Starting phenix.real_space_refine on Sat Dec 28 12:10:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ja5_61290/12_2024/9ja5_61290.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ja5_61290/12_2024/9ja5_61290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ja5_61290/12_2024/9ja5_61290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ja5_61290/12_2024/9ja5_61290.map" model { file = "/net/cci-nas-00/data/ceres_data/9ja5_61290/12_2024/9ja5_61290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ja5_61290/12_2024/9ja5_61290.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.022 sd= 1.765 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 5148 2.51 5 N 1518 2.21 5 O 1761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8469 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1391 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 1 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 3.68, per 1000 atoms: 0.43 Number of scatterers: 8469 At special positions: 0 Unit cell: (85.6, 78.4, 210.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1761 8.00 N 1518 7.00 C 5148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 72.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 211 through 275 removed outlier: 3.983A pdb=" N GLU A 227 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 removed outlier: 3.833A pdb=" N SER A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 318 removed outlier: 3.926A pdb=" N ARG A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 329 removed outlier: 3.917A pdb=" N LEU A 329 " --> pdb=" O ASP A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 329' Processing helix chain 'A' and resid 330 through 339 Processing helix chain 'A' and resid 342 through 347 removed outlier: 3.653A pdb=" N SER A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 546 removed outlier: 3.876A pdb=" N PHE A 546 " --> pdb=" O GLN A 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 275 removed outlier: 3.984A pdb=" N GLU B 227 " --> pdb=" O LYS B 223 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 248 " --> pdb=" O ARG B 244 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 305 removed outlier: 3.833A pdb=" N SER B 305 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 318 removed outlier: 3.927A pdb=" N ARG B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR B 314 " --> pdb=" O ASN B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 329 removed outlier: 3.917A pdb=" N LEU B 329 " --> pdb=" O ASP B 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 326 through 329' Processing helix chain 'B' and resid 330 through 339 Processing helix chain 'B' and resid 342 through 347 removed outlier: 3.653A pdb=" N SER B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 546 removed outlier: 3.877A pdb=" N PHE B 546 " --> pdb=" O GLN B 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 275 removed outlier: 3.983A pdb=" N GLU C 227 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 248 " --> pdb=" O ARG C 244 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 305 removed outlier: 3.832A pdb=" N SER C 305 " --> pdb=" O GLU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 318 removed outlier: 3.927A pdb=" N ARG C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR C 314 " --> pdb=" O ASN C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 329 removed outlier: 3.917A pdb=" N LEU C 329 " --> pdb=" O ASP C 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 326 through 329' Processing helix chain 'C' and resid 330 through 339 Processing helix chain 'C' and resid 342 through 347 removed outlier: 3.654A pdb=" N SER C 347 " --> pdb=" O ALA C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 546 removed outlier: 3.876A pdb=" N PHE C 546 " --> pdb=" O GLN C 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 275 removed outlier: 3.983A pdb=" N GLU D 227 " --> pdb=" O LYS D 223 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN D 248 " --> pdb=" O ARG D 244 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D 253 " --> pdb=" O ASP D 249 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 305 removed outlier: 3.833A pdb=" N SER D 305 " --> pdb=" O GLU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 318 removed outlier: 3.927A pdb=" N ARG D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR D 314 " --> pdb=" O ASN D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 329 removed outlier: 3.918A pdb=" N LEU D 329 " --> pdb=" O ASP D 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 326 through 329' Processing helix chain 'D' and resid 330 through 339 Processing helix chain 'D' and resid 342 through 347 removed outlier: 3.654A pdb=" N SER D 347 " --> pdb=" O ALA D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 546 removed outlier: 3.876A pdb=" N PHE D 546 " --> pdb=" O GLN D 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 275 removed outlier: 3.983A pdb=" N GLU E 227 " --> pdb=" O LYS E 223 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN E 248 " --> pdb=" O ARG E 244 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU E 253 " --> pdb=" O ASP E 249 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG E 255 " --> pdb=" O SER E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 305 removed outlier: 3.833A pdb=" N SER E 305 " --> pdb=" O GLU E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 318 removed outlier: 3.927A pdb=" N ARG E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR E 314 " --> pdb=" O ASN E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 329 removed outlier: 3.917A pdb=" N LEU E 329 " --> pdb=" O ASP E 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 326 through 329' Processing helix chain 'E' and resid 330 through 339 Processing helix chain 'E' and resid 342 through 347 removed outlier: 3.654A pdb=" N SER E 347 " --> pdb=" O ALA E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 546 removed outlier: 3.876A pdb=" N PHE E 546 " --> pdb=" O GLN E 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 275 removed outlier: 3.983A pdb=" N GLU F 227 " --> pdb=" O LYS F 223 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN F 248 " --> pdb=" O ARG F 244 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU F 253 " --> pdb=" O ASP F 249 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG F 255 " --> pdb=" O SER F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 305 removed outlier: 3.833A pdb=" N SER F 305 " --> pdb=" O GLU F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 318 removed outlier: 3.927A pdb=" N ARG F 313 " --> pdb=" O GLU F 309 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR F 314 " --> pdb=" O ASN F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 329 removed outlier: 3.918A pdb=" N LEU F 329 " --> pdb=" O ASP F 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 326 through 329' Processing helix chain 'F' and resid 330 through 339 Processing helix chain 'F' and resid 342 through 347 removed outlier: 3.653A pdb=" N SER F 347 " --> pdb=" O ALA F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 528 through 546 removed outlier: 3.876A pdb=" N PHE F 546 " --> pdb=" O GLN F 542 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1497 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 2.28 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: 2739 1.33 - 1.45: 1018 1.45 - 1.56: 4637 1.56 - 1.68: 0 1.68 - 1.80: 78 Bond restraints: 8472 Sorted by residual: bond pdb=" C LEU E 306 " pdb=" N SER E 307 " ideal model delta sigma weight residual 1.333 1.287 0.045 1.73e-02 3.34e+03 6.92e+00 bond pdb=" C LEU F 306 " pdb=" N SER F 307 " ideal model delta sigma weight residual 1.333 1.287 0.045 1.73e-02 3.34e+03 6.86e+00 bond pdb=" C LEU A 306 " pdb=" N SER A 307 " ideal model delta sigma weight residual 1.333 1.287 0.045 1.73e-02 3.34e+03 6.86e+00 bond pdb=" C LEU B 306 " pdb=" N SER B 307 " ideal model delta sigma weight residual 1.333 1.287 0.045 1.73e-02 3.34e+03 6.84e+00 bond pdb=" C LEU C 306 " pdb=" N SER C 307 " ideal model delta sigma weight residual 1.333 1.287 0.045 1.73e-02 3.34e+03 6.83e+00 ... (remaining 8467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 10499 1.79 - 3.58: 703 3.58 - 5.38: 110 5.38 - 7.17: 52 7.17 - 8.96: 42 Bond angle restraints: 11406 Sorted by residual: angle pdb=" C PHE E 285 " pdb=" CA PHE E 285 " pdb=" CB PHE E 285 " ideal model delta sigma weight residual 110.42 101.46 8.96 1.99e+00 2.53e-01 2.03e+01 angle pdb=" C PHE A 285 " pdb=" CA PHE A 285 " pdb=" CB PHE A 285 " ideal model delta sigma weight residual 110.42 101.48 8.94 1.99e+00 2.53e-01 2.02e+01 angle pdb=" C PHE D 285 " pdb=" CA PHE D 285 " pdb=" CB PHE D 285 " ideal model delta sigma weight residual 110.42 101.49 8.93 1.99e+00 2.53e-01 2.01e+01 angle pdb=" C PHE C 285 " pdb=" CA PHE C 285 " pdb=" CB PHE C 285 " ideal model delta sigma weight residual 110.42 101.50 8.92 1.99e+00 2.53e-01 2.01e+01 angle pdb=" C PHE B 285 " pdb=" CA PHE B 285 " pdb=" CB PHE B 285 " ideal model delta sigma weight residual 110.42 101.52 8.90 1.99e+00 2.53e-01 2.00e+01 ... (remaining 11401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.19: 4433 14.19 - 28.38: 679 28.38 - 42.56: 144 42.56 - 56.75: 24 56.75 - 70.94: 18 Dihedral angle restraints: 5298 sinusoidal: 2322 harmonic: 2976 Sorted by residual: dihedral pdb=" CA PHE C 285 " pdb=" C PHE C 285 " pdb=" N ASN C 286 " pdb=" CA ASN C 286 " ideal model delta harmonic sigma weight residual -180.00 -158.08 -21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA PHE D 285 " pdb=" C PHE D 285 " pdb=" N ASN D 286 " pdb=" CA ASN D 286 " ideal model delta harmonic sigma weight residual -180.00 -158.10 -21.90 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA PHE B 285 " pdb=" C PHE B 285 " pdb=" N ASN B 286 " pdb=" CA ASN B 286 " ideal model delta harmonic sigma weight residual -180.00 -158.10 -21.90 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 5295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 419 0.037 - 0.073: 535 0.073 - 0.110: 171 0.110 - 0.146: 63 0.146 - 0.183: 36 Chirality restraints: 1224 Sorted by residual: chirality pdb=" CA GLU E 238 " pdb=" N GLU E 238 " pdb=" C GLU E 238 " pdb=" CB GLU E 238 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CA SER A 307 " pdb=" N SER A 307 " pdb=" C SER A 307 " pdb=" CB SER A 307 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA GLU A 238 " pdb=" N GLU A 238 " pdb=" C GLU A 238 " pdb=" CB GLU A 238 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.11e-01 ... (remaining 1221 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 285 " -0.035 2.00e-02 2.50e+03 2.92e-02 1.50e+01 pdb=" CG PHE D 285 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE D 285 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE D 285 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 285 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 285 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE D 285 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 285 " 0.034 2.00e-02 2.50e+03 2.92e-02 1.49e+01 pdb=" CG PHE C 285 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE C 285 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 285 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 285 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 285 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 285 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 285 " -0.034 2.00e-02 2.50e+03 2.92e-02 1.49e+01 pdb=" CG PHE F 285 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE F 285 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE F 285 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE F 285 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 285 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE F 285 " -0.005 2.00e-02 2.50e+03 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 316 2.67 - 3.23: 8692 3.23 - 3.79: 12514 3.79 - 4.34: 16572 4.34 - 4.90: 27000 Nonbonded interactions: 65094 Sorted by model distance: nonbonded pdb=" OE2 GLU A 309 " pdb=" O HOH A 701 " model vdw 2.117 3.040 nonbonded pdb=" OE2 GLU D 309 " pdb=" O HOH D 701 " model vdw 2.119 3.040 nonbonded pdb=" O SER A 307 " pdb=" OG SER A 307 " model vdw 2.126 3.040 nonbonded pdb=" O SER D 307 " pdb=" OG SER D 307 " model vdw 2.126 3.040 nonbonded pdb=" O SER F 307 " pdb=" OG SER F 307 " model vdw 2.126 3.040 ... (remaining 65089 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 18.890 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:11.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.066 8472 Z= 0.921 Angle : 1.154 8.958 11406 Z= 0.626 Chirality : 0.064 0.183 1224 Planarity : 0.005 0.029 1518 Dihedral : 14.299 70.938 3342 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.88 % Favored : 87.12 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.25), residues: 978 helix: -0.98 (0.18), residues: 714 sheet: None (None), residues: 0 loop : -3.96 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.006 TRP D 221 PHE 0.068 0.005 PHE D 285 TYR 0.026 0.004 TYR B 314 ARG 0.009 0.001 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.059 Fit side-chains REVERT: A 245 ASP cc_start: 0.7624 (m-30) cc_final: 0.7160 (t0) REVERT: A 301 GLU cc_start: 0.8565 (mp0) cc_final: 0.8319 (mp0) REVERT: A 308 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8698 (tp30) REVERT: A 309 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7225 (tm-30) REVERT: A 323 ASP cc_start: 0.8256 (t0) cc_final: 0.7920 (t0) REVERT: A 527 LEU cc_start: 0.9275 (mp) cc_final: 0.9040 (mp) REVERT: A 531 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7617 (mt-10) REVERT: B 245 ASP cc_start: 0.7507 (m-30) cc_final: 0.7264 (t0) REVERT: B 309 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7530 (tm-30) REVERT: B 323 ASP cc_start: 0.8209 (t0) cc_final: 0.8009 (t0) REVERT: C 245 ASP cc_start: 0.7803 (m-30) cc_final: 0.6917 (OUTLIER) REVERT: C 309 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7433 (tm-30) REVERT: C 323 ASP cc_start: 0.8037 (t0) cc_final: 0.7544 (t0) REVERT: C 326 ASP cc_start: 0.8389 (t0) cc_final: 0.7931 (t0) REVERT: D 245 ASP cc_start: 0.7634 (m-30) cc_final: 0.7380 (OUTLIER) REVERT: D 309 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7308 (tm-30) REVERT: D 323 ASP cc_start: 0.8208 (t0) cc_final: 0.7863 (t0) REVERT: D 326 ASP cc_start: 0.8369 (t0) cc_final: 0.8098 (t70) REVERT: D 527 LEU cc_start: 0.9139 (mp) cc_final: 0.8805 (mt) REVERT: D 531 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7471 (mt-10) REVERT: E 324 GLU cc_start: 0.8450 (tp30) cc_final: 0.7783 (tp30) REVERT: E 534 GLU cc_start: 0.7828 (tp30) cc_final: 0.7434 (tp30) REVERT: F 245 ASP cc_start: 0.7919 (m-30) cc_final: 0.7253 (OUTLIER) REVERT: F 309 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7389 (tm-30) REVERT: F 323 ASP cc_start: 0.8135 (t0) cc_final: 0.7733 (t0) REVERT: F 326 ASP cc_start: 0.8488 (t0) cc_final: 0.8106 (t0) outliers start: 0 outliers final: 3 residues processed: 249 average time/residue: 1.6017 time to fit residues: 417.5779 Evaluate side-chains 213 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 0.0870 chunk 24 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 0.0000 chunk 29 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 87 optimal weight: 0.0020 overall best weight: 0.2570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 ASN ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 ASN ** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8472 Z= 0.207 Angle : 0.660 7.231 11406 Z= 0.347 Chirality : 0.038 0.156 1224 Planarity : 0.004 0.041 1518 Dihedral : 4.784 17.519 1134 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.03 % Allowed : 13.03 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.27), residues: 978 helix: 0.88 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.80 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 221 PHE 0.021 0.002 PHE F 285 TYR 0.007 0.001 TYR D 314 ARG 0.010 0.001 ARG E 222 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 230 time to evaluate : 1.049 Fit side-chains REVERT: A 245 ASP cc_start: 0.7210 (m-30) cc_final: 0.6943 (OUTLIER) REVERT: A 301 GLU cc_start: 0.8577 (mp0) cc_final: 0.8358 (mp0) REVERT: A 309 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7228 (tm-30) REVERT: A 323 ASP cc_start: 0.7979 (t0) cc_final: 0.7527 (t0) REVERT: A 527 LEU cc_start: 0.9150 (mp) cc_final: 0.8934 (mp) REVERT: B 227 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8187 (mp0) REVERT: B 237 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6960 (mmt90) REVERT: B 323 ASP cc_start: 0.8047 (t0) cc_final: 0.7686 (t0) REVERT: C 245 ASP cc_start: 0.7414 (m-30) cc_final: 0.6815 (OUTLIER) REVERT: C 309 GLU cc_start: 0.7286 (tm-30) cc_final: 0.6731 (tm-30) REVERT: C 323 ASP cc_start: 0.7886 (t0) cc_final: 0.7425 (t0) REVERT: D 237 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6844 (mmt90) REVERT: D 309 GLU cc_start: 0.7492 (tm-30) cc_final: 0.6889 (tm-30) REVERT: D 323 ASP cc_start: 0.7907 (t0) cc_final: 0.7480 (t0) REVERT: F 245 ASP cc_start: 0.7539 (m-30) cc_final: 0.7073 (t0) REVERT: F 309 GLU cc_start: 0.7276 (tm-30) cc_final: 0.6698 (tm-30) REVERT: F 316 LYS cc_start: 0.7904 (mttt) cc_final: 0.7647 (mttm) REVERT: F 323 ASP cc_start: 0.8046 (t0) cc_final: 0.7492 (t0) REVERT: F 326 ASP cc_start: 0.7709 (t0) cc_final: 0.7194 (t0) outliers start: 19 outliers final: 9 residues processed: 238 average time/residue: 1.5009 time to fit residues: 375.5838 Evaluate side-chains 219 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 209 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain F residue 286 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8472 Z= 0.333 Angle : 0.688 7.192 11406 Z= 0.356 Chirality : 0.042 0.159 1224 Planarity : 0.005 0.043 1518 Dihedral : 4.762 22.723 1134 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.03 % Allowed : 19.12 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.28), residues: 978 helix: 1.08 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.98 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 221 PHE 0.032 0.003 PHE C 285 TYR 0.008 0.002 TYR B 314 ARG 0.007 0.001 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 1.052 Fit side-chains REVERT: A 245 ASP cc_start: 0.7286 (m-30) cc_final: 0.6965 (OUTLIER) REVERT: A 308 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8700 (tm-30) REVERT: A 309 GLU cc_start: 0.7549 (tm-30) cc_final: 0.6969 (tm-30) REVERT: A 323 ASP cc_start: 0.7950 (t0) cc_final: 0.7533 (t0) REVERT: A 527 LEU cc_start: 0.9113 (mp) cc_final: 0.8893 (mt) REVERT: B 237 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.7102 (mmt90) REVERT: B 308 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8658 (tm-30) REVERT: B 309 GLU cc_start: 0.7393 (tm-30) cc_final: 0.6636 (tm-30) REVERT: C 245 ASP cc_start: 0.7455 (m-30) cc_final: 0.6776 (t0) REVERT: C 308 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8719 (tm-30) REVERT: C 309 GLU cc_start: 0.7421 (tm-30) cc_final: 0.6862 (tm-30) REVERT: C 323 ASP cc_start: 0.7955 (t0) cc_final: 0.7362 (t0) REVERT: C 326 ASP cc_start: 0.7780 (t0) cc_final: 0.7252 (t0) REVERT: D 245 ASP cc_start: 0.7506 (m-30) cc_final: 0.6834 (t0) REVERT: D 308 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8712 (tm-30) REVERT: D 309 GLU cc_start: 0.7505 (tm-30) cc_final: 0.6877 (tm-30) REVERT: D 323 ASP cc_start: 0.7981 (t0) cc_final: 0.7524 (t0) REVERT: E 309 GLU cc_start: 0.7423 (tm-30) cc_final: 0.6697 (tm-30) REVERT: E 323 ASP cc_start: 0.8087 (t0) cc_final: 0.7697 (t0) REVERT: E 534 GLU cc_start: 0.7623 (tp30) cc_final: 0.6996 (tp30) REVERT: F 245 ASP cc_start: 0.7634 (m-30) cc_final: 0.7023 (t0) REVERT: F 309 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6864 (tm-30) REVERT: F 316 LYS cc_start: 0.7997 (mttt) cc_final: 0.7758 (mttm) REVERT: F 323 ASP cc_start: 0.8060 (t0) cc_final: 0.7575 (t0) REVERT: F 326 ASP cc_start: 0.7888 (t0) cc_final: 0.7426 (t0) outliers start: 19 outliers final: 14 residues processed: 228 average time/residue: 1.4660 time to fit residues: 351.6211 Evaluate side-chains 219 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 298 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 0.0980 chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN ** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8472 Z= 0.209 Angle : 0.607 9.267 11406 Z= 0.311 Chirality : 0.037 0.154 1224 Planarity : 0.004 0.039 1518 Dihedral : 4.385 22.211 1134 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.39 % Allowed : 21.47 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.28), residues: 978 helix: 1.92 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.27 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 221 PHE 0.020 0.002 PHE D 285 TYR 0.005 0.001 TYR F 348 ARG 0.008 0.000 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 211 time to evaluate : 1.034 Fit side-chains REVERT: A 245 ASP cc_start: 0.7182 (m-30) cc_final: 0.6911 (t0) REVERT: A 308 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8582 (tm-30) REVERT: A 309 GLU cc_start: 0.7310 (tm-30) cc_final: 0.6676 (tm-30) REVERT: A 323 ASP cc_start: 0.7917 (t0) cc_final: 0.7447 (t0) REVERT: A 527 LEU cc_start: 0.9100 (mp) cc_final: 0.8896 (mt) REVERT: B 237 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7103 (mmt90) REVERT: B 308 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8460 (tm-30) REVERT: B 309 GLU cc_start: 0.7213 (tm-30) cc_final: 0.6406 (tm-30) REVERT: B 323 ASP cc_start: 0.8027 (t0) cc_final: 0.7639 (t0) REVERT: C 221 TRP cc_start: 0.6516 (t60) cc_final: 0.6169 (t60) REVERT: C 245 ASP cc_start: 0.7320 (m-30) cc_final: 0.6757 (t0) REVERT: C 308 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8533 (tm-30) REVERT: C 309 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6694 (tm-30) REVERT: C 323 ASP cc_start: 0.7925 (t0) cc_final: 0.7384 (t0) REVERT: D 245 ASP cc_start: 0.7389 (m-30) cc_final: 0.6883 (t0) REVERT: D 308 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8578 (tm-30) REVERT: D 309 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6606 (tm-30) REVERT: D 323 ASP cc_start: 0.7908 (t0) cc_final: 0.7439 (t0) REVERT: E 241 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7335 (t0) REVERT: E 308 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8584 (tm-30) REVERT: F 245 ASP cc_start: 0.7501 (m-30) cc_final: 0.6983 (t0) REVERT: F 308 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8703 (tm-30) REVERT: F 309 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6662 (tm-30) REVERT: F 316 LYS cc_start: 0.8049 (mttt) cc_final: 0.7819 (mttm) REVERT: F 323 ASP cc_start: 0.8065 (t0) cc_final: 0.7595 (t0) outliers start: 13 outliers final: 9 residues processed: 219 average time/residue: 1.5013 time to fit residues: 345.3120 Evaluate side-chains 214 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain F residue 286 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 79 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8472 Z= 0.221 Angle : 0.603 9.405 11406 Z= 0.308 Chirality : 0.038 0.161 1224 Planarity : 0.004 0.034 1518 Dihedral : 4.302 26.084 1134 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.14 % Allowed : 22.44 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.29), residues: 978 helix: 1.96 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.41 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP B 221 PHE 0.022 0.002 PHE F 285 TYR 0.006 0.001 TYR D 348 ARG 0.009 0.000 ARG E 244 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 1.009 Fit side-chains REVERT: A 245 ASP cc_start: 0.7189 (m-30) cc_final: 0.6896 (t0) REVERT: A 308 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8547 (tm-30) REVERT: A 309 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6701 (tm-30) REVERT: A 323 ASP cc_start: 0.7877 (t0) cc_final: 0.7409 (t0) REVERT: B 237 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.7080 (mmt90) REVERT: B 241 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7174 (t0) REVERT: B 308 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8400 (tm-30) REVERT: B 309 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6442 (tm-30) REVERT: C 211 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7500 (pp-130) REVERT: C 245 ASP cc_start: 0.7315 (m-30) cc_final: 0.6735 (t0) REVERT: C 308 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8461 (tm-30) REVERT: C 309 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6742 (tm-30) REVERT: C 323 ASP cc_start: 0.7898 (t0) cc_final: 0.7370 (t0) REVERT: D 245 ASP cc_start: 0.7450 (m-30) cc_final: 0.6994 (t0) REVERT: D 308 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8535 (tm-30) REVERT: D 309 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6637 (tm-30) REVERT: D 323 ASP cc_start: 0.7913 (t0) cc_final: 0.7472 (t0) REVERT: E 241 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7374 (t0) REVERT: E 286 ASN cc_start: 0.8103 (p0) cc_final: 0.7899 (p0) REVERT: E 308 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8518 (tm-30) REVERT: E 323 ASP cc_start: 0.8048 (t0) cc_final: 0.7591 (t0) REVERT: F 245 ASP cc_start: 0.7520 (m-30) cc_final: 0.6982 (t0) REVERT: F 308 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8744 (tm-30) REVERT: F 309 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6660 (tm-30) REVERT: F 316 LYS cc_start: 0.8019 (mttt) cc_final: 0.7794 (mttm) REVERT: F 323 ASP cc_start: 0.8046 (t0) cc_final: 0.7591 (t0) outliers start: 20 outliers final: 9 residues processed: 222 average time/residue: 1.4125 time to fit residues: 330.2284 Evaluate side-chains 213 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 530 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8472 Z= 0.207 Angle : 0.617 9.318 11406 Z= 0.309 Chirality : 0.038 0.165 1224 Planarity : 0.004 0.034 1518 Dihedral : 4.286 25.910 1134 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.82 % Allowed : 23.61 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.29), residues: 978 helix: 2.15 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.31 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP B 221 PHE 0.018 0.002 PHE F 285 TYR 0.005 0.001 TYR F 348 ARG 0.010 0.001 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 245 ASP cc_start: 0.7184 (m-30) cc_final: 0.6889 (t0) REVERT: A 308 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8525 (tm-30) REVERT: A 309 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6642 (tm-30) REVERT: A 323 ASP cc_start: 0.7872 (t0) cc_final: 0.7402 (t0) REVERT: B 237 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.7045 (mmt90) REVERT: B 241 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7362 (t0) REVERT: B 308 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8373 (tm-30) REVERT: B 309 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6602 (tm-30) REVERT: B 323 ASP cc_start: 0.8001 (t0) cc_final: 0.7640 (t0) REVERT: C 211 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7524 (pp-130) REVERT: C 245 ASP cc_start: 0.7288 (m-30) cc_final: 0.6729 (t0) REVERT: C 308 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8437 (tm-30) REVERT: C 309 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6679 (tm-30) REVERT: C 323 ASP cc_start: 0.7887 (t0) cc_final: 0.7344 (t0) REVERT: D 245 ASP cc_start: 0.7497 (m-30) cc_final: 0.7058 (t0) REVERT: D 308 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8507 (tm-30) REVERT: D 323 ASP cc_start: 0.7888 (t0) cc_final: 0.7400 (t0) REVERT: E 241 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7291 (t0) REVERT: E 308 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8458 (tm-30) REVERT: F 245 ASP cc_start: 0.7502 (m-30) cc_final: 0.6974 (t0) REVERT: F 308 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8673 (tm-30) REVERT: F 316 LYS cc_start: 0.8037 (mttt) cc_final: 0.7817 (mttm) REVERT: F 323 ASP cc_start: 0.7987 (t0) cc_final: 0.7529 (t0) outliers start: 17 outliers final: 8 residues processed: 214 average time/residue: 1.4074 time to fit residues: 317.6136 Evaluate side-chains 211 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 199 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain F residue 286 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8472 Z= 0.212 Angle : 0.619 10.076 11406 Z= 0.307 Chirality : 0.038 0.154 1224 Planarity : 0.004 0.031 1518 Dihedral : 4.241 27.170 1134 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.82 % Allowed : 23.72 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.29), residues: 978 helix: 2.27 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.25 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP B 221 PHE 0.018 0.002 PHE F 285 TYR 0.005 0.001 TYR F 348 ARG 0.009 0.000 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.7216 (m-30) cc_final: 0.6778 (t0) REVERT: A 249 ASP cc_start: 0.7735 (m-30) cc_final: 0.7264 (m-30) REVERT: A 308 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8531 (tm-30) REVERT: A 309 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6630 (tm-30) REVERT: A 323 ASP cc_start: 0.7863 (t0) cc_final: 0.7353 (t0) REVERT: B 227 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: B 241 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7226 (t0) REVERT: B 308 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8372 (tm-30) REVERT: B 309 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6618 (tm-30) REVERT: C 211 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7427 (pp-130) REVERT: C 308 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8406 (tm-30) REVERT: C 309 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6717 (tm-30) REVERT: C 323 ASP cc_start: 0.7865 (t0) cc_final: 0.7330 (t0) REVERT: D 245 ASP cc_start: 0.7481 (m-30) cc_final: 0.7070 (t0) REVERT: D 308 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8515 (tm-30) REVERT: D 309 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6559 (tm-30) REVERT: D 323 ASP cc_start: 0.7888 (t0) cc_final: 0.7425 (t0) REVERT: E 241 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7343 (t0) REVERT: E 308 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8455 (tm-30) REVERT: E 323 ASP cc_start: 0.7996 (t0) cc_final: 0.7571 (t0) REVERT: F 245 ASP cc_start: 0.7517 (m-30) cc_final: 0.6971 (t0) REVERT: F 308 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8645 (tm-30) REVERT: F 316 LYS cc_start: 0.8046 (mttt) cc_final: 0.7761 (mttm) REVERT: F 323 ASP cc_start: 0.7976 (t0) cc_final: 0.7525 (t0) outliers start: 17 outliers final: 7 residues processed: 217 average time/residue: 1.4693 time to fit residues: 335.9695 Evaluate side-chains 214 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain F residue 286 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 72 optimal weight: 0.3980 chunk 84 optimal weight: 0.5980 chunk 88 optimal weight: 0.0770 chunk 80 optimal weight: 3.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8472 Z= 0.185 Angle : 0.616 10.047 11406 Z= 0.303 Chirality : 0.037 0.162 1224 Planarity : 0.004 0.028 1518 Dihedral : 4.154 28.659 1134 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.60 % Allowed : 23.72 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.28), residues: 978 helix: 2.65 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.84 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 221 PHE 0.014 0.001 PHE F 285 TYR 0.005 0.001 TYR F 348 ARG 0.008 0.000 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.7156 (m-30) cc_final: 0.6854 (t0) REVERT: A 308 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8483 (tm-30) REVERT: A 309 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6541 (tm-30) REVERT: A 323 ASP cc_start: 0.7833 (t0) cc_final: 0.7316 (t0) REVERT: B 222 ARG cc_start: 0.8249 (mmp-170) cc_final: 0.7901 (mmp-170) REVERT: B 227 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: B 308 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8390 (tm-30) REVERT: B 309 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6562 (tm-30) REVERT: B 323 ASP cc_start: 0.7977 (t0) cc_final: 0.7618 (t0) REVERT: C 308 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8384 (tm-30) REVERT: C 309 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6627 (tm-30) REVERT: C 323 ASP cc_start: 0.7838 (t0) cc_final: 0.7307 (t0) REVERT: D 308 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8502 (tm-30) REVERT: D 323 ASP cc_start: 0.7859 (t0) cc_final: 0.7394 (t0) REVERT: E 241 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7270 (t0) REVERT: E 308 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8419 (tm-30) REVERT: E 323 ASP cc_start: 0.7945 (t0) cc_final: 0.7522 (t0) REVERT: F 245 ASP cc_start: 0.7470 (m-30) cc_final: 0.6959 (t0) REVERT: F 308 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8506 (tm-30) REVERT: F 316 LYS cc_start: 0.8033 (mttt) cc_final: 0.7748 (mttp) REVERT: F 323 ASP cc_start: 0.7953 (t0) cc_final: 0.7490 (t0) outliers start: 15 outliers final: 7 residues processed: 210 average time/residue: 1.5035 time to fit residues: 332.1831 Evaluate side-chains 202 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 193 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain C residue 215 ARG Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain F residue 286 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.5980 chunk 88 optimal weight: 0.0070 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN ** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8472 Z= 0.229 Angle : 0.652 10.275 11406 Z= 0.320 Chirality : 0.038 0.167 1224 Planarity : 0.004 0.047 1518 Dihedral : 4.256 30.240 1134 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.60 % Allowed : 23.61 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.29), residues: 978 helix: 2.37 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.14 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP B 221 PHE 0.019 0.002 PHE F 285 TYR 0.006 0.001 TYR F 348 ARG 0.010 0.001 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.7250 (m-30) cc_final: 0.6908 (t0) REVERT: A 308 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8505 (tm-30) REVERT: A 309 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6609 (tm-30) REVERT: A 323 ASP cc_start: 0.7852 (t0) cc_final: 0.7370 (t0) REVERT: B 227 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7907 (mp0) REVERT: B 237 ARG cc_start: 0.7463 (mmt90) cc_final: 0.7239 (mpt-90) REVERT: B 308 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8385 (tm-30) REVERT: B 309 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6621 (tm-30) REVERT: C 221 TRP cc_start: 0.7028 (t60) cc_final: 0.6063 (t60) REVERT: C 308 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8386 (tm-30) REVERT: C 309 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6702 (tm-30) REVERT: C 323 ASP cc_start: 0.7835 (t0) cc_final: 0.7325 (t0) REVERT: D 308 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8526 (tm-30) REVERT: D 323 ASP cc_start: 0.7850 (t0) cc_final: 0.7387 (t0) REVERT: E 241 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7169 (t0) REVERT: E 308 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8431 (tm-30) REVERT: F 245 ASP cc_start: 0.7551 (m-30) cc_final: 0.6989 (t0) REVERT: F 308 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8520 (tm-30) REVERT: F 316 LYS cc_start: 0.8052 (mttt) cc_final: 0.7774 (mttm) REVERT: F 323 ASP cc_start: 0.7935 (t0) cc_final: 0.7481 (t0) outliers start: 15 outliers final: 11 residues processed: 200 average time/residue: 1.4294 time to fit residues: 301.1268 Evaluate side-chains 207 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain C residue 215 ARG Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain F residue 286 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 88 optimal weight: 0.0270 chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 0.0470 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN ** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8472 Z= 0.197 Angle : 0.658 11.560 11406 Z= 0.319 Chirality : 0.037 0.158 1224 Planarity : 0.004 0.053 1518 Dihedral : 4.236 29.749 1134 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.60 % Allowed : 23.82 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.29), residues: 978 helix: 2.44 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.07 (0.41), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP A 221 PHE 0.015 0.001 PHE F 285 TYR 0.005 0.001 TYR F 348 ARG 0.008 0.000 ARG B 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.7236 (m-30) cc_final: 0.6890 (t0) REVERT: A 308 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8496 (tm-30) REVERT: A 309 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6511 (tm-30) REVERT: A 323 ASP cc_start: 0.7798 (t0) cc_final: 0.7324 (t0) REVERT: B 227 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: B 237 ARG cc_start: 0.7430 (mmt90) cc_final: 0.7206 (mpt-90) REVERT: B 308 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8399 (tm-30) REVERT: B 309 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6558 (tm-30) REVERT: B 323 ASP cc_start: 0.7947 (t0) cc_final: 0.7578 (t0) REVERT: C 308 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8379 (tm-30) REVERT: C 309 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6649 (tm-30) REVERT: C 323 ASP cc_start: 0.7809 (t0) cc_final: 0.7269 (t0) REVERT: D 308 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8505 (tm-30) REVERT: D 323 ASP cc_start: 0.7847 (t0) cc_final: 0.7428 (t0) REVERT: E 241 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7297 (t0) REVERT: E 308 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8420 (tm-30) REVERT: E 323 ASP cc_start: 0.7947 (t0) cc_final: 0.7531 (t0) REVERT: F 245 ASP cc_start: 0.7523 (m-30) cc_final: 0.6986 (t0) REVERT: F 308 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8511 (tm-30) REVERT: F 309 GLU cc_start: 0.7037 (tm-30) cc_final: 0.6536 (tm-30) REVERT: F 316 LYS cc_start: 0.8026 (mttt) cc_final: 0.7800 (mttm) REVERT: F 323 ASP cc_start: 0.7936 (t0) cc_final: 0.7469 (t0) outliers start: 15 outliers final: 11 residues processed: 201 average time/residue: 1.4320 time to fit residues: 303.1522 Evaluate side-chains 201 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain F residue 286 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 0.0970 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN ** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.161371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118697 restraints weight = 9405.741| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.75 r_work: 0.3247 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8472 Z= 0.219 Angle : 0.675 11.557 11406 Z= 0.328 Chirality : 0.038 0.159 1224 Planarity : 0.004 0.044 1518 Dihedral : 4.292 30.626 1134 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.07 % Allowed : 24.47 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.29), residues: 978 helix: 2.44 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.07 (0.41), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP A 221 PHE 0.017 0.002 PHE F 285 TYR 0.006 0.001 TYR F 348 ARG 0.008 0.001 ARG B 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5196.54 seconds wall clock time: 92 minutes 34.30 seconds (5554.30 seconds total)