Starting phenix.real_space_refine on Wed Sep 17 10:35:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9enb_19830/09_2025/9enb_19830.cif Found real_map, /net/cci-nas-00/data/ceres_data/9enb_19830/09_2025/9enb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9enb_19830/09_2025/9enb_19830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9enb_19830/09_2025/9enb_19830.map" model { file = "/net/cci-nas-00/data/ceres_data/9enb_19830/09_2025/9enb_19830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9enb_19830/09_2025/9enb_19830.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 2.55, per 1000 atoms: 0.31 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: 0.88 Conformation dependent library (CDL) restraints added in 228.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.21 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: 1.37 Time building geometry restraints manager: 1.16 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=" CB MET A 316 " pdb=" CG MET A 316 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.36e+00 bond pdb=" CG PRO A 321 " pdb=" CD PRO A 321 " ideal model delta sigma weight residual 1.503 1.465 0.038 3.40e-02 8.65e+02 1.22e+00 bond pdb=" CG PRO B 321 " pdb=" CD PRO B 321 " ideal model delta sigma weight residual 1.503 1.466 0.037 3.40e-02 8.65e+02 1.18e+00 bond pdb=" CB TRP B 74 " pdb=" CG TRP B 74 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 8.41e-01 bond pdb=" C4' A D 38 " pdb=" O4' A D 38 " ideal model delta sigma weight residual 1.451 1.438 0.013 1.50e-02 4.44e+03 8.00e-01 ... (remaining 8735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 12032 1.23 - 2.46: 390 2.46 - 3.69: 68 3.69 - 4.92: 16 4.92 - 6.15: 4 Bond angle restraints: 12510 Sorted by residual: angle pdb=" C2' U C 39 " pdb=" C1' U C 39 " pdb=" N1 U C 39 " ideal model delta sigma weight residual 112.00 116.38 -4.38 1.50e+00 4.44e-01 8.53e+00 angle pdb=" N PHE A 320 " pdb=" CA PHE A 320 " pdb=" C PHE A 320 " ideal model delta sigma weight residual 109.81 115.96 -6.15 2.21e+00 2.05e-01 7.74e+00 angle pdb=" N PHE B 320 " pdb=" CA PHE B 320 " pdb=" C PHE B 320 " ideal model delta sigma weight residual 109.81 115.72 -5.91 2.21e+00 2.05e-01 7.15e+00 angle pdb=" C2' A D 38 " pdb=" C1' A D 38 " pdb=" N9 A D 38 " ideal model delta sigma weight residual 112.00 115.62 -3.62 1.50e+00 4.44e-01 5.81e+00 angle pdb=" CA PHE A 320 " pdb=" C PHE A 320 " pdb=" N PRO A 321 " ideal model delta sigma weight residual 118.44 121.76 -3.32 1.59e+00 3.96e-01 4.37e+00 ... (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: 2.490 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.780 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:7.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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= 0.261 Angle : 0.554 6.147 12514 Z= 0.292 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 aren 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 covalent geometry : bond 0.00590 ( 8740) covalent geometry : angle 0.55375 (12510) SS BOND : bond 0.00888 ( 2) SS BOND : angle 1.17487 ( 4) hydrogen bonds : bond 0.17213 ( 313) hydrogen bonds : angle 5.56689 ( 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 : 0.235 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: 0.6998 time to fit residues: 22.3460 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 : 0.255 ------------------------------------------------------------------------------- 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: 8.9990 chunk 62 optimal weight: 8.9990 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: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3589 r_free = 0.3589 target = 0.092776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.064519 restraints weight = 17744.228| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.18 r_work: 0.2898 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8742 Z= 0.168 Angle : 0.527 6.112 12514 Z= 0.276 Chirality : 0.037 0.253 1482 Planarity : 0.004 0.041 1076 Dihedral : 22.108 176.543 2954 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.97 % Allowed : 23.30 % Favored : 74.73 % 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 aren not related in a simple way. whole: 0.40 (0.34), residues: 620 helix: 1.61 (0.39), residues: 166 sheet: 1.65 (0.58), residues: 68 loop : -0.62 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 106 TYR 0.007 0.001 TYR A 216 PHE 0.017 0.001 PHE B 320 TRP 0.006 0.001 TRP B 74 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8740) covalent geometry : angle 0.52624 (12510) SS BOND : bond 0.00806 ( 2) SS BOND : angle 1.07258 ( 4) hydrogen bonds : bond 0.05684 ( 313) hydrogen bonds : angle 3.85911 ( 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 37 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.244 Fit side-chains REVERT: A 72 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8290 (mpp) REVERT: A 259 GLN cc_start: 0.8511 (mt0) cc_final: 0.7768 (mt0) REVERT: A 412 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.7083 (ttpt) REVERT: B 72 MET cc_start: 0.8647 (mmm) cc_final: 0.8180 (mmm) outliers start: 11 outliers final: 1 residues processed: 34 average time/residue: 0.6068 time to fit residues: 22.0434 Evaluate side-chains 29 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain B residue 74 TRP 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: 2.9990 chunk 8 optimal weight: 0.0770 chunk 4 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3601 r_free = 0.3601 target = 0.093559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.065350 restraints weight = 17624.616| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.18 r_work: 0.2925 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1023 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= 0.138 Angle : 0.496 5.969 12514 Z= 0.260 Chirality : 0.036 0.245 1482 Planarity : 0.004 0.040 1076 Dihedral : 22.028 176.711 2948 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.33 % Allowed : 23.66 % 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 aren not related in a simple way. whole: 0.48 (0.33), residues: 620 helix: 1.84 (0.39), residues: 166 sheet: 1.66 (0.59), residues: 60 loop : -0.59 (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 216 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 covalent geometry : bond 0.00300 ( 8740) covalent geometry : angle 0.49576 (12510) SS BOND : bond 0.00718 ( 2) SS BOND : angle 0.93918 ( 4) hydrogen bonds : bond 0.05255 ( 313) hydrogen bonds : angle 3.60875 ( 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 40 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.167 Fit side-chains REVERT: A 259 GLN cc_start: 0.8426 (mt0) cc_final: 0.7777 (mt0) REVERT: A 412 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.7089 (ttpp) REVERT: B 72 MET cc_start: 0.8639 (mmm) cc_final: 0.8014 (mmm) outliers start: 13 outliers final: 4 residues processed: 36 average time/residue: 0.5970 time to fit residues: 22.9536 Evaluate side-chains 31 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 67 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 11 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3579 r_free = 0.3579 target = 0.092307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.063754 restraints weight = 18034.908| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.23 r_work: 0.2888 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8742 Z= 0.198 Angle : 0.529 6.093 12514 Z= 0.278 Chirality : 0.038 0.242 1482 Planarity : 0.004 0.043 1076 Dihedral : 22.024 176.639 2948 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.61 % Allowed : 24.19 % 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 aren not related in a simple way. whole: 0.49 (0.33), residues: 620 helix: 1.73 (0.38), residues: 166 sheet: 1.55 (0.55), residues: 72 loop : -0.57 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 187 TYR 0.008 0.001 TYR A 216 PHE 0.017 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 covalent geometry : bond 0.00445 ( 8740) covalent geometry : angle 0.52826 (12510) SS BOND : bond 0.00911 ( 2) SS BOND : angle 1.21731 ( 4) hydrogen bonds : bond 0.05862 ( 313) hydrogen bonds : angle 3.68603 ( 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 35 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.180 Fit side-chains REVERT: A 259 GLN cc_start: 0.8445 (mt0) cc_final: 0.7797 (mt0) REVERT: A 412 LYS cc_start: 0.7482 (ttpp) cc_final: 0.7268 (ttpp) REVERT: B 72 MET cc_start: 0.8730 (mmm) cc_final: 0.8007 (mmm) REVERT: B 228 MET cc_start: 0.8606 (mtp) cc_final: 0.8192 (mtm) outliers start: 9 outliers final: 5 residues processed: 34 average time/residue: 0.5681 time to fit residues: 20.7645 Evaluate side-chains 31 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 316 MET 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: 5.9990 chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 0.0170 chunk 75 optimal weight: 8.9990 overall best weight: 1.6824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3624 r_free = 0.3624 target = 0.094204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.066023 restraints weight = 17902.776| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.19 r_work: 0.2957 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8742 Z= 0.181 Angle : 0.518 6.070 12514 Z= 0.271 Chirality : 0.037 0.242 1482 Planarity : 0.004 0.042 1076 Dihedral : 22.010 176.787 2948 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.79 % Allowed : 23.84 % 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 aren not related in a simple way. whole: 0.49 (0.33), residues: 620 helix: 1.78 (0.38), residues: 166 sheet: 1.54 (0.55), residues: 72 loop : -0.60 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 187 TYR 0.008 0.001 TYR A 216 PHE 0.017 0.001 PHE B 320 TRP 0.007 0.001 TRP B 74 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8740) covalent geometry : angle 0.51729 (12510) SS BOND : bond 0.00861 ( 2) SS BOND : angle 1.12687 ( 4) hydrogen bonds : bond 0.05660 ( 313) hydrogen bonds : angle 3.63251 ( 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 37 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 412 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.7092 (ttpp) REVERT: B 72 MET cc_start: 0.8740 (mmm) cc_final: 0.8052 (mmm) REVERT: B 228 MET cc_start: 0.8638 (mtp) cc_final: 0.8233 (mtm) outliers start: 10 outliers final: 5 residues processed: 35 average time/residue: 0.6097 time to fit residues: 22.8560 Evaluate side-chains 33 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 40 optimal weight: 0.3980 chunk 64 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3611 r_free = 0.3611 target = 0.093404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.065175 restraints weight = 17767.840| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.20 r_work: 0.2938 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8742 Z= 0.232 Angle : 0.550 6.182 12514 Z= 0.289 Chirality : 0.039 0.238 1482 Planarity : 0.004 0.044 1076 Dihedral : 22.031 177.026 2948 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.79 % Allowed : 23.84 % 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 aren not related in a simple way. whole: 0.39 (0.33), residues: 620 helix: 1.66 (0.38), residues: 166 sheet: 1.47 (0.54), residues: 72 loop : -0.64 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 187 TYR 0.010 0.001 TYR A 216 PHE 0.017 0.001 PHE A 94 TRP 0.007 0.001 TRP B 74 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00524 ( 8740) covalent geometry : angle 0.55004 (12510) SS BOND : bond 0.00992 ( 2) SS BOND : angle 1.31268 ( 4) hydrogen bonds : bond 0.06193 ( 313) hydrogen bonds : angle 3.71583 ( 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 36 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.199 Fit side-chains REVERT: A 259 GLN cc_start: 0.8422 (mt0) cc_final: 0.7787 (mt0) REVERT: A 412 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7215 (ttpp) REVERT: B 72 MET cc_start: 0.8766 (mmm) cc_final: 0.8056 (mmm) REVERT: B 228 MET cc_start: 0.8648 (mtp) cc_final: 0.8234 (mtm) outliers start: 10 outliers final: 4 residues processed: 32 average time/residue: 0.6552 time to fit residues: 22.3016 Evaluate side-chains 31 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 62 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3616 r_free = 0.3616 target = 0.093698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.065440 restraints weight = 18068.790| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.22 r_work: 0.2935 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8742 Z= 0.205 Angle : 0.544 8.665 12514 Z= 0.285 Chirality : 0.038 0.240 1482 Planarity : 0.004 0.043 1076 Dihedral : 22.036 177.060 2948 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.08 % Allowed : 24.55 % 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 aren not related in a simple way. whole: 0.41 (0.33), residues: 620 helix: 1.70 (0.38), residues: 166 sheet: 1.47 (0.54), residues: 72 loop : -0.64 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 187 TYR 0.009 0.001 TYR A 216 PHE 0.017 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 covalent geometry : bond 0.00460 ( 8740) covalent geometry : angle 0.54375 (12510) SS BOND : bond 0.00930 ( 2) SS BOND : angle 1.21444 ( 4) hydrogen bonds : bond 0.06021 ( 313) hydrogen bonds : angle 3.69261 ( 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 32 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.182 Fit side-chains REVERT: A 259 GLN cc_start: 0.8419 (mt0) cc_final: 0.7781 (mt0) REVERT: A 412 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.7189 (ttpp) REVERT: B 72 MET cc_start: 0.8754 (mmm) cc_final: 0.8069 (mmm) REVERT: B 228 MET cc_start: 0.8640 (mtp) cc_final: 0.8214 (mtm) outliers start: 6 outliers final: 4 residues processed: 30 average time/residue: 0.6370 time to fit residues: 20.4508 Evaluate side-chains 31 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3621 r_free = 0.3621 target = 0.093968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.065842 restraints weight = 17869.767| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.18 r_work: 0.2939 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.0920 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= 0.187 Angle : 0.531 6.110 12514 Z= 0.279 Chirality : 0.038 0.241 1482 Planarity : 0.004 0.043 1076 Dihedral : 22.037 177.070 2948 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.25 % Allowed : 24.55 % 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 aren not related in a simple way. whole: 0.45 (0.33), residues: 620 helix: 1.75 (0.38), residues: 166 sheet: 1.48 (0.54), residues: 72 loop : -0.62 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 193 TYR 0.008 0.001 TYR A 216 PHE 0.017 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 covalent geometry : bond 0.00419 ( 8740) covalent geometry : angle 0.53027 (12510) SS BOND : bond 0.00883 ( 2) SS BOND : angle 1.15685 ( 4) hydrogen bonds : bond 0.05887 ( 313) hydrogen bonds : angle 3.67480 ( 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 34 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.294 Fit side-chains REVERT: A 259 GLN cc_start: 0.8426 (mt0) cc_final: 0.7800 (mt0) REVERT: A 412 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.7161 (ttpp) REVERT: B 72 MET cc_start: 0.8749 (mmm) cc_final: 0.8063 (mmm) REVERT: B 228 MET cc_start: 0.8643 (mtp) cc_final: 0.8221 (mtm) outliers start: 7 outliers final: 4 residues processed: 33 average time/residue: 0.6388 time to fit residues: 22.5901 Evaluate side-chains 31 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 65 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 11 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.092871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.064626 restraints weight = 17908.830| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.20 r_work: 0.2921 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8742 Z= 0.275 Angle : 0.581 6.217 12514 Z= 0.305 Chirality : 0.041 0.235 1482 Planarity : 0.004 0.044 1076 Dihedral : 22.056 177.396 2948 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.08 % Allowed : 24.73 % 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 aren not related in a simple way. whole: 0.30 (0.33), residues: 620 helix: 1.56 (0.38), residues: 166 sheet: 1.43 (0.54), residues: 72 loop : -0.69 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 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 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00621 ( 8740) covalent geometry : angle 0.58037 (12510) SS BOND : bond 0.01076 ( 2) SS BOND : angle 1.41424 ( 4) hydrogen bonds : bond 0.06554 ( 313) hydrogen bonds : angle 3.78045 ( 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 32 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.264 Fit side-chains REVERT: A 259 GLN cc_start: 0.8418 (mt0) cc_final: 0.7799 (mt0) REVERT: A 412 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7318 (ttpp) REVERT: B 72 MET cc_start: 0.8805 (mmm) cc_final: 0.8085 (mmm) outliers start: 6 outliers final: 4 residues processed: 31 average time/residue: 0.6663 time to fit residues: 22.0652 Evaluate side-chains 31 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 63 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3654 r_free = 0.3654 target = 0.095942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.067732 restraints weight = 17739.632| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.21 r_work: 0.2993 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8742 Z= 0.117 Angle : 0.482 6.028 12514 Z= 0.252 Chirality : 0.035 0.233 1482 Planarity : 0.004 0.043 1076 Dihedral : 22.004 177.405 2948 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.90 % Allowed : 25.09 % 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 aren not related in a simple way. whole: 0.57 (0.33), residues: 620 helix: 2.06 (0.38), residues: 166 sheet: 1.64 (0.60), residues: 60 loop : -0.59 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 280 TYR 0.005 0.001 TYR A 216 PHE 0.018 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 covalent geometry : bond 0.00252 ( 8740) covalent geometry : angle 0.48232 (12510) SS BOND : bond 0.00689 ( 2) SS BOND : angle 0.77561 ( 4) hydrogen bonds : bond 0.04892 ( 313) hydrogen bonds : angle 3.49272 ( 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 33 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.253 Fit side-chains REVERT: A 259 GLN cc_start: 0.8498 (mt0) cc_final: 0.7900 (mt0) REVERT: A 412 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.7095 (ttpp) REVERT: B 72 MET cc_start: 0.8746 (mmm) cc_final: 0.8023 (mmm) REVERT: B 228 MET cc_start: 0.8690 (mtp) cc_final: 0.8298 (mtm) outliers start: 5 outliers final: 3 residues processed: 32 average time/residue: 0.6277 time to fit residues: 21.5289 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 : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 49 optimal weight: 0.0170 chunk 56 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3620 r_free = 0.3620 target = 0.094167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.066055 restraints weight = 17797.950| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.19 r_work: 0.2945 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1147 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= 0.155 Angle : 0.499 6.053 12514 Z= 0.261 Chirality : 0.036 0.220 1482 Planarity : 0.004 0.044 1076 Dihedral : 21.975 177.542 2948 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % 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 aren not related in a simple way. whole: 0.56 (0.33), residues: 620 helix: 2.03 (0.38), residues: 166 sheet: 1.66 (0.60), residues: 60 loop : -0.59 (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 0.017 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 covalent geometry : bond 0.00344 ( 8740) covalent geometry : angle 0.49907 (12510) SS BOND : bond 0.00786 ( 2) SS BOND : angle 1.01557 ( 4) hydrogen bonds : bond 0.05365 ( 313) hydrogen bonds : angle 3.54168 ( 742) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2169.10 seconds wall clock time: 37 minutes 46.36 seconds (2266.36 seconds total)