Starting phenix.real_space_refine on Thu Mar 13 12:40:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zo9_14844/03_2025/7zo9_14844_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zo9_14844/03_2025/7zo9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zo9_14844/03_2025/7zo9_14844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zo9_14844/03_2025/7zo9_14844.map" model { file = "/net/cci-nas-00/data/ceres_data/7zo9_14844/03_2025/7zo9_14844_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zo9_14844/03_2025/7zo9_14844_neut.cif" } resolution = 3.5 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= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 17.21, per 1000 atoms: 1.97 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: 4.51 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 1.00 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: 3.30 Time building geometry restraints manager: 4.03 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: 0.04 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: 47.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 42.380 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.610 ------------------------------------------------------------------------------- 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= 0.229 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 : 10.83 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 (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 (0.26), 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 TRP 0.016 0.002 TRP A 8 HIS 0.005 0.001 HIS B 117 PHE 0.027 0.002 PHE B 133 TYR 0.015 0.002 TYR A 169 ARG 0.004 0.000 ARG B 479 *********************** 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 : 0.900 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: 0.1939 time to fit residues: 49.7061 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 : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 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 47 GLN 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 = 0.4012 r_free = 0.4012 target = 0.148770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.118652 restraints weight = 97626.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.125358 restraints weight = 21190.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.129851 restraints weight = 9415.265| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8886 Z= 0.194 Angle : 0.649 9.519 12060 Z= 0.322 Chirality : 0.042 0.197 1422 Planarity : 0.004 0.037 1530 Dihedral : 7.417 94.603 1234 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.41 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 (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: 1.05 (0.26), residues: 1112 helix: 1.63 (0.19), residues: 714 sheet: -0.24 (0.62), residues: 62 loop : -1.15 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 8 HIS 0.005 0.001 HIS B 117 PHE 0.024 0.002 PHE B 133 TYR 0.014 0.002 TYR A 169 ARG 0.008 0.001 ARG B 303 *********************** 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 167 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.884 Fit side-chains REVERT: A 156 MET cc_start: 0.6486 (ptt) cc_final: 0.6193 (ptp) REVERT: A 167 VAL cc_start: 0.8692 (t) cc_final: 0.8488 (p) REVERT: A 534 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6243 (ptp-170) REVERT: B 156 MET cc_start: 0.6492 (ptt) cc_final: 0.6194 (ptp) REVERT: B 167 VAL cc_start: 0.8690 (t) cc_final: 0.8482 (p) REVERT: B 534 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6263 (ptp-170) outliers start: 12 outliers final: 4 residues processed: 159 average time/residue: 0.1513 time to fit residues: 36.5564 Evaluate side-chains 142 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 56 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 80 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 chunk 94 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.148516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118970 restraints weight = 86978.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.125617 restraints weight = 20200.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.129910 restraints weight = 9182.272| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1605 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= 0.195 Angle : 0.630 8.456 12060 Z= 0.311 Chirality : 0.042 0.189 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.237 91.978 1234 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.23 % Favored : 94.58 % Rotamer: Outliers : 1.62 % Allowed : 12.55 % Favored : 85.82 % 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: 1.09 (0.26), residues: 1112 helix: 1.69 (0.20), residues: 716 sheet: -0.58 (0.61), residues: 62 loop : -1.15 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 62 HIS 0.005 0.001 HIS B 117 PHE 0.018 0.001 PHE A 295 TYR 0.013 0.001 TYR A 169 ARG 0.006 0.000 ARG B 303 *********************** 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 154 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.910 Fit side-chains REVERT: A 156 MET cc_start: 0.6533 (ptt) cc_final: 0.6194 (ptp) REVERT: A 534 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6287 (ptp-170) REVERT: B 156 MET cc_start: 0.6521 (ptt) cc_final: 0.6178 (ptp) REVERT: B 534 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6319 (ptp-170) outliers start: 15 outliers final: 10 residues processed: 148 average time/residue: 0.1622 time to fit residues: 36.4257 Evaluate side-chains 143 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 253 SER 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 19 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 253 SER 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 33 optimal weight: 0.4980 chunk 80 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 0.0770 chunk 56 optimal weight: 4.9990 chunk 109 optimal weight: 0.1980 chunk 76 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.149167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.119379 restraints weight = 94125.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.125973 restraints weight = 22446.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.130301 restraints weight = 10201.918| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8886 Z= 0.169 Angle : 0.615 9.027 12060 Z= 0.299 Chirality : 0.041 0.188 1422 Planarity : 0.004 0.041 1530 Dihedral : 7.109 93.631 1234 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.42 % Favored : 94.40 % Rotamer: Outliers : 2.06 % Allowed : 12.99 % Favored : 84.96 % 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: 1.29 (0.26), residues: 1112 helix: 1.85 (0.20), residues: 712 sheet: -0.53 (0.60), residues: 62 loop : -1.05 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 106 HIS 0.005 0.001 HIS B 117 PHE 0.014 0.001 PHE B 295 TYR 0.009 0.001 TYR B 169 ARG 0.005 0.000 ARG A 303 *********************** 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 165 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.939 Fit side-chains REVERT: A 41 LEU cc_start: 0.9132 (mm) cc_final: 0.8660 (mp) REVERT: A 156 MET cc_start: 0.6512 (ptt) cc_final: 0.6181 (ptp) REVERT: A 534 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6032 (ptp-170) REVERT: B 41 LEU cc_start: 0.9152 (mm) cc_final: 0.8699 (mp) REVERT: B 156 MET cc_start: 0.6512 (ptt) cc_final: 0.6168 (ptp) REVERT: B 534 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6053 (ptp-170) outliers start: 19 outliers final: 11 residues processed: 159 average time/residue: 0.1526 time to fit residues: 36.8831 Evaluate side-chains 144 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 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 378 ILE Chi-restraints excluded: chain B residue 534 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.147247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.117791 restraints weight = 107437.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.126357 restraints weight = 26852.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.132018 restraints weight = 9052.981| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8886 Z= 0.231 Angle : 0.654 8.307 12060 Z= 0.322 Chirality : 0.043 0.185 1422 Planarity : 0.004 0.040 1530 Dihedral : 7.145 96.924 1234 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.51 % Favored : 94.31 % Rotamer: Outliers : 1.73 % Allowed : 15.15 % Favored : 83.12 % 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: 1.15 (0.26), residues: 1112 helix: 1.70 (0.19), residues: 716 sheet: -0.40 (0.57), residues: 62 loop : -1.05 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 8 HIS 0.004 0.001 HIS A 191 PHE 0.022 0.002 PHE B 295 TYR 0.015 0.001 TYR B 169 ARG 0.005 0.000 ARG B 303 *********************** 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 154 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.954 Fit side-chains REVERT: A 41 LEU cc_start: 0.9053 (mm) cc_final: 0.8621 (mp) REVERT: A 156 MET cc_start: 0.6636 (ptt) cc_final: 0.6280 (ptp) REVERT: A 534 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.5847 (ptp-170) REVERT: B 41 LEU cc_start: 0.9050 (mm) cc_final: 0.8616 (mp) REVERT: B 156 MET cc_start: 0.6643 (ptt) cc_final: 0.6285 (ptp) REVERT: B 534 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6033 (ptp-170) outliers start: 16 outliers final: 10 residues processed: 146 average time/residue: 0.1565 time to fit residues: 34.4962 Evaluate side-chains 148 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 258 LEU Chi-restraints excluded: chain A residue 279 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 148 ILE Chi-restraints excluded: chain B residue 534 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 103 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.147277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.118101 restraints weight = 100304.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.125554 restraints weight = 26850.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.130067 restraints weight = 9830.806| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8886 Z= 0.216 Angle : 0.655 8.637 12060 Z= 0.319 Chirality : 0.042 0.182 1422 Planarity : 0.004 0.040 1530 Dihedral : 7.149 98.994 1234 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.60 % Favored : 94.22 % Rotamer: Outliers : 1.62 % Allowed : 15.58 % Favored : 82.79 % 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: 1.12 (0.26), residues: 1112 helix: 1.66 (0.19), residues: 716 sheet: -0.44 (0.56), residues: 62 loop : -1.02 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 8 HIS 0.005 0.001 HIS A 117 PHE 0.025 0.002 PHE B 133 TYR 0.015 0.001 TYR A 169 ARG 0.005 0.000 ARG B 303 *********************** 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 158 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.878 Fit side-chains REVERT: A 41 LEU cc_start: 0.9050 (mm) cc_final: 0.8596 (mp) REVERT: A 156 MET cc_start: 0.6655 (ptt) cc_final: 0.6297 (ptp) REVERT: B 156 MET cc_start: 0.6649 (ptt) cc_final: 0.6283 (ptp) outliers start: 15 outliers final: 11 residues processed: 152 average time/residue: 0.1688 time to fit residues: 37.8778 Evaluate side-chains 147 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 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 146 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 542 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.148267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.119102 restraints weight = 100945.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.126598 restraints weight = 26550.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.133431 restraints weight = 9791.267| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2053 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= 0.191 Angle : 0.652 8.834 12060 Z= 0.313 Chirality : 0.042 0.190 1422 Planarity : 0.004 0.040 1530 Dihedral : 7.127 102.469 1234 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.42 % Favored : 94.40 % Rotamer: Outliers : 1.41 % Allowed : 16.34 % Favored : 82.25 % 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: 1.17 (0.26), residues: 1112 helix: 1.73 (0.19), residues: 716 sheet: -0.52 (0.55), residues: 62 loop : -1.06 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 106 HIS 0.005 0.001 HIS A 117 PHE 0.025 0.001 PHE B 133 TYR 0.012 0.001 TYR B 169 ARG 0.004 0.000 ARG B 303 *********************** 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 154 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 1.034 Fit side-chains REVERT: A 41 LEU cc_start: 0.9003 (mm) cc_final: 0.8568 (mp) REVERT: A 156 MET cc_start: 0.6650 (ptt) cc_final: 0.6290 (ptp) REVERT: B 156 MET cc_start: 0.6649 (ptt) cc_final: 0.6303 (ptp) outliers start: 13 outliers final: 12 residues processed: 148 average time/residue: 0.1560 time to fit residues: 35.0555 Evaluate side-chains 147 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 258 LEU Chi-restraints excluded: chain A residue 378 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 146 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 542 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 0.2980 chunk 67 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 78 optimal weight: 0.0570 chunk 36 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.150165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.121000 restraints weight = 89747.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.127361 restraints weight = 22024.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.131545 restraints weight = 10091.923| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- 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 = 0.21 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 = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2246 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= 0.165 Angle : 0.647 9.417 12060 Z= 0.305 Chirality : 0.041 0.189 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.075 105.972 1234 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.23 % Favored : 94.58 % Rotamer: Outliers : 1.52 % Allowed : 15.91 % Favored : 82.58 % 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: 1.29 (0.26), residues: 1112 helix: 1.86 (0.20), residues: 712 sheet: -0.52 (0.57), residues: 60 loop : -1.06 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 106 HIS 0.005 0.001 HIS A 117 PHE 0.023 0.001 PHE B 133 TYR 0.015 0.001 TYR A 263 ARG 0.004 0.000 ARG A 303 *********************** 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 160 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9018 (mm) cc_final: 0.8570 (mp) REVERT: A 156 MET cc_start: 0.6606 (ptt) cc_final: 0.6263 (ptp) REVERT: B 156 MET cc_start: 0.6617 (ptt) cc_final: 0.6248 (ptp) REVERT: B 283 GLN cc_start: 0.7772 (mt0) cc_final: 0.7471 (pt0) outliers start: 14 outliers final: 11 residues processed: 151 average time/residue: 0.1485 time to fit residues: 34.2710 Evaluate side-chains 150 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 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 284 LEU Chi-restraints excluded: chain B residue 378 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 89 optimal weight: 0.0870 chunk 90 optimal weight: 50.0000 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.150872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.120765 restraints weight = 97817.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.127447 restraints weight = 21275.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.131845 restraints weight = 9483.071| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3796 r_free = 0.3796 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3796 r_free = 0.3796 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2329 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= 0.169 Angle : 0.662 9.682 12060 Z= 0.310 Chirality : 0.042 0.188 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.076 108.171 1234 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.32 % Favored : 94.49 % Rotamer: Outliers : 1.08 % Allowed : 17.53 % 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 (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: 1.24 (0.26), residues: 1112 helix: 1.84 (0.19), residues: 714 sheet: -0.21 (0.54), residues: 74 loop : -1.25 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 106 HIS 0.005 0.001 HIS A 117 PHE 0.023 0.001 PHE B 133 TYR 0.013 0.001 TYR B 263 ARG 0.004 0.000 ARG A 303 *********************** 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 161 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9001 (mm) cc_final: 0.8571 (mp) REVERT: A 156 MET cc_start: 0.6536 (ptt) cc_final: 0.6172 (ptp) REVERT: B 41 LEU cc_start: 0.8962 (mm) cc_final: 0.8492 (mp) REVERT: B 156 MET cc_start: 0.6535 (ptt) cc_final: 0.6173 (ptp) outliers start: 10 outliers final: 10 residues processed: 155 average time/residue: 0.1591 time to fit residues: 37.3557 Evaluate side-chains 155 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 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 378 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 0.0000 chunk 33 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.150441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.121017 restraints weight = 86409.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.128667 restraints weight = 24837.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.134660 restraints weight = 9252.963| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3800 r_free = 0.3800 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3800 r_free = 0.3800 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2350 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= 0.184 Angle : 0.660 9.459 12060 Z= 0.312 Chirality : 0.042 0.184 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.070 108.678 1234 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.42 % Favored : 94.40 % Rotamer: Outliers : 1.19 % Allowed : 18.18 % 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 (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: 1.17 (0.26), residues: 1112 helix: 1.75 (0.19), residues: 718 sheet: -0.48 (0.57), residues: 60 loop : -1.15 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 106 HIS 0.005 0.001 HIS B 117 PHE 0.022 0.001 PHE A 133 TYR 0.013 0.001 TYR B 263 ARG 0.004 0.000 ARG A 303 ********************** 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 155 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9003 (mm) cc_final: 0.8485 (mp) REVERT: A 156 MET cc_start: 0.6537 (ptt) cc_final: 0.6137 (ptp) REVERT: A 283 GLN cc_start: 0.7454 (mt0) cc_final: 0.7239 (pt0) REVERT: B 41 LEU cc_start: 0.8946 (mm) cc_final: 0.8485 (mp) REVERT: B 156 MET cc_start: 0.6515 (ptt) cc_final: 0.6129 (ptp) outliers start: 11 outliers final: 11 residues processed: 149 average time/residue: 0.1694 time to fit residues: 37.6381 Evaluate side-chains 156 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 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 378 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 46 optimal weight: 0.0050 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 4 optimal weight: 0.1980 chunk 58 optimal weight: 0.0670 chunk 66 optimal weight: 0.6980 overall best weight: 0.2932 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.152047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.121108 restraints weight = 109887.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.127990 restraints weight = 23633.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.132564 restraints weight = 10561.587| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 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 = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8886 Z= 0.156 Angle : 0.651 9.868 12060 Z= 0.305 Chirality : 0.041 0.182 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.056 109.383 1234 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.14 % Favored : 94.68 % Rotamer: Outliers : 1.08 % Allowed : 18.18 % Favored : 80.74 % 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: 1.27 (0.26), residues: 1112 helix: 1.87 (0.20), residues: 714 sheet: -0.17 (0.56), residues: 70 loop : -1.25 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 106 HIS 0.005 0.001 HIS A 117 PHE 0.026 0.001 PHE B 133 TYR 0.013 0.001 TYR B 263 ARG 0.004 0.000 ARG A 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3176.86 seconds wall clock time: 56 minutes 32.71 seconds (3392.71 seconds total)