Starting phenix.real_space_refine on Tue Mar 3 21:55:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zo9_14844/03_2026/7zo9_14844_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zo9_14844/03_2026/7zo9_14844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zo9_14844/03_2026/7zo9_14844_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zo9_14844/03_2026/7zo9_14844_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zo9_14844/03_2026/7zo9_14844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zo9_14844/03_2026/7zo9_14844.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.090 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 64 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians V 2 8.30 5 P 4 5.49 5 S 44 5.16 5 C 5526 2.51 5 N 1534 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8730 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4333 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} Conformer: "B" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} bond proxies already assigned to first conformer: 4380 Conformer: "C" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} bond proxies already assigned to first conformer: 4380 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 4.58, per 1000 atoms: 0.52 Number of scatterers: 8730 At special positions: 0 Unit cell: (85.075, 76.875, 131.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) V 2 22.97 S 44 16.00 P 4 15.00 O 1620 8.00 N 1534 7.00 C 5526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 989.2 milliseconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 4 sheets defined 68.3% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 removed outlier: 4.420A pdb=" N LYS A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 46 removed outlier: 4.026A pdb=" N THR A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 56 through 101 removed outlier: 3.593A pdb=" N LEU A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.627A pdb=" N HIS A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 154 removed outlier: 3.881A pdb=" N SER A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Proline residue: A 149 - end of helix removed outlier: 3.536A pdb=" N MET A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 203 removed outlier: 3.507A pdb=" N SER A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 213 through 231 removed outlier: 3.660A pdb=" N ALA A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 264 removed outlier: 3.727A pdb=" N LEU A 236 " --> pdb=" O GLN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 314 removed outlier: 3.717A pdb=" N ASP A 274 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 382 Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.610A pdb=" N ALA A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 437 through 448 removed outlier: 3.610A pdb=" N VAL A 441 " --> pdb=" O THR A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 455 removed outlier: 4.710A pdb=" N PHE A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 474 through 489 Processing helix chain 'A' and resid 503 through 519 removed outlier: 3.769A pdb=" N ALA A 513 " --> pdb=" O LYS A 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 17 through 46 removed outlier: 4.026A pdb=" N THR B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 56 through 101 removed outlier: 3.592A pdb=" N LEU B 60 " --> pdb=" O PHE B 56 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.627A pdb=" N HIS B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 154 removed outlier: 3.880A pdb=" N SER B 125 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Proline residue: B 149 - end of helix removed outlier: 3.537A pdb=" N MET B 154 " --> pdb=" O VAL B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 203 removed outlier: 3.507A pdb=" N SER B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA B 186 " --> pdb=" O ASP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 213 through 231 removed outlier: 3.661A pdb=" N ALA B 231 " --> pdb=" O ASN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 264 removed outlier: 3.727A pdb=" N LEU B 236 " --> pdb=" O GLN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 314 removed outlier: 3.716A pdb=" N ASP B 274 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ILE B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 382 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.609A pdb=" N ALA B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 431 Processing helix chain 'B' and resid 437 through 448 removed outlier: 3.612A pdb=" N VAL B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 455 removed outlier: 4.711A pdb=" N PHE B 453 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 474 through 489 Processing helix chain 'B' and resid 503 through 519 removed outlier: 3.768A pdb=" N ALA B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.941A pdb=" N VAL A 340 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA A 389 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 414 removed outlier: 6.589A pdb=" N LEU A 493 " --> pdb=" O PHE A 524 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE A 526 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU A 495 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ALA A 365 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.941A pdb=" N VAL B 340 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA B 389 " --> pdb=" O VAL B 340 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 411 through 414 removed outlier: 6.589A pdb=" N LEU B 493 " --> pdb=" O PHE B 524 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ILE B 526 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU B 495 " --> pdb=" O ILE B 526 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA B 365 " --> pdb=" O LEU B 540 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1696 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: 1.12 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 2962 1.36 - 1.50: 2174 1.50 - 1.64: 3656 1.64 - 1.77: 0 1.77 - 1.91: 94 Bond restraints: 8886 Sorted by residual: bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.38e+00 bond pdb=" C4 ADP A 601 " pdb=" C5 ADP A 601 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" CA PHE A 133 " pdb=" C PHE A 133 " ideal model delta sigma weight residual 1.524 1.511 0.013 1.28e-02 6.10e+03 1.06e+00 bond pdb=" CB PRO A 149 " pdb=" CG PRO A 149 " ideal model delta sigma weight residual 1.492 1.441 0.051 5.00e-02 4.00e+02 1.04e+00 bond pdb=" CB GLN B 512 " pdb=" CG GLN B 512 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.02e+00 ... (remaining 8881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 11761 1.69 - 3.38: 225 3.38 - 5.07: 58 5.07 - 6.76: 14 6.76 - 8.45: 2 Bond angle restraints: 12060 Sorted by residual: angle pdb=" CA GLN A 512 " pdb=" CB GLN A 512 " pdb=" CG GLN A 512 " ideal model delta sigma weight residual 114.10 120.28 -6.18 2.00e+00 2.50e-01 9.55e+00 angle pdb=" CA GLN B 512 " pdb=" CB GLN B 512 " pdb=" CG GLN B 512 " ideal model delta sigma weight residual 114.10 120.27 -6.17 2.00e+00 2.50e-01 9.52e+00 angle pdb=" CB MET B 24 " pdb=" CG MET B 24 " pdb=" SD MET B 24 " ideal model delta sigma weight residual 112.70 121.15 -8.45 3.00e+00 1.11e-01 7.94e+00 angle pdb=" CB MET A 24 " pdb=" CG MET A 24 " pdb=" SD MET A 24 " ideal model delta sigma weight residual 112.70 121.14 -8.44 3.00e+00 1.11e-01 7.92e+00 angle pdb=" CA GLY A 390 " pdb=" C GLY A 390 " pdb=" N ARG A 391 " ideal model delta sigma weight residual 114.75 117.22 -2.47 9.90e-01 1.02e+00 6.21e+00 ... (remaining 12055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.74: 4979 25.74 - 51.49: 297 51.49 - 77.23: 28 77.23 - 102.98: 0 102.98 - 128.72: 4 Dihedral angle restraints: 5308 sinusoidal: 2074 harmonic: 3234 Sorted by residual: dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual 300.00 171.28 128.72 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" O1B ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PB ADP B 601 " pdb=" PA ADP B 601 " ideal model delta sinusoidal sigma weight residual 300.00 171.30 128.70 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual 300.00 178.78 121.23 1 2.00e+01 2.50e-03 3.64e+01 ... (remaining 5305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 734 0.026 - 0.051: 399 0.051 - 0.077: 186 0.077 - 0.102: 75 0.102 - 0.128: 28 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA ILE A 492 " pdb=" N ILE A 492 " pdb=" C ILE A 492 " pdb=" CB ILE A 492 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE B 492 " pdb=" N ILE B 492 " pdb=" C ILE B 492 " pdb=" CB ILE B 492 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA VAL B 414 " pdb=" N VAL B 414 " pdb=" C VAL B 414 " pdb=" CB VAL B 414 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 1419 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 134 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C MET A 134 " -0.058 2.00e-02 2.50e+03 pdb=" O MET A 134 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG A 135 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 134 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C MET B 134 " 0.057 2.00e-02 2.50e+03 pdb=" O MET B 134 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG B 135 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 135 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C ARG B 135 " -0.039 2.00e-02 2.50e+03 pdb=" O ARG B 135 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN B 136 " 0.013 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 237 2.71 - 3.26: 9645 3.26 - 3.81: 14346 3.81 - 4.35: 16587 4.35 - 4.90: 27932 Nonbonded interactions: 68747 Sorted by model distance: nonbonded pdb=" O SER B 458 " pdb=" OG1 THR B 463 " model vdw 2.164 3.040 nonbonded pdb=" O SER A 458 " pdb=" OG1 THR A 463 " model vdw 2.165 3.040 nonbonded pdb=" O GLU B 17 " pdb=" OG1 THR B 21 " model vdw 2.246 3.040 nonbonded pdb=" O GLU A 17 " pdb=" OG1 THR A 21 " model vdw 2.247 3.040 nonbonded pdb=" O ILE A 100 " pdb=" NE2 GLN B 209 " model vdw 2.318 3.120 ... (remaining 68742 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.560 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 : 0.003 0.051 8886 Z= 0.158 Angle : 0.631 8.455 12060 Z= 0.325 Chirality : 0.041 0.128 1422 Planarity : 0.005 0.045 1530 Dihedral : 15.326 128.721 3212 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.13 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.26), residues: 1112 helix: 1.11 (0.20), residues: 706 sheet: -0.25 (0.56), residues: 80 loop : -1.41 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 479 TYR 0.015 0.002 TYR A 169 PHE 0.027 0.002 PHE B 133 TRP 0.016 0.002 TRP A 8 HIS 0.005 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8886) covalent geometry : angle 0.63097 (12060) hydrogen bonds : bond 0.14624 ( 576) hydrogen bonds : angle 5.92692 ( 1696) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.322 Fit side-chains REVERT: A 156 MET cc_start: 0.6351 (ptt) cc_final: 0.6052 (ptp) REVERT: B 156 MET cc_start: 0.6389 (ptt) cc_final: 0.6087 (ptp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.0703 time to fit residues: 18.3471 Evaluate side-chains 137 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN ** A 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN B 47 GLN B 283 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.147802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.117515 restraints weight = 104357.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.124203 restraints weight = 21673.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.128722 restraints weight = 9547.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.131573 restraints weight = 5520.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.133504 restraints weight = 3811.450| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3796 r_free = 0.3796 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3796 r_free = 0.3796 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8886 Z= 0.146 Angle : 0.655 9.268 12060 Z= 0.326 Chirality : 0.042 0.197 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.427 95.248 1234 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.23 % Favored : 94.58 % Rotamer: Outliers : 1.30 % Allowed : 10.06 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.26), residues: 1112 helix: 1.56 (0.19), residues: 718 sheet: -0.24 (0.62), residues: 62 loop : -1.13 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 303 TYR 0.016 0.002 TYR B 169 PHE 0.025 0.002 PHE B 133 TRP 0.010 0.001 TRP B 8 HIS 0.005 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8886) covalent geometry : angle 0.65492 (12060) hydrogen bonds : bond 0.05071 ( 576) hydrogen bonds : angle 4.44222 ( 1696) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.294 Fit side-chains REVERT: A 156 MET cc_start: 0.6530 (ptt) cc_final: 0.6260 (ptp) REVERT: A 167 VAL cc_start: 0.8725 (t) cc_final: 0.8518 (p) REVERT: A 534 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6207 (ptp-170) REVERT: B 156 MET cc_start: 0.6499 (ptt) cc_final: 0.6212 (ptp) REVERT: B 167 VAL cc_start: 0.8718 (t) cc_final: 0.8510 (p) REVERT: B 534 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6210 (ptp-170) outliers start: 12 outliers final: 4 residues processed: 158 average time/residue: 0.0614 time to fit residues: 14.9437 Evaluate side-chains 143 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 534 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.148889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.119143 restraints weight = 97951.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.126728 restraints weight = 25983.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.131416 restraints weight = 9960.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.134916 restraints weight = 5829.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.134581 restraints weight = 4751.358| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8886 Z= 0.135 Angle : 0.635 8.571 12060 Z= 0.313 Chirality : 0.042 0.181 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.241 92.084 1234 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.42 % Favored : 94.40 % Rotamer: Outliers : 1.52 % Allowed : 12.12 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.26), residues: 1112 helix: 1.69 (0.20), residues: 716 sheet: -0.64 (0.60), residues: 62 loop : -1.15 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 303 TYR 0.013 0.001 TYR A 169 PHE 0.023 0.002 PHE A 133 TRP 0.013 0.002 TRP A 62 HIS 0.005 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8886) covalent geometry : angle 0.63504 (12060) hydrogen bonds : bond 0.04688 ( 576) hydrogen bonds : angle 4.25132 ( 1696) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.329 Fit side-chains REVERT: A 156 MET cc_start: 0.6554 (ptt) cc_final: 0.6223 (ptp) REVERT: A 534 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6265 (ptp-170) REVERT: B 156 MET cc_start: 0.6538 (ptt) cc_final: 0.6205 (ptp) REVERT: B 534 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6336 (ptp-170) outliers start: 14 outliers final: 7 residues processed: 143 average time/residue: 0.0658 time to fit residues: 14.4020 Evaluate side-chains 140 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 534 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 90 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 80 optimal weight: 0.0970 chunk 4 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 overall best weight: 1.0078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.147579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.116492 restraints weight = 105060.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.123224 restraints weight = 22992.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.127749 restraints weight = 10359.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.130696 restraints weight = 6098.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.132609 restraints weight = 4253.824| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3780 r_free = 0.3780 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3780 r_free = 0.3780 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8886 Z= 0.141 Angle : 0.637 8.500 12060 Z= 0.313 Chirality : 0.042 0.177 1422 Planarity : 0.004 0.040 1530 Dihedral : 7.179 94.172 1234 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.69 % Favored : 94.13 % Rotamer: Outliers : 2.38 % Allowed : 13.53 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.26), residues: 1112 helix: 1.64 (0.20), residues: 718 sheet: -0.50 (0.59), residues: 60 loop : -1.07 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 303 TYR 0.014 0.001 TYR A 169 PHE 0.024 0.002 PHE B 133 TRP 0.011 0.001 TRP B 8 HIS 0.005 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8886) covalent geometry : angle 0.63656 (12060) hydrogen bonds : bond 0.04725 ( 576) hydrogen bonds : angle 4.23073 ( 1696) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.308 Fit side-chains REVERT: A 41 LEU cc_start: 0.9103 (mm) cc_final: 0.8661 (mp) REVERT: A 156 MET cc_start: 0.6592 (ptt) cc_final: 0.6280 (ptp) REVERT: A 534 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.5873 (ptp-170) REVERT: B 41 LEU cc_start: 0.9110 (mm) cc_final: 0.8654 (mp) REVERT: B 156 MET cc_start: 0.6635 (ptt) cc_final: 0.6317 (ptp) REVERT: B 534 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.5908 (ptp-170) outliers start: 22 outliers final: 15 residues processed: 153 average time/residue: 0.0613 time to fit residues: 14.5081 Evaluate side-chains 147 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 62 TRP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 542 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 88 optimal weight: 0.0670 chunk 85 optimal weight: 0.9990 chunk 43 optimal weight: 0.0370 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.149763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.119243 restraints weight = 102728.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.125941 restraints weight = 23153.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.130326 restraints weight = 10450.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.133180 restraints weight = 6157.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.135062 restraints weight = 4316.090| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8886 Z= 0.120 Angle : 0.633 9.285 12060 Z= 0.305 Chirality : 0.041 0.192 1422 Planarity : 0.004 0.041 1530 Dihedral : 7.091 95.616 1234 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.05 % Favored : 94.77 % Rotamer: Outliers : 1.73 % Allowed : 14.94 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.26), residues: 1112 helix: 1.85 (0.20), residues: 710 sheet: -0.67 (0.58), residues: 62 loop : -1.04 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 303 TYR 0.008 0.001 TYR B 169 PHE 0.023 0.001 PHE B 133 TRP 0.008 0.001 TRP B 8 HIS 0.004 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8886) covalent geometry : angle 0.63322 (12060) hydrogen bonds : bond 0.04266 ( 576) hydrogen bonds : angle 4.08822 ( 1696) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.337 Fit side-chains REVERT: A 41 LEU cc_start: 0.9010 (mm) cc_final: 0.8553 (mp) REVERT: A 156 MET cc_start: 0.6589 (ptt) cc_final: 0.6271 (ptp) REVERT: B 41 LEU cc_start: 0.9044 (mm) cc_final: 0.8607 (mp) REVERT: B 156 MET cc_start: 0.6580 (ptt) cc_final: 0.6262 (ptp) outliers start: 16 outliers final: 14 residues processed: 157 average time/residue: 0.0644 time to fit residues: 15.6687 Evaluate side-chains 147 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 62 TRP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 378 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.148794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.119175 restraints weight = 89310.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.125714 restraints weight = 20438.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.130035 restraints weight = 9224.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.132860 restraints weight = 5425.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.134674 restraints weight = 3778.982| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3834 r_free = 0.3834 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3834 r_free = 0.3834 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8886 Z= 0.128 Angle : 0.650 9.049 12060 Z= 0.310 Chirality : 0.042 0.184 1422 Planarity : 0.004 0.040 1530 Dihedral : 7.083 98.412 1234 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.78 % Favored : 94.04 % Rotamer: Outliers : 1.95 % Allowed : 15.15 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.26), residues: 1112 helix: 1.74 (0.20), residues: 718 sheet: -0.52 (0.58), residues: 60 loop : -0.98 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 303 TYR 0.011 0.001 TYR A 169 PHE 0.026 0.002 PHE A 295 TRP 0.011 0.001 TRP A 106 HIS 0.005 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8886) covalent geometry : angle 0.64991 (12060) hydrogen bonds : bond 0.04379 ( 576) hydrogen bonds : angle 4.05958 ( 1696) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.335 Fit side-chains REVERT: A 41 LEU cc_start: 0.8988 (mm) cc_final: 0.8532 (mp) REVERT: A 156 MET cc_start: 0.6616 (ptt) cc_final: 0.6293 (ptp) REVERT: B 41 LEU cc_start: 0.8999 (mm) cc_final: 0.8548 (mp) REVERT: B 156 MET cc_start: 0.6614 (ptt) cc_final: 0.6292 (ptp) outliers start: 18 outliers final: 17 residues processed: 153 average time/residue: 0.0704 time to fit residues: 16.0443 Evaluate side-chains 156 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 62 TRP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 378 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.0070 chunk 48 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.151169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.121317 restraints weight = 94508.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.127893 restraints weight = 20820.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.132307 restraints weight = 9344.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.135108 restraints weight = 5472.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.136983 restraints weight = 3813.583| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8886 Z= 0.118 Angle : 0.638 9.833 12060 Z= 0.303 Chirality : 0.041 0.188 1422 Planarity : 0.004 0.041 1530 Dihedral : 7.045 101.519 1234 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.23 % Favored : 94.58 % Rotamer: Outliers : 1.62 % Allowed : 16.02 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.26), residues: 1112 helix: 1.87 (0.20), residues: 712 sheet: -0.51 (0.58), residues: 60 loop : -1.03 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 303 TYR 0.008 0.001 TYR A 169 PHE 0.022 0.001 PHE A 133 TRP 0.012 0.001 TRP B 106 HIS 0.005 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8886) covalent geometry : angle 0.63751 (12060) hydrogen bonds : bond 0.04115 ( 576) hydrogen bonds : angle 4.00771 ( 1696) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.296 Fit side-chains REVERT: A 41 LEU cc_start: 0.8964 (mm) cc_final: 0.8511 (mp) REVERT: A 156 MET cc_start: 0.6539 (ptt) cc_final: 0.6217 (ptp) REVERT: B 41 LEU cc_start: 0.8973 (mm) cc_final: 0.8517 (mp) REVERT: B 156 MET cc_start: 0.6431 (ptt) cc_final: 0.6113 (ptp) outliers start: 15 outliers final: 14 residues processed: 157 average time/residue: 0.0710 time to fit residues: 16.7941 Evaluate side-chains 155 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 62 TRP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 378 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 61 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS B 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.142553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.111607 restraints weight = 101670.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.118027 restraints weight = 23050.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.122334 restraints weight = 10573.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.125176 restraints weight = 6320.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.127019 restraints weight = 4466.459| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3708 r_free = 0.3708 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3708 r_free = 0.3708 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8886 Z= 0.233 Angle : 0.761 8.449 12060 Z= 0.373 Chirality : 0.046 0.168 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.312 108.899 1234 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.42 % Favored : 94.40 % Rotamer: Outliers : 2.06 % Allowed : 16.56 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.25), residues: 1112 helix: 1.42 (0.19), residues: 704 sheet: -0.41 (0.59), residues: 62 loop : -1.37 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 408 TYR 0.028 0.003 TYR A 169 PHE 0.019 0.002 PHE A 295 TRP 0.020 0.002 TRP A 8 HIS 0.007 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00562 ( 8886) covalent geometry : angle 0.76143 (12060) hydrogen bonds : bond 0.05693 ( 576) hydrogen bonds : angle 4.36930 ( 1696) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.299 Fit side-chains REVERT: A 62 TRP cc_start: 0.7309 (OUTLIER) cc_final: 0.6805 (t60) REVERT: A 156 MET cc_start: 0.7076 (ptt) cc_final: 0.6727 (ptp) REVERT: B 62 TRP cc_start: 0.7296 (OUTLIER) cc_final: 0.6805 (t60) REVERT: B 156 MET cc_start: 0.7074 (ptt) cc_final: 0.6713 (ptp) REVERT: B 283 GLN cc_start: 0.7961 (mt0) cc_final: 0.7611 (pt0) outliers start: 19 outliers final: 13 residues processed: 148 average time/residue: 0.0746 time to fit residues: 16.1037 Evaluate side-chains 148 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 62 TRP Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 542 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 97 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.147756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.118164 restraints weight = 89287.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.125427 restraints weight = 25953.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129921 restraints weight = 9897.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.132633 restraints weight = 5745.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.132780 restraints weight = 4529.431| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8886 Z= 0.134 Angle : 0.679 9.017 12060 Z= 0.323 Chirality : 0.043 0.207 1422 Planarity : 0.004 0.040 1530 Dihedral : 7.200 109.132 1234 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.05 % Favored : 94.77 % Rotamer: Outliers : 1.30 % Allowed : 17.75 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.26), residues: 1112 helix: 1.57 (0.19), residues: 716 sheet: -0.45 (0.58), residues: 62 loop : -1.23 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 303 TYR 0.014 0.001 TYR B 263 PHE 0.025 0.002 PHE B 133 TRP 0.013 0.001 TRP B 106 HIS 0.005 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8886) covalent geometry : angle 0.67884 (12060) hydrogen bonds : bond 0.04604 ( 576) hydrogen bonds : angle 4.13742 ( 1696) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6862 (ptt) cc_final: 0.6510 (ptp) REVERT: A 283 GLN cc_start: 0.7650 (pt0) cc_final: 0.7384 (mt0) REVERT: B 156 MET cc_start: 0.6856 (ptt) cc_final: 0.6502 (ptp) outliers start: 12 outliers final: 11 residues processed: 148 average time/residue: 0.0681 time to fit residues: 15.1467 Evaluate side-chains 152 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 62 TRP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 53 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 92 optimal weight: 0.0270 chunk 89 optimal weight: 8.9990 chunk 82 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.149291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.118796 restraints weight = 111572.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.125456 restraints weight = 22615.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.129889 restraints weight = 9919.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.132807 restraints weight = 5739.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.134760 restraints weight = 3961.872| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8886 Z= 0.124 Angle : 0.672 9.429 12060 Z= 0.318 Chirality : 0.042 0.213 1422 Planarity : 0.004 0.040 1530 Dihedral : 7.158 110.078 1234 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.42 % Favored : 94.40 % Rotamer: Outliers : 1.30 % Allowed : 18.18 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.26), residues: 1112 helix: 1.67 (0.20), residues: 718 sheet: -0.63 (0.57), residues: 60 loop : -1.15 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 303 TYR 0.014 0.001 TYR B 263 PHE 0.023 0.001 PHE B 133 TRP 0.012 0.001 TRP B 106 HIS 0.005 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8886) covalent geometry : angle 0.67213 (12060) hydrogen bonds : bond 0.04339 ( 576) hydrogen bonds : angle 4.08556 ( 1696) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6782 (ptt) cc_final: 0.6435 (ptp) REVERT: A 283 GLN cc_start: 0.7548 (pt0) cc_final: 0.7266 (mt0) REVERT: B 156 MET cc_start: 0.6779 (ptt) cc_final: 0.6430 (ptp) outliers start: 12 outliers final: 10 residues processed: 148 average time/residue: 0.0679 time to fit residues: 15.0590 Evaluate side-chains 150 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 62 TRP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 258 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.0000 chunk 75 optimal weight: 0.5980 chunk 53 optimal weight: 9.9990 chunk 43 optimal weight: 0.0470 chunk 0 optimal weight: 3.9990 overall best weight: 0.4482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.150826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.121164 restraints weight = 108497.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.129056 restraints weight = 28123.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.135567 restraints weight = 9900.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.135134 restraints weight = 4811.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.135719 restraints weight = 5171.245| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8886 Z= 0.121 Angle : 0.665 9.599 12060 Z= 0.313 Chirality : 0.042 0.209 1422 Planarity : 0.004 0.040 1530 Dihedral : 7.129 110.748 1234 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.14 % Favored : 94.68 % Rotamer: Outliers : 1.08 % Allowed : 18.29 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.26), residues: 1112 helix: 1.77 (0.20), residues: 714 sheet: -0.58 (0.58), residues: 60 loop : -1.05 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 303 TYR 0.015 0.001 TYR A 263 PHE 0.024 0.002 PHE B 133 TRP 0.011 0.001 TRP B 106 HIS 0.005 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8886) covalent geometry : angle 0.66458 (12060) hydrogen bonds : bond 0.04195 ( 576) hydrogen bonds : angle 4.03127 ( 1696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1481.68 seconds wall clock time: 26 minutes 16.41 seconds (1576.41 seconds total)