Starting phenix.real_space_refine on Thu Mar 13 00:43:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ja5_61290/03_2025/9ja5_61290.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ja5_61290/03_2025/9ja5_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_61290/03_2025/9ja5_61290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ja5_61290/03_2025/9ja5_61290.map" model { file = "/net/cci-nas-00/data/ceres_data/9ja5_61290/03_2025/9ja5_61290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ja5_61290/03_2025/9ja5_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.93, per 1000 atoms: 0.58 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: 2.18 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: 0.72 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: 1.92 Time building geometry restraints manager: 2.51 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 5.020 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: 0.470 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.490 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.100 ------------------------------------------------------------------------------- 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 : 0.926 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: 1.4892 time to fit residues: 388.7201 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 : 0.917 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.165470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.121594 restraints weight = 9255.961| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.69 r_work: 0.3303 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 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 : 1.005 Fit side-chains REVERT: A 245 ASP cc_start: 0.7396 (m-30) cc_final: 0.6915 (OUTLIER) REVERT: A 301 GLU cc_start: 0.8380 (mp0) cc_final: 0.8096 (mp0) REVERT: A 309 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7276 (tm-30) REVERT: A 323 ASP cc_start: 0.7744 (t0) cc_final: 0.7228 (t0) REVERT: A 527 LEU cc_start: 0.9101 (mp) cc_final: 0.8834 (mp) REVERT: B 227 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8444 (mp0) REVERT: B 245 ASP cc_start: 0.7417 (m-30) cc_final: 0.7011 (t0) REVERT: B 323 ASP cc_start: 0.7838 (t0) cc_final: 0.7407 (t0) REVERT: C 245 ASP cc_start: 0.7501 (m-30) cc_final: 0.6743 (OUTLIER) REVERT: C 309 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6559 (tm-30) REVERT: C 323 ASP cc_start: 0.7596 (t0) cc_final: 0.7121 (t0) REVERT: D 245 ASP cc_start: 0.7575 (m-30) cc_final: 0.7193 (OUTLIER) REVERT: D 309 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6827 (tm-30) REVERT: D 323 ASP cc_start: 0.7668 (t0) cc_final: 0.7174 (t0) REVERT: F 245 ASP cc_start: 0.7760 (m-30) cc_final: 0.7079 (t0) REVERT: F 309 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6532 (tm-30) REVERT: F 316 LYS cc_start: 0.7416 (mttt) cc_final: 0.7206 (mttm) REVERT: F 323 ASP cc_start: 0.7802 (t0) cc_final: 0.7209 (t0) REVERT: F 326 ASP cc_start: 0.7534 (t0) cc_final: 0.6966 (t0) outliers start: 19 outliers final: 9 residues processed: 238 average time/residue: 1.3854 time to fit residues: 347.3522 Evaluate side-chains 225 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 218 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 C residue 225 THR Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 225 THR 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 31 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.158740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.115298 restraints weight = 9425.448| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.68 r_work: 0.3216 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8472 Z= 0.246 Angle : 0.634 6.987 11406 Z= 0.329 Chirality : 0.039 0.154 1224 Planarity : 0.005 0.041 1518 Dihedral : 4.545 22.720 1134 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 1.50 % Allowed : 18.70 % Favored : 79.81 % 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: 0.13 (0.28), residues: 978 helix: 1.21 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.90 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 221 PHE 0.027 0.002 PHE C 285 TYR 0.007 0.001 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 240 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 1.087 Fit side-chains REVERT: A 245 ASP cc_start: 0.7439 (m-30) cc_final: 0.6940 (OUTLIER) REVERT: A 308 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8672 (tm-30) REVERT: A 309 GLU cc_start: 0.7530 (tm-30) cc_final: 0.6872 (tm-30) REVERT: A 323 ASP cc_start: 0.7781 (t0) cc_final: 0.7236 (t0) REVERT: B 222 ARG cc_start: 0.8274 (mmp-170) cc_final: 0.8061 (mmp-170) REVERT: B 245 ASP cc_start: 0.7395 (m-30) cc_final: 0.7145 (t0) REVERT: B 308 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8593 (tm-30) REVERT: B 309 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6515 (tm-30) REVERT: B 323 ASP cc_start: 0.7930 (t0) cc_final: 0.7487 (t0) REVERT: C 221 TRP cc_start: 0.6651 (t60) cc_final: 0.6011 (t60) REVERT: C 222 ARG cc_start: 0.7764 (mmp-170) cc_final: 0.7522 (mmp-170) REVERT: C 245 ASP cc_start: 0.7576 (m-30) cc_final: 0.6802 (t0) REVERT: C 308 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8640 (tm-30) REVERT: C 309 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6684 (tm-30) REVERT: C 323 ASP cc_start: 0.7681 (t0) cc_final: 0.7072 (t0) REVERT: D 245 ASP cc_start: 0.7626 (m-30) cc_final: 0.7203 (t0) REVERT: D 308 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8661 (tm-30) REVERT: D 309 GLU cc_start: 0.7443 (tm-30) cc_final: 0.6758 (tm-30) REVERT: D 323 ASP cc_start: 0.7786 (t0) cc_final: 0.7244 (t0) REVERT: E 309 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6600 (tm-30) REVERT: E 323 ASP cc_start: 0.7891 (t0) cc_final: 0.7451 (t0) REVERT: F 245 ASP cc_start: 0.7832 (m-30) cc_final: 0.7062 (t0) REVERT: F 309 GLU cc_start: 0.7271 (tm-30) cc_final: 0.6764 (tm-30) REVERT: F 323 ASP cc_start: 0.7844 (t0) cc_final: 0.7299 (t0) REVERT: F 326 ASP cc_start: 0.7583 (t0) cc_final: 0.7042 (t0) outliers start: 14 outliers final: 11 residues processed: 234 average time/residue: 1.4855 time to fit residues: 366.1292 Evaluate side-chains 217 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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 286 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain C 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 286 ASN 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 84 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.159609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.115910 restraints weight = 9289.557| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.70 r_work: 0.3213 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8472 Z= 0.242 Angle : 0.620 9.141 11406 Z= 0.318 Chirality : 0.039 0.148 1224 Planarity : 0.004 0.031 1518 Dihedral : 4.423 22.674 1134 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.92 % Allowed : 20.19 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.82 (0.28), residues: 978 helix: 1.71 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.59 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B 221 PHE 0.024 0.002 PHE C 285 TYR 0.006 0.001 TYR B 314 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 227 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 1.300 Fit side-chains REVERT: A 245 ASP cc_start: 0.7410 (m-30) cc_final: 0.6907 (t0) REVERT: A 308 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8595 (tm-30) REVERT: A 309 GLU cc_start: 0.7428 (tm-30) cc_final: 0.6707 (tm-30) REVERT: A 323 ASP cc_start: 0.7723 (t0) cc_final: 0.7179 (t0) REVERT: B 245 ASP cc_start: 0.7362 (m-30) cc_final: 0.6916 (t0) REVERT: B 249 ASP cc_start: 0.7989 (m-30) cc_final: 0.7756 (m-30) REVERT: B 308 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8415 (tm-30) REVERT: B 309 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6402 (tm-30) REVERT: B 323 ASP cc_start: 0.7898 (t0) cc_final: 0.7448 (t0) REVERT: C 221 TRP cc_start: 0.6708 (t60) cc_final: 0.6214 (t60) REVERT: C 245 ASP cc_start: 0.7492 (m-30) cc_final: 0.6722 (t0) REVERT: C 249 ASP cc_start: 0.8061 (m-30) cc_final: 0.7733 (m-30) REVERT: C 308 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8497 (tm-30) REVERT: C 309 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6589 (tm-30) REVERT: C 323 ASP cc_start: 0.7712 (t0) cc_final: 0.7138 (t0) REVERT: D 245 ASP cc_start: 0.7600 (m-30) cc_final: 0.7175 (t0) REVERT: D 308 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8566 (tm-30) REVERT: D 309 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6601 (tm-30) REVERT: D 323 ASP cc_start: 0.7740 (t0) cc_final: 0.7193 (t0) REVERT: E 241 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7584 (t0) REVERT: E 308 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8553 (tm-30) REVERT: F 245 ASP cc_start: 0.7781 (m-30) cc_final: 0.7035 (t0) REVERT: F 308 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8649 (tm-30) REVERT: F 309 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6567 (tm-30) REVERT: F 323 ASP cc_start: 0.7877 (t0) cc_final: 0.7351 (t0) REVERT: F 326 ASP cc_start: 0.7476 (t0) cc_final: 0.6959 (t0) outliers start: 18 outliers final: 12 residues processed: 218 average time/residue: 1.4218 time to fit residues: 326.3790 Evaluate side-chains 214 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 A residue 530 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 530 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 82 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.159465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.115647 restraints weight = 9339.749| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.70 r_work: 0.3207 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8472 Z= 0.239 Angle : 0.600 9.017 11406 Z= 0.308 Chirality : 0.038 0.155 1224 Planarity : 0.004 0.029 1518 Dihedral : 4.335 23.485 1134 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.31 % Allowed : 21.15 % Favored : 75.53 % 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: 1.19 (0.29), residues: 978 helix: 1.98 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.45 (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 242 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 245 ASP cc_start: 0.7420 (m-30) cc_final: 0.6912 (t0) REVERT: A 308 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8528 (tm-30) REVERT: A 309 GLU cc_start: 0.7384 (tm-30) cc_final: 0.6650 (tm-30) REVERT: A 323 ASP cc_start: 0.7679 (t0) cc_final: 0.7161 (t0) REVERT: B 244 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7668 (ttp80) REVERT: B 245 ASP cc_start: 0.7405 (m-30) cc_final: 0.7172 (t0) REVERT: B 308 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8359 (tm-30) REVERT: B 309 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6345 (tm-30) REVERT: B 323 ASP cc_start: 0.7928 (t0) cc_final: 0.7446 (t0) REVERT: C 211 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7901 (pp-130) REVERT: C 245 ASP cc_start: 0.7489 (m-30) cc_final: 0.6744 (t0) REVERT: C 308 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8497 (tm-30) REVERT: C 309 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6618 (tm-30) REVERT: C 323 ASP cc_start: 0.7691 (t0) cc_final: 0.7086 (t0) REVERT: D 245 ASP cc_start: 0.7550 (m-30) cc_final: 0.7120 (t0) REVERT: D 308 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8513 (tm-30) REVERT: D 309 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6566 (tm-30) REVERT: D 323 ASP cc_start: 0.7719 (t0) cc_final: 0.7140 (t0) REVERT: E 241 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7704 (t0) REVERT: E 286 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7720 (p0) REVERT: E 308 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8489 (tm-30) REVERT: E 323 ASP cc_start: 0.7855 (t0) cc_final: 0.7327 (t0) REVERT: F 211 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7776 (pp-130) REVERT: F 245 ASP cc_start: 0.7806 (m-30) cc_final: 0.7053 (t0) REVERT: F 308 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8689 (tm-30) REVERT: F 323 ASP cc_start: 0.7851 (t0) cc_final: 0.7350 (t0) outliers start: 31 outliers final: 13 residues processed: 226 average time/residue: 1.4313 time to fit residues: 342.3258 Evaluate side-chains 219 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 B residue 225 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 530 THR 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 D residue 225 THR Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 232 LEU 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 211 MET Chi-restraints excluded: chain F residue 225 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 31 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 50 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** D 540 GLN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.160038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.115625 restraints weight = 9335.502| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.73 r_work: 0.3205 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8472 Z= 0.237 Angle : 0.628 10.741 11406 Z= 0.313 Chirality : 0.039 0.152 1224 Planarity : 0.004 0.041 1518 Dihedral : 4.382 26.095 1134 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.35 % Allowed : 22.86 % Favored : 74.79 % 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: 1.35 (0.28), residues: 978 helix: 2.10 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.37 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 221 PHE 0.022 0.002 PHE F 285 TYR 0.005 0.001 TYR D 348 ARG 0.007 0.000 ARG E 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 226 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.912 Fit side-chains REVERT: A 245 ASP cc_start: 0.7439 (m-30) cc_final: 0.6915 (t0) REVERT: A 308 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8521 (tm-30) REVERT: A 309 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6613 (tm-30) REVERT: A 323 ASP cc_start: 0.7682 (t0) cc_final: 0.7153 (t0) REVERT: A 527 LEU cc_start: 0.8249 (pt) cc_final: 0.7917 (pp) REVERT: B 222 ARG cc_start: 0.8340 (mmp-170) cc_final: 0.8017 (mmp-170) REVERT: B 227 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8214 (mp0) REVERT: B 237 ARG cc_start: 0.7509 (mmt90) cc_final: 0.7014 (mpt180) REVERT: B 244 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7634 (ttp80) REVERT: B 245 ASP cc_start: 0.7478 (m-30) cc_final: 0.6987 (t0) REVERT: B 308 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8339 (tm-30) REVERT: B 309 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6582 (tm-30) REVERT: C 211 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7900 (pp-130) REVERT: C 245 ASP cc_start: 0.7477 (m-30) cc_final: 0.6747 (t0) REVERT: C 308 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8392 (tm-30) REVERT: C 309 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6564 (tm-30) REVERT: C 323 ASP cc_start: 0.7672 (t0) cc_final: 0.7089 (t0) REVERT: D 211 MET cc_start: 0.8264 (pp-130) cc_final: 0.8026 (pp-130) REVERT: D 308 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8481 (tm-30) REVERT: D 309 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6540 (tm-30) REVERT: D 323 ASP cc_start: 0.7705 (t0) cc_final: 0.7170 (t0) REVERT: E 241 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7521 (t0) REVERT: E 308 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8460 (tm-30) REVERT: F 211 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7768 (pp-130) REVERT: F 245 ASP cc_start: 0.7810 (m-30) cc_final: 0.7055 (t0) REVERT: F 308 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8621 (tm-30) REVERT: F 323 ASP cc_start: 0.7857 (t0) cc_final: 0.7351 (t0) outliers start: 22 outliers final: 12 residues processed: 214 average time/residue: 1.4613 time to fit residues: 329.3052 Evaluate side-chains 218 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 211 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 232 LEU 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 211 MET Chi-restraints excluded: chain F residue 225 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 76 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.161308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117137 restraints weight = 9390.111| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.72 r_work: 0.3224 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8472 Z= 0.217 Angle : 0.618 10.179 11406 Z= 0.308 Chirality : 0.038 0.182 1224 Planarity : 0.004 0.044 1518 Dihedral : 4.295 26.632 1134 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.46 % Allowed : 22.86 % 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: 1.51 (0.29), residues: 978 helix: 2.23 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.33 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 221 PHE 0.019 0.002 PHE F 285 TYR 0.005 0.001 TYR F 348 ARG 0.007 0.000 ARG E 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 240 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 1.031 Fit side-chains REVERT: A 245 ASP cc_start: 0.7432 (m-30) cc_final: 0.6894 (t0) REVERT: A 308 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8516 (tm-30) REVERT: A 309 GLU cc_start: 0.7314 (tm-30) cc_final: 0.6574 (tm-30) REVERT: A 323 ASP cc_start: 0.7641 (t0) cc_final: 0.7052 (t0) REVERT: A 527 LEU cc_start: 0.8368 (pt) cc_final: 0.8123 (pp) REVERT: B 227 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: B 237 ARG cc_start: 0.7516 (mmt90) cc_final: 0.7009 (mpt180) REVERT: B 245 ASP cc_start: 0.7479 (m-30) cc_final: 0.6950 (t0) REVERT: B 308 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8325 (tm-30) REVERT: B 309 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6640 (tm-30) REVERT: B 323 ASP cc_start: 0.7907 (t0) cc_final: 0.7453 (t0) REVERT: C 211 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7763 (pp-130) REVERT: C 245 ASP cc_start: 0.7441 (m-30) cc_final: 0.6670 (t0) REVERT: C 249 ASP cc_start: 0.8027 (m-30) cc_final: 0.7660 (m-30) REVERT: C 308 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8349 (tm-30) REVERT: C 309 GLU cc_start: 0.7071 (tm-30) cc_final: 0.6557 (tm-30) REVERT: C 323 ASP cc_start: 0.7649 (t0) cc_final: 0.7072 (t0) REVERT: D 308 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8491 (tm-30) REVERT: D 309 GLU cc_start: 0.7260 (tm-30) cc_final: 0.6500 (tm-30) REVERT: D 323 ASP cc_start: 0.7699 (t0) cc_final: 0.7159 (t0) REVERT: E 241 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7651 (t0) REVERT: E 308 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8420 (tm-30) REVERT: E 323 ASP cc_start: 0.7817 (t0) cc_final: 0.7324 (t0) REVERT: F 211 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7756 (pp-130) REVERT: F 245 ASP cc_start: 0.7780 (m-30) cc_final: 0.7027 (t0) REVERT: F 308 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8579 (tm-30) REVERT: F 309 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6375 (tm-30) REVERT: F 323 ASP cc_start: 0.7817 (t0) cc_final: 0.7304 (t0) outliers start: 23 outliers final: 15 residues processed: 229 average time/residue: 1.4038 time to fit residues: 338.6006 Evaluate side-chains 224 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 A residue 534 GLU 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 211 MET 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 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 E residue 530 THR Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 225 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 78 optimal weight: 0.0070 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.160539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.117689 restraints weight = 9559.581| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.76 r_work: 0.3212 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3624 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= 0.204 Angle : 0.633 10.200 11406 Z= 0.314 Chirality : 0.038 0.195 1224 Planarity : 0.004 0.046 1518 Dihedral : 4.263 29.448 1134 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 1.92 % Allowed : 23.50 % 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: 1.67 (0.29), residues: 978 helix: 2.34 (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 0.039 0.003 TRP B 221 PHE 0.017 0.002 PHE D 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 225 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 207 time to evaluate : 0.985 Fit side-chains REVERT: A 245 ASP cc_start: 0.7146 (m-30) cc_final: 0.6615 (t0) REVERT: A 308 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8402 (tm-30) REVERT: A 309 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6362 (tm-30) REVERT: A 323 ASP cc_start: 0.7370 (t0) cc_final: 0.6803 (t0) REVERT: A 527 LEU cc_start: 0.8477 (pt) cc_final: 0.8159 (pp) REVERT: B 227 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: B 237 ARG cc_start: 0.7248 (mmt90) cc_final: 0.6724 (mpt180) REVERT: B 245 ASP cc_start: 0.7172 (m-30) cc_final: 0.6634 (t0) REVERT: B 296 ARG cc_start: 0.8452 (mmp80) cc_final: 0.8221 (mmp-170) REVERT: B 308 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8197 (tm-30) REVERT: B 309 GLU cc_start: 0.6846 (tm-30) cc_final: 0.6420 (tm-30) REVERT: B 323 ASP cc_start: 0.7627 (t0) cc_final: 0.7149 (t0) REVERT: C 308 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8194 (tm-30) REVERT: C 309 GLU cc_start: 0.6815 (tm-30) cc_final: 0.6323 (tm-30) REVERT: C 323 ASP cc_start: 0.7372 (t0) cc_final: 0.6781 (t0) REVERT: D 308 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8396 (tm-30) REVERT: D 323 ASP cc_start: 0.7441 (t0) cc_final: 0.6877 (t0) REVERT: E 241 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7431 (t0) REVERT: E 308 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8263 (tm-30) REVERT: E 323 ASP cc_start: 0.7537 (t0) cc_final: 0.7062 (t0) REVERT: F 211 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7797 (pp-130) REVERT: F 245 ASP cc_start: 0.7518 (m-30) cc_final: 0.6776 (t0) REVERT: F 308 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8433 (tm-30) REVERT: F 323 ASP cc_start: 0.7565 (t0) cc_final: 0.7050 (t0) outliers start: 18 outliers final: 11 residues processed: 215 average time/residue: 1.5461 time to fit residues: 349.6755 Evaluate side-chains 208 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 A residue 534 GLU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 225 THR 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 211 MET Chi-restraints excluded: chain F residue 225 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 84 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.160836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.116643 restraints weight = 9436.768| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.74 r_work: 0.3217 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3610 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= 0.230 Angle : 0.660 10.205 11406 Z= 0.326 Chirality : 0.039 0.201 1224 Planarity : 0.004 0.038 1518 Dihedral : 4.364 29.885 1134 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.35 % Allowed : 23.40 % Favored : 74.25 % 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: 1.70 (0.29), residues: 978 helix: 2.37 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.27 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP E 221 PHE 0.020 0.002 PHE D 285 TYR 0.006 0.001 TYR F 348 ARG 0.010 0.000 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 218 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 245 ASP cc_start: 0.7448 (m-30) cc_final: 0.6909 (t0) REVERT: A 308 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8495 (tm-30) REVERT: A 309 GLU cc_start: 0.7336 (tm-30) cc_final: 0.6580 (tm-30) REVERT: A 323 ASP cc_start: 0.7626 (t0) cc_final: 0.7068 (t0) REVERT: A 527 LEU cc_start: 0.8521 (pt) cc_final: 0.8220 (pp) REVERT: B 227 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: B 237 ARG cc_start: 0.7489 (mmt90) cc_final: 0.6952 (mpt180) REVERT: B 245 ASP cc_start: 0.7451 (m-30) cc_final: 0.6907 (t0) REVERT: B 296 ARG cc_start: 0.8558 (mmp80) cc_final: 0.8251 (mmp-170) REVERT: B 308 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8328 (tm-30) REVERT: B 309 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6549 (tm-30) REVERT: B 323 ASP cc_start: 0.7879 (t0) cc_final: 0.7406 (t0) REVERT: C 308 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8318 (tm-30) REVERT: C 309 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6537 (tm-30) REVERT: C 323 ASP cc_start: 0.7616 (t0) cc_final: 0.7029 (t0) REVERT: D 308 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8500 (tm-30) REVERT: D 309 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6471 (tm-30) REVERT: D 323 ASP cc_start: 0.7696 (t0) cc_final: 0.7161 (t0) REVERT: E 241 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7405 (t0) REVERT: E 308 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8374 (tm-30) REVERT: F 211 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7722 (pp-130) REVERT: F 245 ASP cc_start: 0.7777 (m-30) cc_final: 0.7015 (t0) REVERT: F 308 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8462 (tm-30) REVERT: F 323 ASP cc_start: 0.7788 (t0) cc_final: 0.7285 (t0) outliers start: 22 outliers final: 13 residues processed: 206 average time/residue: 1.3727 time to fit residues: 297.9800 Evaluate side-chains 209 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 A residue 534 GLU 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 D residue 225 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 225 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 14 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 40 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.161535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.117380 restraints weight = 9384.091| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.73 r_work: 0.3226 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8472 Z= 0.223 Angle : 0.665 11.548 11406 Z= 0.326 Chirality : 0.038 0.160 1224 Planarity : 0.004 0.046 1518 Dihedral : 4.427 29.297 1134 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.82 % Allowed : 24.36 % Favored : 73.82 % 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: 1.73 (0.29), residues: 978 helix: 2.39 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.25 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP E 221 PHE 0.019 0.002 PHE F 285 TYR 0.005 0.001 TYR F 348 ARG 0.010 0.000 ARG C 222 ********************** 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 212 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 245 ASP cc_start: 0.7452 (m-30) cc_final: 0.6908 (t0) REVERT: A 308 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8497 (tm-30) REVERT: A 309 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6530 (tm-30) REVERT: A 323 ASP cc_start: 0.7610 (t0) cc_final: 0.7026 (t0) REVERT: A 527 LEU cc_start: 0.8536 (pt) cc_final: 0.8235 (pp) REVERT: B 227 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: B 237 ARG cc_start: 0.7494 (mmt90) cc_final: 0.7073 (mpt180) REVERT: B 245 ASP cc_start: 0.7426 (m-30) cc_final: 0.6896 (t0) REVERT: B 296 ARG cc_start: 0.8559 (mmp80) cc_final: 0.8245 (mmp-170) REVERT: B 308 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8343 (tm-30) REVERT: B 309 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6534 (tm-30) REVERT: B 323 ASP cc_start: 0.7853 (t0) cc_final: 0.7392 (t0) REVERT: C 211 MET cc_start: 0.8878 (ppp) cc_final: 0.8644 (ppp) REVERT: C 308 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8326 (tm-30) REVERT: C 309 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6511 (tm-30) REVERT: C 323 ASP cc_start: 0.7593 (t0) cc_final: 0.7021 (t0) REVERT: D 211 MET cc_start: 0.8865 (ppp) cc_final: 0.8635 (ppp) REVERT: D 308 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8505 (tm-30) REVERT: D 309 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6405 (tm-30) REVERT: D 323 ASP cc_start: 0.7688 (t0) cc_final: 0.7125 (t0) REVERT: E 221 TRP cc_start: 0.7464 (t60) cc_final: 0.7018 (t60) REVERT: E 241 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7635 (t0) REVERT: E 308 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8396 (tm-30) REVERT: E 323 ASP cc_start: 0.7799 (t0) cc_final: 0.7325 (t0) REVERT: F 211 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7663 (pp-130) REVERT: F 245 ASP cc_start: 0.7784 (m-30) cc_final: 0.7016 (t0) REVERT: F 308 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8452 (tm-30) REVERT: F 323 ASP cc_start: 0.7769 (t0) cc_final: 0.7268 (t0) outliers start: 17 outliers final: 13 residues processed: 201 average time/residue: 1.4627 time to fit residues: 309.0644 Evaluate side-chains 205 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 534 GLU 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 D residue 225 THR Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 225 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 65 optimal weight: 0.1980 chunk 86 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 52 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 532 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 = 0.3897 r_free = 0.3897 target = 0.161246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118652 restraints weight = 9571.119| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.77 r_work: 0.3118 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8472 Z= 0.203 Angle : 0.648 11.589 11406 Z= 0.317 Chirality : 0.038 0.151 1224 Planarity : 0.004 0.060 1518 Dihedral : 4.330 29.896 1134 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 1.71 % Allowed : 24.68 % Favored : 73.61 % 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: 1.84 (0.29), residues: 978 helix: 2.47 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.20 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP E 221 PHE 0.017 0.002 PHE D 285 TYR 0.006 0.001 TYR F 348 ARG 0.009 0.000 ARG B 244 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7951.75 seconds wall clock time: 139 minutes 6.74 seconds (8346.74 seconds total)