" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1527 Classifications: {'RNA': 72} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 29, 'rna3p_pyr': 31} Link IDs: {'rna2p': 12, 'rna3p': 59} Chain: "D" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1527 Classifications: {'RNA': 72} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 30, 'rna3p_pyr': 30} Link IDs: {'rna2p': 12, 'rna3p': 59} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.59, per 1000 atoms: 0.19 Number of scatterers: 8264 At special positions: 0 Unit cell: (104.009, 131.068, 68.4936, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 142 15.00 Mg 6 11.99 O 1942 8.00 N 1440 7.00 C 4700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS A 327 " distance=2.04 Simple disulfide: pdb=" SG CYS B 114 " - pdb=" SG CYS B 327 " distance=2.04 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: 0.58 Conformation dependent library (CDL) restraints added in 290.4 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1208 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 4 sheets defined 36.6% alpha, 24.2% beta 45 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 removed outlier: 3.725A pdb=" N ALA A 59 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS A 60 " --> pdb=" O PHE A 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 60' Processing helix chain 'A' and resid 72 through 76 removed outlier: 4.442A pdb=" N GLY A 75 " --> pdb=" O MET A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 100 removed outlier: 3.514A pdb=" N LYS A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.531A pdb=" N SER A 109 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 168 removed outlier: 4.059A pdb=" N VAL A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 223 through 226 removed outlier: 4.248A pdb=" N CYS A 226 " --> pdb=" O ARG A 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 226' Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 277 through 291 removed outlier: 3.536A pdb=" N LEU A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 303 removed outlier: 3.577A pdb=" N GLU A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 369 Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.723A pdb=" N ALA B 59 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B 60 " --> pdb=" O PHE B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 60' Processing helix chain 'B' and resid 72 through 76 removed outlier: 4.425A pdb=" N GLY B 75 " --> pdb=" O MET B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 100 removed outlier: 3.564A pdb=" N LYS B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.501A pdb=" N THR B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 168 removed outlier: 4.046A pdb=" N VAL B 167 " --> pdb=" O ILE B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 removed outlier: 3.553A pdb=" N GLN B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 226 removed outlier: 4.206A pdb=" N CYS B 226 " --> pdb=" O ARG B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 259 through 262 Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.534A pdb=" N LEU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 303 removed outlier: 3.526A pdb=" N GLU B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 369 Processing helix chain 'B' and resid 413 through 417 Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113 removed outlier: 5.269A pdb=" N PHE A 124 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR A 71 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY A 61 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N HIS A 64 " --> pdb=" O PRO A 179 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA A 66 " --> pdb=" O TRP A 177 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TRP A 177 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG A 68 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113 removed outlier: 6.426A pdb=" N ASP A 326 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN A 126 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N LYS A 328 " --> pdb=" O GLN A 126 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N ILE A 128 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR A 194 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS A 327 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU A 192 " --> pdb=" O CYS A 327 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU A 264 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU A 248 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLN A 266 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL A 246 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU A 268 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA A 244 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR A 270 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 113 removed outlier: 5.349A pdb=" N PHE B 124 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR B 71 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B 61 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N HIS B 64 " --> pdb=" O PRO B 179 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA B 66 " --> pdb=" O TRP B 177 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TRP B 177 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG B 68 " --> pdb=" O LEU B 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 113 removed outlier: 6.447A pdb=" N ASP B 326 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLN B 126 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N LYS B 328 " --> pdb=" O GLN B 126 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N ILE B 128 " --> pdb=" O LYS B 328 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR B 194 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS B 327 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU B 192 " --> pdb=" O CYS B 327 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU B 264 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU B 248 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN B 266 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL B 246 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU B 268 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA B 244 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR B 270 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 239 " --> pdb=" O HIS B 220 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 534 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 118 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1876 1.33 - 1.45: 2667 1.45 - 1.57: 3859 1.57 - 1.69: 284 1.69 - 1.81: 54 Bond restraints: 8740 Sorted by residual: bond pdb=" N1 C D 27 " pdb=" C6 C D 27 " ideal model delta sigma weight residual 1.367 1.356 0.011 6.00e-03 2.78e+04 3.66e+00 bond pdb=" N1 C C 27 " pdb=" C6 C C 27 " ideal model delta sigma weight residual 1.367 1.356 0.011 6.00e-03 2.78e+04 3.63e+00 bond pdb=" C5 G C 29 " pdb=" C4 G C 29 " ideal model delta sigma weight residual 1.379 1.366 0.013 7.00e-03 2.04e+04 3.28e+00 bond pdb=" C5 G D 29 " pdb=" C4 G D 29 " ideal model delta sigma weight residual 1.379 1.367 0.012 7.00e-03 2.04e+04 2.82e+00 bond pdb=" N7 A C 58 " pdb=" C5 A C 58 " ideal model delta sigma weight residual 1.388 1.378 0.010 6.00e-03 2.78e+04 2.80e+00 ... (remaining 8735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 12031 1.23 - 2.46: 391 2.46 - 3.69: 68 3.69 - 4.92: 16 4.92 - 6.15: 4 Bond angle restraints: 12510 Sorted by residual: angle pdb=" C1' C C 48 " pdb=" N1 C C 48 " pdb=" C2 C C 48 " ideal model delta sigma weight residual 118.80 124.64 -5.84 1.10e+00 8.26e-01 2.82e+01 angle pdb=" C1' C D 48 " pdb=" N1 C D 48 " pdb=" C2 C D 48 " ideal model delta sigma weight residual 118.80 124.62 -5.82 1.10e+00 8.26e-01 2.80e+01 angle pdb=" N1 C C 48 " pdb=" C2 C C 48 " pdb=" O2 C C 48 " ideal model delta sigma weight residual 118.90 121.84 -2.94 6.00e-01 2.78e+00 2.40e+01 angle pdb=" N1 C D 48 " pdb=" C2 C D 48 " pdb=" O2 C D 48 " ideal model delta sigma weight residual 118.90 121.81 -2.91 6.00e-01 2.78e+00 2.35e+01 angle pdb=" O2 C C 48 " pdb=" C2 C C 48 " pdb=" N3 C C 48 " ideal model delta sigma weight residual 121.90 118.78 3.12 7.00e-01 2.04e+00 1.99e+01 ... (remaining 12505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 4977 35.54 - 71.08: 401 71.08 - 106.62: 56 106.62 - 142.16: 3 142.16 - 177.70: 5 Dihedral angle restraints: 5442 sinusoidal: 3578 harmonic: 1864 Sorted by residual: dihedral pdb=" O4' C C 48 " pdb=" C1' C C 48 " pdb=" N1 C C 48 " pdb=" C2 C C 48 " ideal model delta sinusoidal sigma weight residual -160.00 -8.90 -151.10 1 1.50e+01 4.44e-03 8.00e+01 dihedral pdb=" O4' C D 48 " pdb=" C1' C D 48 " pdb=" N1 C D 48 " pdb=" C2 C D 48 " ideal model delta sinusoidal sigma weight residual -160.00 -9.07 -150.93 1 1.50e+01 4.44e-03 8.00e+01 dihedral pdb=" O4' U C 34 " pdb=" C1' U C 34 " pdb=" N1 U C 34 " pdb=" C2 U C 34 " ideal model delta sinusoidal sigma weight residual -128.00 48.64 -176.64 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 5439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1217 0.048 - 0.096: 214 0.096 - 0.145: 47 0.145 - 0.193: 2 0.193 - 0.241: 2 Chirality restraints: 1482 Sorted by residual: chirality pdb=" C1' A D 38 " pdb=" O4' A D 38 " pdb=" C2' A D 38 " pdb=" N9 A D 38 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1' U C 39 " pdb=" O4' U C 39 " pdb=" C2' U C 39 " pdb=" N1 U C 39 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA PHE A 320 " pdb=" N PHE A 320 " pdb=" C PHE A 320 " pdb=" CB PHE A 320 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.97e-01 ... (remaining 1479 not shown) Planarity restraints: 1076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D 38 " -0.027 2.00e-02 2.50e+03 1.35e-02 5.03e+00 pdb=" N9 A D 38 " 0.035 2.00e-02 2.50e+03 pdb=" C8 A D 38 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A D 38 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A D 38 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A D 38 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A D 38 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A D 38 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A D 38 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A D 38 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A D 38 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 39 " 0.022 2.00e-02 2.50e+03 1.33e-02 3.97e+00 pdb=" N1 U C 39 " -0.032 2.00e-02 2.50e+03 pdb=" C2 U C 39 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U C 39 " 0.000 2.00e-02 2.50e+03 pdb=" N3 U C 39 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U C 39 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U C 39 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U C 39 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U C 39 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 320 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO B 321 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 321 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 321 " -0.024 5.00e-02 4.00e+02 ... (remaining 1073 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 429 2.70 - 3.25: 7178 3.25 - 3.80: 14293 3.80 - 4.35: 18866 4.35 - 4.90: 28528 Nonbonded interactions: 69294 Sorted by model distance: nonbonded pdb=" OP2 G D 9 " pdb="MG MG D 102 " model vdw 2.149 2.170 nonbonded pdb=" OP2 G C 9 " pdb="MG MG C 102 " model vdw 2.162 2.170 nonbonded pdb=" OE2 GLU B 294 " pdb=" OH TYR B 411 " model vdw 2.225 3.040 nonbonded pdb=" O2' G C 36 " pdb=" OP2 A C 37 " model vdw 2.244 3.040 nonbonded pdb=" OE2 GLU A 294 " pdb=" OH TYR A 411 " model vdw 2.250 3.040 ... (remaining 69289 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.860 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 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 : 0.006 0.042 8742 Z= 0.382 Angle : 0.554 6.147 12514 Z= 0.415 Chirality : 0.039 0.241 1482 Planarity : 0.004 0.042 1076 Dihedral : 22.369 177.702 4228 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.72 % Allowed : 25.27 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.33), residues: 620 helix: 0.93 (0.39), residues: 166 sheet: 1.03 (0.56), residues: 82 loop : -0.78 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 133 TYR 0.009 0.001 TYR A 216 PHE 0.016 0.001 PHE B 320 TRP 0.012 0.001 TRP B 74 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.38 ( 8740) covalent geometry : angle 0.55386 / 0.41 (12510) SS BOND : bond 0.00888 / 0.44 ( 2) SS BOND : angle 1.17487 / 0.61 ( 4) hydrogen bonds : bond 0.17213 / 11.60 ( 313) hydrogen bonds : angle 5.56689 / 3.79 ( 742) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.159 Fit side-chains REVERT: A 259 GLN cc_start: 0.7892 (mt0) cc_final: 0.7497 (mt0) REVERT: A 412 LYS cc_start: 0.7486 (ttpp) cc_final: 0.7278 (ttpp) REVERT: B 72 MET cc_start: 0.8292 (mmm) cc_final: 0.7783 (mmm) outliers start: 4 outliers final: 3 residues processed: 30 average time/residue: 0.5749 time to fit residues: 18.3411 Evaluate side-chains 28 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 415 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.092040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.063870 restraints weight = 17709.903| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.16 r_work: 0.2894 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.0523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8742 Z= 0.165 Angle : 0.499 6.372 12514 Z= 0.288 Chirality : 0.038 0.256 1482 Planarity : 0.004 0.040 1076 Dihedral : 22.186 177.635 2954 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.15 % Allowed : 22.58 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.33), residues: 620 helix: 1.51 (0.40), residues: 166 sheet: 1.65 (0.56), residues: 72 loop : -0.66 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 106 TYR 0.007 0.001 TYR B 197 PHE 0.018 0.001 PHE B 320 TRP 0.006 0.001 TRP B 74 HIS 0.006 0.002 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 8740) covalent geometry : angle 0.49846 / 0.29 (12510) SS BOND : bond 0.00727 / 0.36 ( 2) SS BOND : angle 1.01737 / 0.52 ( 4) hydrogen bonds : bond 0.06708 / 4.55 ( 313) hydrogen bonds : angle 4.11198 / 2.84 ( 742) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.264 Fit side-chains REVERT: A 259 GLN cc_start: 0.8513 (mt0) cc_final: 0.7760 (mt0) REVERT: A 412 LYS cc_start: 0.7322 (ttpp) cc_final: 0.7102 (ttpp) REVERT: B 72 MET cc_start: 0.8710 (mmm) cc_final: 0.8276 (mmm) outliers start: 12 outliers final: 2 residues processed: 36 average time/residue: 0.5639 time to fit residues: 21.8844 Evaluate side-chains 28 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 230 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.093290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.064861 restraints weight = 17606.578| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.24 r_work: 0.2916 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8742 Z= 0.126 Angle : 0.462 7.543 12514 Z= 0.265 Chirality : 0.036 0.256 1482 Planarity : 0.004 0.040 1076 Dihedral : 22.134 177.075 2948 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.97 % Allowed : 22.76 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.33), residues: 620 helix: 1.79 (0.39), residues: 166 sheet: 1.60 (0.59), residues: 60 loop : -0.66 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 193 TYR 0.006 0.001 TYR A 216 PHE 0.016 0.001 PHE B 320 TRP 0.008 0.001 TRP B 74 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 8740) covalent geometry : angle 0.46135 / 0.27 (12510) SS BOND : bond 0.00701 / 0.35 ( 2) SS BOND : angle 0.98428 / 0.51 ( 4) hydrogen bonds : bond 0.05767 / 3.90 ( 313) hydrogen bonds : angle 3.78308 / 2.62 ( 742) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.263 Fit side-chains REVERT: A 259 GLN cc_start: 0.8513 (mt0) cc_final: 0.7804 (mt0) REVERT: B 72 MET cc_start: 0.8646 (mmm) cc_final: 0.8150 (mmm) outliers start: 11 outliers final: 2 residues processed: 34 average time/residue: 0.5439 time to fit residues: 19.9761 Evaluate side-chains 28 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain B residue 74 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 67 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.091041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.062689 restraints weight = 18038.823| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.18 r_work: 0.2856 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.0666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8742 Z= 0.279 Angle : 0.547 6.262 12514 Z= 0.312 Chirality : 0.042 0.248 1482 Planarity : 0.004 0.047 1076 Dihedral : 22.105 177.087 2948 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.61 % Allowed : 24.01 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.33), residues: 620 helix: 1.50 (0.38), residues: 166 sheet: 1.50 (0.53), residues: 72 loop : -0.67 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 133 TYR 0.012 0.001 TYR A 216 PHE 0.019 0.002 PHE A 94 TRP 0.007 0.001 TRP B 74 HIS 0.004 0.002 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.28 ( 8740) covalent geometry : angle 0.54650 / 0.31 (12510) SS BOND : bond 0.01154 / 0.58 ( 2) SS BOND : angle 1.45352 / 0.75 ( 4) hydrogen bonds : bond 0.07059 / 4.76 ( 313) hydrogen bonds : angle 3.91257 / 2.70 ( 742) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.244 Fit side-chains REVERT: A 259 GLN cc_start: 0.8392 (mt0) cc_final: 0.7726 (mt0) REVERT: B 72 MET cc_start: 0.8741 (mmm) cc_final: 0.8113 (mmm) outliers start: 9 outliers final: 4 residues processed: 32 average time/residue: 0.5382 time to fit residues: 18.5727 Evaluate side-chains 29 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 71 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.093384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.064934 restraints weight = 17720.046| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.23 r_work: 0.2920 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8742 Z= 0.120 Angle : 0.453 7.023 12514 Z= 0.262 Chirality : 0.036 0.261 1482 Planarity : 0.004 0.041 1076 Dihedral : 22.125 176.747 2948 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.72 % Allowed : 24.37 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.33), residues: 620 helix: 1.79 (0.38), residues: 166 sheet: 1.59 (0.59), residues: 60 loop : -0.65 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 166 TYR 0.006 0.001 TYR A 197 PHE 0.016 0.001 PHE B 320 TRP 0.008 0.001 TRP B 74 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 8740) covalent geometry : angle 0.45322 / 0.26 (12510) SS BOND : bond 0.00695 / 0.35 ( 2) SS BOND : angle 0.98960 / 0.51 ( 4) hydrogen bonds : bond 0.05636 / 3.81 ( 313) hydrogen bonds : angle 3.67878 / 2.55 ( 742) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.244 Fit side-chains REVERT: A 259 GLN cc_start: 0.8457 (mt0) cc_final: 0.7818 (mt0) REVERT: B 72 MET cc_start: 0.8671 (mmm) cc_final: 0.8067 (mmm) outliers start: 4 outliers final: 1 residues processed: 29 average time/residue: 0.6471 time to fit residues: 20.1188 Evaluate side-chains 26 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.091570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.063218 restraints weight = 17595.409| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.16 r_work: 0.2876 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8742 Z= 0.239 Angle : 0.512 6.193 12514 Z= 0.292 Chirality : 0.040 0.249 1482 Planarity : 0.004 0.046 1076 Dihedral : 22.070 176.877 2948 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.25 % Allowed : 24.37 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.33), residues: 620 helix: 1.63 (0.38), residues: 166 sheet: 1.50 (0.55), residues: 64 loop : -0.66 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 187 TYR 0.011 0.001 TYR A 216 PHE 0.018 0.002 PHE A 94 TRP 0.007 0.001 TRP B 74 HIS 0.004 0.002 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.24 ( 8740) covalent geometry : angle 0.51107 / 0.29 (12510) SS BOND : bond 0.01041 / 0.52 ( 2) SS BOND : angle 1.30959 / 0.67 ( 4) hydrogen bonds : bond 0.06506 / 4.39 ( 313) hydrogen bonds : angle 3.76279 / 2.60 ( 742) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.309 Fit side-chains REVERT: A 72 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8431 (mtp) REVERT: A 259 GLN cc_start: 0.8420 (mt0) cc_final: 0.7780 (mt0) REVERT: B 72 MET cc_start: 0.8724 (mmm) cc_final: 0.8036 (mmm) outliers start: 7 outliers final: 4 residues processed: 28 average time/residue: 0.6030 time to fit residues: 18.1610 Evaluate side-chains 29 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 415 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 62 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 0.0570 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.093027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.064453 restraints weight = 17882.423| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.25 r_work: 0.2907 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8742 Z= 0.132 Angle : 0.453 5.887 12514 Z= 0.262 Chirality : 0.037 0.256 1482 Planarity : 0.004 0.041 1076 Dihedral : 22.090 176.689 2948 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.08 % Allowed : 24.91 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.33), residues: 620 helix: 1.81 (0.38), residues: 166 sheet: 1.62 (0.59), residues: 60 loop : -0.64 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 68 TYR 0.005 0.001 TYR A 197 PHE 0.017 0.001 PHE B 320 TRP 0.008 0.001 TRP B 74 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8740) covalent geometry : angle 0.45256 / 0.26 (12510) SS BOND : bond 0.00736 / 0.37 ( 2) SS BOND : angle 0.99515 / 0.51 ( 4) hydrogen bonds : bond 0.05668 / 3.84 ( 313) hydrogen bonds : angle 3.64332 / 2.52 ( 742) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.243 Fit side-chains REVERT: A 259 GLN cc_start: 0.8439 (mt0) cc_final: 0.7816 (mt0) REVERT: B 72 MET cc_start: 0.8690 (mmm) cc_final: 0.8043 (mmm) outliers start: 6 outliers final: 3 residues processed: 30 average time/residue: 0.4993 time to fit residues: 16.1672 Evaluate side-chains 28 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 415 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 66 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.092069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.063693 restraints weight = 17657.700| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.17 r_work: 0.2883 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8742 Z= 0.197 Angle : 0.485 6.106 12514 Z= 0.279 Chirality : 0.039 0.249 1482 Planarity : 0.004 0.044 1076 Dihedral : 22.061 176.790 2948 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.43 % Allowed : 24.37 % Favored : 74.19 % 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: 0.40 (0.33), residues: 620 helix: 1.74 (0.38), residues: 166 sheet: 1.51 (0.56), residues: 64 loop : -0.63 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 133 TYR 0.010 0.001 TYR A 216 PHE 0.016 0.001 PHE A 94 TRP 0.007 0.001 TRP B 74 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 ( 8740) covalent geometry : angle 0.48459 / 0.28 (12510) SS BOND : bond 0.00939 / 0.47 ( 2) SS BOND : angle 1.18622 / 0.61 ( 4) hydrogen bonds : bond 0.06151 / 4.16 ( 313) hydrogen bonds : angle 3.69224 / 2.55 ( 742) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.171 Fit side-chains REVERT: A 72 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8433 (mtp) REVERT: A 259 GLN cc_start: 0.8439 (mt0) cc_final: 0.7790 (mt0) REVERT: B 72 MET cc_start: 0.8706 (mmm) cc_final: 0.8007 (mmm) outliers start: 8 outliers final: 5 residues processed: 30 average time/residue: 0.5444 time to fit residues: 17.4788 Evaluate side-chains 31 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 415 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 65 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 11 optimal weight: 0.0670 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 55 optimal weight: 0.5980 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.092605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.064150 restraints weight = 17749.268| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.22 r_work: 0.2894 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8742 Z= 0.144 Angle : 0.464 5.939 12514 Z= 0.269 Chirality : 0.037 0.253 1482 Planarity : 0.004 0.042 1076 Dihedral : 22.084 176.722 2948 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.72 % Allowed : 24.91 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.33), residues: 620 helix: 1.84 (0.38), residues: 166 sheet: 1.58 (0.59), residues: 60 loop : -0.65 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 133 TYR 0.007 0.001 TYR A 216 PHE 0.018 0.001 PHE B 320 TRP 0.007 0.001 TRP B 74 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 8740) covalent geometry : angle 0.46339 / 0.27 (12510) SS BOND : bond 0.00816 / 0.41 ( 2) SS BOND : angle 1.11490 / 0.57 ( 4) hydrogen bonds : bond 0.05863 / 3.97 ( 313) hydrogen bonds : angle 3.67740 / 2.55 ( 742) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.253 Fit side-chains REVERT: A 259 GLN cc_start: 0.8435 (mt0) cc_final: 0.7802 (mt0) REVERT: B 72 MET cc_start: 0.8732 (mmm) cc_final: 0.8060 (mmm) outliers start: 4 outliers final: 4 residues processed: 28 average time/residue: 0.5761 time to fit residues: 17.3525 Evaluate side-chains 29 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 415 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 63 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 chunk 42 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 16 optimal weight: 0.0020 chunk 60 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.094633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.066247 restraints weight = 17549.297| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.23 r_work: 0.2947 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8742 Z= 0.097 Angle : 0.422 5.868 12514 Z= 0.245 Chirality : 0.035 0.251 1482 Planarity : 0.004 0.043 1076 Dihedral : 22.053 176.994 2948 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.72 % Allowed : 25.09 % Favored : 74.19 % 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: 0.67 (0.33), residues: 620 helix: 2.20 (0.38), residues: 166 sheet: 1.80 (0.61), residues: 60 loop : -0.57 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.004 0.001 TYR A 211 PHE 0.017 0.001 PHE B 320 TRP 0.008 0.001 TRP B 74 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.10 ( 8740) covalent geometry : angle 0.42199 / 0.25 (12510) SS BOND : bond 0.00519 / 0.26 ( 2) SS BOND : angle 0.73772 / 0.38 ( 4) hydrogen bonds : bond 0.05032 / 3.40 ( 313) hydrogen bonds : angle 3.49431 / 2.43 ( 742) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.253 Fit side-chains REVERT: A 259 GLN cc_start: 0.8454 (mt0) cc_final: 0.7820 (mt0) REVERT: B 72 MET cc_start: 0.8646 (mmm) cc_final: 0.7982 (mmm) outliers start: 4 outliers final: 4 residues processed: 29 average time/residue: 0.5032 time to fit residues: 15.6513 Evaluate side-chains 29 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 415 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 49 optimal weight: 0.0670 chunk 56 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.093915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.065532 restraints weight = 17780.937| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.21 r_work: 0.2930 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8742 Z= 0.122 Angle : 0.432 5.998 12514 Z= 0.249 Chirality : 0.036 0.241 1482 Planarity : 0.004 0.043 1076 Dihedral : 22.020 176.896 2948 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.90 % Allowed : 24.91 % Favored : 74.19 % 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: 0.73 (0.33), residues: 620 helix: 2.25 (0.38), residues: 166 sheet: 1.78 (0.61), residues: 60 loop : -0.53 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 193 TYR 0.005 0.001 TYR A 216 PHE 0.016 0.001 PHE B 320 TRP 0.008 0.001 TRP B 74 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 8740) covalent geometry : angle 0.43143 / 0.25 (12510) SS BOND : bond 0.00717 / 0.36 ( 2) SS BOND : angle 0.86210 / 0.44 ( 4) hydrogen bonds : bond 0.05209 / 3.52 ( 313) hydrogen bonds : angle 3.49482 / 2.43 ( 742) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1841.43 seconds wall clock time: 32 minutes 11.31 seconds (1931.31 seconds total)