Starting phenix.real_space_refine on Thu Feb 13 10:16:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zo9_14844/02_2025/7zo9_14844_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zo9_14844/02_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_14844/02_2025/7zo9_14844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zo9_14844/02_2025/7zo9_14844.map" model { file = "/net/cci-nas-00/data/ceres_data/7zo9_14844/02_2025/7zo9_14844_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zo9_14844/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 10.81, per 1000 atoms: 1.24 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: 2.57 Conformation dependent library (CDL) restraints added in 3.1 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: 0.68 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: 2.48 Time building geometry restraints manager: 2.86 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 31.060 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.830 ------------------------------------------------------------------------------- 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 : 1.004 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: 0.1792 time to fit residues: 45.7727 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 : 0.925 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.125367 restraints weight = 21189.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.129846 restraints weight = 9412.233| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 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 = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3746 ------------------------------------------------------------------------------- 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 : 0.971 Fit side-chains REVERT: A 156 MET cc_start: 0.6486 (ptt) cc_final: 0.6194 (ptp) REVERT: A 167 VAL cc_start: 0.8693 (t) cc_final: 0.8489 (p) REVERT: A 534 ARG cc_start: 0.6901 (OUTLIER) cc_final: 0.6242 (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: 0.6917 (OUTLIER) cc_final: 0.6264 (ptp-170) outliers start: 12 outliers final: 4 residues processed: 159 average time/residue: 0.1655 time to fit residues: 39.7252 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 : 0.926 ------------------------------------------------------------------------------- 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: 0.6980 chunk 81 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 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: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4016 r_free = 0.4016 target = 0.150152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.120668 restraints weight = 89136.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.128656 restraints weight = 24762.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.133003 restraints weight = 9396.403| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1633 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= 0.186 Angle : 0.627 8.640 12060 Z= 0.308 Chirality : 0.042 0.193 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.231 92.059 1234 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.21 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: 1.14 (0.26), residues: 1112 helix: 1.76 (0.20), residues: 712 sheet: -0.57 (0.61), residues: 62 loop : -1.17 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 62 HIS 0.005 0.001 HIS B 117 PHE 0.017 0.001 PHE A 295 TYR 0.012 0.001 TYR A 169 ARG 0.007 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 155 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.914 Fit side-chains REVERT: A 156 MET cc_start: 0.6489 (ptt) cc_final: 0.6131 (ptp) REVERT: A 534 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6259 (ptp-170) REVERT: B 156 MET cc_start: 0.6472 (ptt) cc_final: 0.6121 (ptp) REVERT: B 534 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6314 (ptp-170) outliers start: 15 outliers final: 9 residues processed: 149 average time/residue: 0.1744 time to fit residues: 38.7413 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 : 1.022 ------------------------------------------------------------------------------- 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 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 378 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: 0.0270 chunk 80 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 0.0670 chunk 56 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.150897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.120969 restraints weight = 92234.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.127698 restraints weight = 20906.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.132156 restraints weight = 9383.225| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1843 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= 0.172 Angle : 0.622 9.035 12060 Z= 0.302 Chirality : 0.041 0.195 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.148 93.207 1234 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.32 % Favored : 94.49 % Rotamer: Outliers : 1.62 % Allowed : 13.20 % Favored : 85.17 % 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: 1.23 (0.26), residues: 1112 helix: 1.80 (0.20), residues: 712 sheet: -0.58 (0.59), residues: 62 loop : -1.05 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 62 HIS 0.005 0.001 HIS B 117 PHE 0.021 0.001 PHE B 295 TYR 0.009 0.001 TYR A 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 163 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.972 Fit side-chains REVERT: A 7 TYR cc_start: 0.8449 (m-10) cc_final: 0.8118 (m-10) REVERT: A 156 MET cc_start: 0.6509 (ptt) cc_final: 0.6196 (ptp) REVERT: A 534 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6018 (ptp-170) REVERT: B 7 TYR cc_start: 0.8428 (m-10) cc_final: 0.8170 (m-10) REVERT: B 156 MET cc_start: 0.6521 (ptt) cc_final: 0.6180 (ptp) REVERT: B 534 ARG cc_start: 0.6872 (OUTLIER) cc_final: 0.6048 (ptp-170) outliers start: 15 outliers final: 9 residues processed: 155 average time/residue: 0.1593 time to fit residues: 37.5060 Evaluate side-chains 145 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 58 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.147441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.117309 restraints weight = 105294.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.123983 restraints weight = 21949.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.128272 restraints weight = 9663.754| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1813 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= 0.221 Angle : 0.651 8.435 12060 Z= 0.319 Chirality : 0.043 0.199 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.149 96.005 1234 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.32 % Favored : 94.49 % Rotamer: Outliers : 1.62 % Allowed : 14.94 % Favored : 83.44 % 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: 1.13 (0.26), residues: 1112 helix: 1.65 (0.19), residues: 720 sheet: -0.45 (0.59), residues: 60 loop : -1.02 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 62 HIS 0.004 0.001 HIS A 117 PHE 0.022 0.002 PHE A 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 155 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.948 Fit side-chains REVERT: A 156 MET cc_start: 0.6630 (ptt) cc_final: 0.6282 (ptp) REVERT: A 534 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.5964 (ptp-170) REVERT: B 156 MET cc_start: 0.6628 (ptt) cc_final: 0.6283 (ptp) REVERT: B 534 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.5994 (ptp-170) outliers start: 15 outliers final: 10 residues processed: 146 average time/residue: 0.1612 time to fit residues: 35.5213 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 : 0.907 ------------------------------------------------------------------------------- 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 152 MET 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 A residue 542 MET Chi-restraints excluded: chain B residue 19 THR 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 534 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 103 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.149158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.119438 restraints weight = 99765.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.126789 restraints weight = 26038.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.133227 restraints weight = 9771.386| |-----------------------------------------------------------------------------| 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 = 0.31 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 = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2033 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= 0.191 Angle : 0.652 8.948 12060 Z= 0.313 Chirality : 0.042 0.187 1422 Planarity : 0.004 0.040 1530 Dihedral : 7.118 98.437 1234 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.32 % Favored : 94.49 % Rotamer: Outliers : 1.41 % Allowed : 15.91 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.26), residues: 1112 helix: 1.73 (0.19), residues: 716 sheet: -0.39 (0.57), residues: 62 loop : -1.04 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 8 HIS 0.005 0.001 HIS B 117 PHE 0.023 0.001 PHE B 133 TYR 0.012 0.001 TYR B 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 156 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.962 Fit side-chains REVERT: A 156 MET cc_start: 0.6577 (ptt) cc_final: 0.6232 (ptp) REVERT: B 156 MET cc_start: 0.6569 (ptt) cc_final: 0.6231 (ptp) outliers start: 13 outliers final: 11 residues processed: 148 average time/residue: 0.1733 time to fit residues: 37.6844 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 : 0.962 ------------------------------------------------------------------------------- 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 152 MET 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 146 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 378 ILE 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: 3.9990 chunk 100 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 0.1980 chunk 57 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.147889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.118058 restraints weight = 98033.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.124567 restraints weight = 21318.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.128813 restraints weight = 9501.358| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2061 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= 0.196 Angle : 0.659 8.786 12060 Z= 0.316 Chirality : 0.042 0.189 1422 Planarity : 0.004 0.040 1530 Dihedral : 7.117 101.919 1234 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.42 % Favored : 94.40 % Rotamer: Outliers : 1.41 % Allowed : 16.56 % Favored : 82.03 % 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: -0.43 (0.57), 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 B 117 PHE 0.027 0.002 PHE A 295 TYR 0.013 0.001 TYR B 169 ARG 0.004 0.000 ARG A 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 150 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.911 Fit side-chains REVERT: A 156 MET cc_start: 0.6650 (ptt) cc_final: 0.6305 (ptp) REVERT: A 283 GLN cc_start: 0.7617 (pt0) cc_final: 0.7399 (mt0) REVERT: B 156 MET cc_start: 0.6648 (ptt) cc_final: 0.6294 (ptp) outliers start: 13 outliers final: 13 residues processed: 141 average time/residue: 0.1566 time to fit residues: 33.7125 Evaluate side-chains 147 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 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 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 542 MET Chi-restraints excluded: chain B residue 19 THR 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 542 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 78 optimal weight: 0.0980 chunk 36 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.149417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.119897 restraints weight = 89734.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.126349 restraints weight = 20415.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.130571 restraints weight = 9215.418| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2215 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= 0.177 Angle : 0.651 9.456 12060 Z= 0.309 Chirality : 0.042 0.188 1422 Planarity : 0.004 0.040 1530 Dihedral : 7.097 106.512 1234 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.32 % Favored : 94.49 % Rotamer: Outliers : 1.30 % Allowed : 16.56 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.26), residues: 1112 helix: 1.80 (0.20), residues: 716 sheet: -0.49 (0.58), residues: 60 loop : -1.06 (0.36), residues: 336 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 0.024 0.002 PHE A 295 TYR 0.016 0.001 TYR B 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 154 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.946 Fit side-chains REVERT: A 156 MET cc_start: 0.6619 (ptt) cc_final: 0.6275 (ptp) REVERT: B 156 MET cc_start: 0.6608 (ptt) cc_final: 0.6253 (ptp) outliers start: 12 outliers final: 10 residues processed: 145 average time/residue: 0.1603 time to fit residues: 35.4470 Evaluate side-chains 145 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 152 MET 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 146 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 152 MET 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: 2.9990 chunk 69 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 89 optimal weight: 0.3980 chunk 90 optimal weight: 0.0770 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 103 optimal weight: 0.0570 chunk 12 optimal weight: 0.6980 overall best weight: 0.3856 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.151743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.121177 restraints weight = 100106.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.127936 restraints weight = 22329.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.132419 restraints weight = 10083.558| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2418 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= 0.159 Angle : 0.657 9.938 12060 Z= 0.308 Chirality : 0.041 0.188 1422 Planarity : 0.004 0.040 1530 Dihedral : 7.080 108.619 1234 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.23 % Favored : 94.58 % Rotamer: Outliers : 1.08 % Allowed : 17.32 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.26), residues: 1112 helix: 1.94 (0.20), residues: 712 sheet: -0.27 (0.54), residues: 76 loop : -1.21 (0.35), residues: 324 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 0.021 0.001 PHE A 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 157 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.8918 (mm) cc_final: 0.8437 (mp) REVERT: A 156 MET cc_start: 0.6464 (ptt) cc_final: 0.6092 (ptp) REVERT: A 283 GLN cc_start: 0.7606 (pt0) cc_final: 0.7320 (mt0) REVERT: B 156 MET cc_start: 0.6466 (ptt) cc_final: 0.6093 (ptp) outliers start: 10 outliers final: 9 residues processed: 150 average time/residue: 0.1782 time to fit residues: 38.9545 Evaluate side-chains 147 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 152 MET 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 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: 0.0970 chunk 65 optimal weight: 0.5980 chunk 3 optimal weight: 0.0980 chunk 108 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 93 optimal weight: 0.4980 chunk 72 optimal weight: 0.0000 chunk 48 optimal weight: 0.0010 chunk 100 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 overall best weight: 0.1388 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.152640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.123923 restraints weight = 85718.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.131444 restraints weight = 25006.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.138090 restraints weight = 9496.706| |-----------------------------------------------------------------------------| 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) = 0.136 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3834 r_free = 0.3834 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2640 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= 0.152 Angle : 0.645 10.292 12060 Z= 0.303 Chirality : 0.041 0.191 1422 Planarity : 0.004 0.040 1530 Dihedral : 7.066 109.485 1234 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.32 % Favored : 94.49 % Rotamer: Outliers : 0.87 % Allowed : 17.86 % Favored : 81.28 % 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: 1.36 (0.26), residues: 1112 helix: 1.96 (0.19), residues: 708 sheet: -0.25 (0.54), residues: 76 loop : -1.20 (0.36), 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 0.018 0.001 PHE A 453 TYR 0.014 0.001 TYR A 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 165 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.8928 (mm) cc_final: 0.8439 (mp) REVERT: B 41 LEU cc_start: 0.8894 (mm) cc_final: 0.8352 (mp) outliers start: 8 outliers final: 8 residues processed: 161 average time/residue: 0.1994 time to fit residues: 46.1518 Evaluate side-chains 151 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 3.9990 chunk 14 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.150048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.119323 restraints weight = 106440.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.125939 restraints weight = 22448.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.130410 restraints weight = 9930.436| |-----------------------------------------------------------------------------| 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 = 0.26 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 = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8886 Z= 0.216 Angle : 0.676 9.514 12060 Z= 0.324 Chirality : 0.043 0.184 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.074 110.316 1234 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.32 % Favored : 94.49 % Rotamer: Outliers : 0.87 % Allowed : 19.37 % Favored : 79.76 % 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: 1.21 (0.26), residues: 1112 helix: 1.76 (0.19), residues: 714 sheet: -0.08 (0.57), residues: 70 loop : -1.14 (0.35), residues: 328 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 0.023 0.002 PHE A 133 TYR 0.014 0.002 TYR A 263 ARG 0.004 0.000 ARG B 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2830.54 seconds wall clock time: 51 minutes 32.30 seconds (3092.30 seconds total)