Starting phenix.real_space_refine on Tue Mar 3 22:12:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7znu_14814/03_2026/7znu_14814_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7znu_14814/03_2026/7znu_14814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7znu_14814/03_2026/7znu_14814_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7znu_14814/03_2026/7znu_14814_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7znu_14814/03_2026/7znu_14814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7znu_14814/03_2026/7znu_14814.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.044 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 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8730 Number of models: 1 Model: "" Number of chains: 4 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: "B" 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} Chain: "B" 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} Time building chain proxies: 4.90, per 1000 atoms: 0.56 Number of scatterers: 8730 At special positions: 0 Unit cell: (68.06, 91.02, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) V 2 22.97 S 44 16.00 P 4 15.00 O 1620 8.00 N 1534 7.00 C 5526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 1.0 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: 36 helices and 4 sheets defined 68.1% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 17 through 49 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 55 through 102 removed outlier: 4.423A pdb=" N LEU A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 110 removed outlier: 3.702A pdb=" N HIS A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 154 removed outlier: 3.726A pdb=" N HIS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 155 through 204 removed outlier: 4.073A pdb=" N SER A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASP A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLY A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 210 removed outlier: 3.548A pdb=" N VAL A 208 " --> pdb=" O ASN A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 231 removed outlier: 3.872A pdb=" N ALA A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 267 removed outlier: 3.772A pdb=" N LEU A 236 " --> pdb=" O GLN A 232 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 267 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 316 removed outlier: 4.663A pdb=" N ALA A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LYS A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR A 316 " --> pdb=" O MET A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 382 Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.661A pdb=" N ARG A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 430 Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 476 through 489 removed outlier: 3.520A pdb=" N ASP A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 519 Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.790A pdb=" N THR A 532 " --> pdb=" O ARG A 529 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A 533 " --> pdb=" O LEU A 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 529 through 533' Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 17 through 49 Proline residue: B 39 - end of helix removed outlier: 3.664A pdb=" N ILE B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 102 removed outlier: 4.437A pdb=" N LEU B 59 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 110 removed outlier: 3.552A pdb=" N HIS B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 154 Proline residue: B 149 - end of helix Processing helix chain 'B' and resid 155 through 203 removed outlier: 4.050A pdb=" N SER B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ASP B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLY B 183 " --> pdb=" O LYS B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 213 through 231 removed outlier: 4.101A pdb=" N ALA B 231 " --> pdb=" O ASN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 267 removed outlier: 4.684A pdb=" N VAL B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 236 " --> pdb=" O GLN B 232 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS B 267 " --> pdb=" O TYR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 315 removed outlier: 4.712A pdb=" N ALA B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 382 Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.616A pdb=" N ARG B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 430 Processing helix chain 'B' and resid 437 through 448 Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 476 through 489 removed outlier: 3.509A pdb=" N ASP B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 519 Processing helix chain 'B' and resid 529 through 533 removed outlier: 3.623A pdb=" N THR B 532 " --> pdb=" O ARG B 529 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL B 533 " --> pdb=" O LEU B 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 529 through 533' Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.871A pdb=" N PHE A 356 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE A 335 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 391 " --> pdb=" O ASP A 338 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A 340 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 6.996A 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 413 removed outlier: 6.302A pdb=" N ALA A 412 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP A 496 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU A 493 " --> pdb=" O PHE A 524 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE A 526 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU A 495 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALA A 365 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N MET A 542 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL A 367 " --> pdb=" O MET A 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.729A pdb=" N ARG B 391 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 411 through 414 removed outlier: 6.579A pdb=" N ALA B 412 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASP B 496 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL B 414 " --> pdb=" O ASP B 496 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B 493 " --> pdb=" O PHE B 524 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE B 526 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 495 " --> pdb=" O ILE B 526 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ALA B 365 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N MET B 542 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 367 " --> pdb=" O MET B 542 " (cutoff:3.500A) 592 hydrogen bonds defined for protein. 1741 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 2955 1.36 - 1.50: 2158 1.50 - 1.64: 3679 1.64 - 1.77: 0 1.77 - 1.91: 94 Bond restraints: 8886 Sorted by residual: bond pdb=" N SER B 473 " pdb=" CA SER B 473 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.26e+00 bond pdb=" N SER A 473 " pdb=" CA SER A 473 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.85e+00 bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.26e+00 bond pdb=" C4 ADP A 601 " pdb=" C5 ADP A 601 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.16e+00 bond pdb=" CA SER A 473 " pdb=" CB SER A 473 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.69e-02 3.50e+03 1.06e+00 ... (remaining 8881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 11455 1.25 - 2.51: 479 2.51 - 3.76: 79 3.76 - 5.01: 37 5.01 - 6.27: 10 Bond angle restraints: 12060 Sorted by residual: angle pdb=" N VAL A 16 " pdb=" CA VAL A 16 " pdb=" C VAL A 16 " ideal model delta sigma weight residual 111.56 107.98 3.58 8.60e-01 1.35e+00 1.74e+01 angle pdb=" N ILE B 454 " pdb=" CA ILE B 454 " pdb=" C ILE B 454 " ideal model delta sigma weight residual 113.53 109.76 3.77 9.80e-01 1.04e+00 1.48e+01 angle pdb=" N HIS B 451 " pdb=" CA HIS B 451 " pdb=" C HIS B 451 " ideal model delta sigma weight residual 114.04 110.19 3.85 1.24e+00 6.50e-01 9.66e+00 angle pdb=" CA MET A 154 " pdb=" C MET A 154 " pdb=" O MET A 154 " ideal model delta sigma weight residual 121.50 117.85 3.65 1.25e+00 6.40e-01 8.53e+00 angle pdb=" CA MET B 154 " pdb=" C MET B 154 " pdb=" O MET B 154 " ideal model delta sigma weight residual 121.50 117.86 3.64 1.25e+00 6.40e-01 8.50e+00 ... (remaining 12055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.61: 4944 23.61 - 47.22: 329 47.22 - 70.83: 25 70.83 - 94.44: 6 94.44 - 118.05: 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 -60.00 -178.06 118.05 1 2.00e+01 2.50e-03 3.53e+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 -60.00 -176.41 116.41 1 2.00e+01 2.50e-03 3.47e+01 dihedral pdb=" C5' ADP B 601 " pdb=" O5' ADP B 601 " pdb=" PA ADP B 601 " pdb=" O2A ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 -174.82 114.83 1 2.00e+01 2.50e-03 3.41e+01 ... (remaining 5305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 797 0.026 - 0.051: 368 0.051 - 0.077: 170 0.077 - 0.103: 76 0.103 - 0.129: 11 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA ILE B 392 " pdb=" N ILE B 392 " pdb=" C ILE B 392 " pdb=" CB ILE B 392 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE A 526 " pdb=" N ILE A 526 " pdb=" C ILE A 526 " pdb=" CB ILE A 526 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.43e-01 chirality pdb=" CA ILE A 392 " pdb=" N ILE A 392 " pdb=" C ILE A 392 " pdb=" CB ILE A 392 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 ... (remaining 1419 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 134 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C MET B 134 " -0.037 2.00e-02 2.50e+03 pdb=" O MET B 134 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG B 135 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 134 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.92e+00 pdb=" C MET A 134 " -0.034 2.00e-02 2.50e+03 pdb=" O MET A 134 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 135 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 278 " -0.008 2.00e-02 2.50e+03 9.66e-03 1.63e+00 pdb=" CG PHE B 278 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE B 278 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 278 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 278 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 278 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 278 " 0.000 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 377 2.72 - 3.26: 9517 3.26 - 3.81: 14748 3.81 - 4.35: 16017 4.35 - 4.90: 27578 Nonbonded interactions: 68237 Sorted by model distance: nonbonded pdb=" OE1 GLN B 478 " pdb=" OG SER B 500 " model vdw 2.173 3.040 nonbonded pdb=" O SER B 458 " pdb=" OG1 THR B 463 " model vdw 2.189 3.040 nonbonded pdb=" OE2 GLU A 343 " pdb=" OH TYR A 352 " model vdw 2.212 3.040 nonbonded pdb=" O TYR A 263 " pdb=" OG1 THR A 266 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASP B 327 " pdb=" OG SER B 403 " model vdw 2.249 3.040 ... (remaining 68232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 251 or resid 253 through 602)) selection = (chain 'B' and (resid 1 through 251 or resid 253 through 602)) } 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: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.260 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 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 0.029 8886 Z= 0.152 Angle : 0.635 6.267 12060 Z= 0.366 Chirality : 0.038 0.129 1422 Planarity : 0.003 0.030 1530 Dihedral : 15.162 118.054 3212 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.16 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.25), residues: 1112 helix: 2.47 (0.19), residues: 702 sheet: -2.10 (0.65), residues: 58 loop : -1.87 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 391 TYR 0.012 0.001 TYR A 13 PHE 0.022 0.001 PHE B 278 TRP 0.015 0.001 TRP A 62 HIS 0.005 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8886) covalent geometry : angle 0.63544 (12060) hydrogen bonds : bond 0.10602 ( 592) hydrogen bonds : angle 4.65362 ( 1741) *********************** 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 312 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.7310 (p) cc_final: 0.7059 (p) REVERT: A 21 THR cc_start: 0.9315 (m) cc_final: 0.9065 (p) REVERT: A 68 PHE cc_start: 0.6427 (m-10) cc_final: 0.6222 (m-10) REVERT: A 71 MET cc_start: 0.7901 (mtm) cc_final: 0.7603 (ptm) REVERT: A 154 MET cc_start: 0.7756 (mmp) cc_final: 0.7389 (mmp) REVERT: A 233 PHE cc_start: 0.7204 (m-10) cc_final: 0.6955 (m-80) REVERT: A 254 MET cc_start: 0.8603 (mmm) cc_final: 0.8382 (mmm) REVERT: A 278 PHE cc_start: 0.7952 (m-10) cc_final: 0.7454 (m-10) REVERT: A 482 ILE cc_start: 0.8396 (pt) cc_final: 0.8072 (mt) REVERT: A 503 ASP cc_start: 0.7668 (t70) cc_final: 0.7377 (t70) REVERT: B 1 MET cc_start: 0.6247 (mtm) cc_final: 0.4158 (tpt) REVERT: B 41 LEU cc_start: 0.8747 (mt) cc_final: 0.8224 (tp) REVERT: B 68 PHE cc_start: 0.8091 (t80) cc_final: 0.7545 (t80) REVERT: B 96 TYR cc_start: 0.9327 (t80) cc_final: 0.9113 (t80) REVERT: B 181 LYS cc_start: 0.8236 (ptmm) cc_final: 0.7958 (tttt) REVERT: B 288 ARG cc_start: 0.8433 (mtt-85) cc_final: 0.7314 (mtt90) REVERT: B 299 THR cc_start: 0.9280 (m) cc_final: 0.8975 (p) REVERT: B 437 THR cc_start: 0.6264 (t) cc_final: 0.5852 (p) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.0965 time to fit residues: 40.6625 Evaluate side-chains 183 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 0.3980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.0470 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.0870 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN B 184 GLN B 298 GLN B 349 GLN B 478 GLN B 512 GLN B 519 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.106786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.084814 restraints weight = 201374.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.090275 restraints weight = 59869.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.093758 restraints weight = 29260.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.095955 restraints weight = 17521.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.097476 restraints weight = 12052.632| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2955 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= 0.156 Angle : 0.780 14.024 12060 Z= 0.377 Chirality : 0.045 0.205 1422 Planarity : 0.004 0.040 1530 Dihedral : 7.367 97.215 1234 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.49 % Rotamer: Outliers : 1.62 % Allowed : 16.88 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.25), residues: 1112 helix: 2.27 (0.19), residues: 708 sheet: -1.76 (0.80), residues: 44 loop : -1.87 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 222 TYR 0.016 0.001 TYR B 352 PHE 0.036 0.002 PHE B 281 TRP 0.037 0.002 TRP B 239 HIS 0.004 0.001 HIS B 546 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8886) covalent geometry : angle 0.77977 (12060) hydrogen bonds : bond 0.04715 ( 592) hydrogen bonds : angle 4.26709 ( 1741) *********************** 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 220 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 205 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8759 (tp) cc_final: 0.8298 (tt) REVERT: A 71 MET cc_start: 0.7875 (mtm) cc_final: 0.7639 (ptm) REVERT: A 130 TRP cc_start: 0.8003 (m-10) cc_final: 0.7480 (m-10) REVERT: A 154 MET cc_start: 0.7864 (mmp) cc_final: 0.7542 (mmp) REVERT: A 270 MET cc_start: 0.5400 (tpp) cc_final: 0.3624 (tpp) REVERT: A 297 ASN cc_start: 0.8223 (m110) cc_final: 0.7244 (m110) REVERT: A 482 ILE cc_start: 0.8473 (pt) cc_final: 0.8047 (mt) REVERT: A 503 ASP cc_start: 0.7580 (t70) cc_final: 0.7338 (t70) REVERT: B 1 MET cc_start: 0.6266 (mtm) cc_final: 0.3998 (tpt) REVERT: B 41 LEU cc_start: 0.8666 (mt) cc_final: 0.8159 (tp) REVERT: B 96 TYR cc_start: 0.9137 (t80) cc_final: 0.8914 (t80) REVERT: B 102 MET cc_start: 0.8010 (tpp) cc_final: 0.7770 (mmm) REVERT: B 169 TYR cc_start: 0.8350 (m-80) cc_final: 0.7929 (m-80) REVERT: B 181 LYS cc_start: 0.7851 (ptmm) cc_final: 0.7609 (tttt) REVERT: B 239 TRP cc_start: 0.6905 (m-10) cc_final: 0.5928 (m-10) REVERT: B 288 ARG cc_start: 0.8704 (mtt-85) cc_final: 0.8118 (mtt90) REVERT: B 384 VAL cc_start: 0.7684 (OUTLIER) cc_final: 0.7181 (m) outliers start: 15 outliers final: 9 residues processed: 216 average time/residue: 0.0864 time to fit residues: 26.4152 Evaluate side-chains 170 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 515 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 HIS A 478 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.103266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.081881 restraints weight = 182606.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.087479 restraints weight = 55754.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.091198 restraints weight = 26350.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.093689 restraints weight = 15028.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.094406 restraints weight = 10125.085| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8886 Z= 0.168 Angle : 0.775 14.438 12060 Z= 0.385 Chirality : 0.047 0.320 1422 Planarity : 0.004 0.041 1530 Dihedral : 7.407 99.305 1234 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.51 % Favored : 95.40 % Rotamer: Outliers : 1.84 % Allowed : 20.02 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.25), residues: 1112 helix: 2.11 (0.19), residues: 716 sheet: -1.41 (0.88), residues: 44 loop : -1.59 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 271 TYR 0.010 0.002 TYR A 96 PHE 0.049 0.003 PHE B 281 TRP 0.051 0.003 TRP A 239 HIS 0.005 0.001 HIS A 442 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8886) covalent geometry : angle 0.77526 (12060) hydrogen bonds : bond 0.04889 ( 592) hydrogen bonds : angle 4.31859 ( 1741) *********************** 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 179 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7996 (mtm) cc_final: 0.7681 (ptm) REVERT: A 254 MET cc_start: 0.8567 (mmm) cc_final: 0.8223 (ttp) REVERT: A 297 ASN cc_start: 0.8273 (m110) cc_final: 0.6855 (m110) REVERT: A 312 MET cc_start: 0.7509 (tpt) cc_final: 0.7237 (tpt) REVERT: A 482 ILE cc_start: 0.8557 (pt) cc_final: 0.8185 (mt) REVERT: A 503 ASP cc_start: 0.7658 (t70) cc_final: 0.7454 (t70) REVERT: B 1 MET cc_start: 0.6343 (mtm) cc_final: 0.4020 (tpt) REVERT: B 169 TYR cc_start: 0.8529 (m-80) cc_final: 0.7987 (m-80) REVERT: B 181 LYS cc_start: 0.7894 (ptmm) cc_final: 0.7605 (tttm) REVERT: B 239 TRP cc_start: 0.6698 (m-10) cc_final: 0.5916 (m-10) REVERT: B 288 ARG cc_start: 0.8574 (mtt-85) cc_final: 0.8129 (mtt90) REVERT: B 297 ASN cc_start: 0.8016 (m-40) cc_final: 0.7680 (t0) outliers start: 17 outliers final: 10 residues processed: 170 average time/residue: 0.0766 time to fit residues: 19.1278 Evaluate side-chains 160 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 464 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 32 optimal weight: 0.0270 chunk 105 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 298 GLN A 451 HIS ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.104242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.082886 restraints weight = 195759.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.089207 restraints weight = 61031.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.092466 restraints weight = 25621.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.095218 restraints weight = 13747.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.095814 restraints weight = 9238.651| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4091 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= 0.142 Angle : 0.768 14.707 12060 Z= 0.372 Chirality : 0.044 0.229 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.369 101.890 1234 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 1.41 % Allowed : 22.40 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.25), residues: 1112 helix: 2.06 (0.19), residues: 718 sheet: -0.92 (1.21), residues: 24 loop : -1.58 (0.28), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 477 TYR 0.036 0.001 TYR B 96 PHE 0.047 0.002 PHE B 281 TRP 0.078 0.003 TRP A 239 HIS 0.003 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8886) covalent geometry : angle 0.76759 (12060) hydrogen bonds : bond 0.04812 ( 592) hydrogen bonds : angle 4.21334 ( 1741) *********************** 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 172 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7967 (mtm) cc_final: 0.7678 (ptm) REVERT: A 254 MET cc_start: 0.8575 (mmm) cc_final: 0.8194 (ttp) REVERT: A 482 ILE cc_start: 0.8500 (pt) cc_final: 0.8171 (mt) REVERT: A 503 ASP cc_start: 0.7592 (t70) cc_final: 0.7377 (t70) REVERT: B 1 MET cc_start: 0.6298 (mtm) cc_final: 0.3931 (tpt) REVERT: B 102 MET cc_start: 0.7786 (mmm) cc_final: 0.6950 (mmt) REVERT: B 169 TYR cc_start: 0.8431 (m-80) cc_final: 0.7944 (m-80) REVERT: B 181 LYS cc_start: 0.7908 (ptmm) cc_final: 0.7574 (tttm) REVERT: B 239 TRP cc_start: 0.6660 (m-10) cc_final: 0.5805 (m-10) REVERT: B 285 MET cc_start: 0.8849 (ptm) cc_final: 0.8529 (ptp) REVERT: B 288 ARG cc_start: 0.8528 (mtt-85) cc_final: 0.8076 (mtt90) REVERT: B 297 ASN cc_start: 0.7898 (m-40) cc_final: 0.7412 (t0) outliers start: 13 outliers final: 10 residues processed: 167 average time/residue: 0.0689 time to fit residues: 17.3078 Evaluate side-chains 164 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 464 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 45 optimal weight: 0.0870 chunk 38 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 451 HIS ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.103367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.082240 restraints weight = 192480.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.087692 restraints weight = 55864.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.090675 restraints weight = 26818.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.092538 restraints weight = 17419.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.095371 restraints weight = 12007.162| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8886 Z= 0.142 Angle : 0.745 14.258 12060 Z= 0.363 Chirality : 0.044 0.322 1422 Planarity : 0.004 0.034 1530 Dihedral : 7.324 102.760 1234 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.73 % Allowed : 21.65 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.25), residues: 1112 helix: 2.01 (0.19), residues: 728 sheet: -1.04 (1.13), residues: 24 loop : -1.70 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 400 TYR 0.033 0.001 TYR B 96 PHE 0.051 0.002 PHE B 281 TRP 0.082 0.003 TRP A 239 HIS 0.024 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8886) covalent geometry : angle 0.74476 (12060) hydrogen bonds : bond 0.04731 ( 592) hydrogen bonds : angle 4.22257 ( 1741) *********************** 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 178 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7977 (mtm) cc_final: 0.7702 (ptm) REVERT: A 130 TRP cc_start: 0.8037 (m-10) cc_final: 0.7529 (m-10) REVERT: A 254 MET cc_start: 0.8607 (mmm) cc_final: 0.8179 (ttp) REVERT: A 270 MET cc_start: 0.5435 (ptp) cc_final: 0.5185 (mtt) REVERT: A 482 ILE cc_start: 0.8487 (pt) cc_final: 0.8163 (mt) REVERT: A 503 ASP cc_start: 0.7650 (t70) cc_final: 0.7441 (t70) REVERT: B 1 MET cc_start: 0.6357 (mtm) cc_final: 0.3968 (tpt) REVERT: B 169 TYR cc_start: 0.8424 (m-80) cc_final: 0.7946 (m-80) REVERT: B 181 LYS cc_start: 0.7824 (ptmm) cc_final: 0.7497 (tttm) REVERT: B 239 TRP cc_start: 0.6603 (m-10) cc_final: 0.5939 (m-10) REVERT: B 285 MET cc_start: 0.8825 (ptm) cc_final: 0.8511 (ptp) REVERT: B 297 ASN cc_start: 0.7911 (m-40) cc_final: 0.7706 (t0) REVERT: B 525 ILE cc_start: 0.8690 (mt) cc_final: 0.8398 (mp) outliers start: 16 outliers final: 13 residues processed: 171 average time/residue: 0.0692 time to fit residues: 18.0821 Evaluate side-chains 170 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 464 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 34 optimal weight: 0.0970 chunk 84 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 204 ASN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.103335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.082646 restraints weight = 170645.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.088539 restraints weight = 56592.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.092477 restraints weight = 23724.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.094477 restraints weight = 11997.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.094548 restraints weight = 8702.264| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8886 Z= 0.138 Angle : 0.743 13.797 12060 Z= 0.364 Chirality : 0.044 0.211 1422 Planarity : 0.004 0.034 1530 Dihedral : 7.261 103.425 1234 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.38 % Allowed : 21.86 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.25), residues: 1112 helix: 2.01 (0.19), residues: 730 sheet: -0.98 (1.10), residues: 24 loop : -1.59 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 271 TYR 0.030 0.002 TYR B 96 PHE 0.049 0.002 PHE B 281 TRP 0.028 0.002 TRP A 239 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8886) covalent geometry : angle 0.74257 (12060) hydrogen bonds : bond 0.04681 ( 592) hydrogen bonds : angle 4.20573 ( 1741) *********************** 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 184 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8047 (mtm) cc_final: 0.7742 (ptm) REVERT: A 130 TRP cc_start: 0.8062 (m-10) cc_final: 0.7545 (m-10) REVERT: A 254 MET cc_start: 0.8619 (mmm) cc_final: 0.8085 (ttp) REVERT: A 482 ILE cc_start: 0.8522 (pt) cc_final: 0.8212 (mt) REVERT: A 503 ASP cc_start: 0.7611 (t70) cc_final: 0.7322 (t70) REVERT: A 542 MET cc_start: 0.7659 (ppp) cc_final: 0.7313 (ppp) REVERT: B 1 MET cc_start: 0.6415 (mtm) cc_final: 0.4114 (tpt) REVERT: B 24 MET cc_start: 0.8229 (tpt) cc_final: 0.7963 (tpt) REVERT: B 102 MET cc_start: 0.7800 (mmm) cc_final: 0.6475 (mmt) REVERT: B 169 TYR cc_start: 0.8493 (m-80) cc_final: 0.8030 (m-80) REVERT: B 181 LYS cc_start: 0.7768 (ptmm) cc_final: 0.7407 (tttm) REVERT: B 239 TRP cc_start: 0.6550 (m-10) cc_final: 0.5922 (m-10) REVERT: B 288 ARG cc_start: 0.8814 (mmt90) cc_final: 0.8145 (mtt90) REVERT: B 457 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.7222 (tmtt) REVERT: B 525 ILE cc_start: 0.8694 (mt) cc_final: 0.8399 (mp) outliers start: 22 outliers final: 15 residues processed: 175 average time/residue: 0.0706 time to fit residues: 18.5966 Evaluate side-chains 169 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 464 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 0.0970 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.102922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.081962 restraints weight = 181478.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.087700 restraints weight = 56878.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.091934 restraints weight = 24420.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.094087 restraints weight = 12015.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.094716 restraints weight = 8352.032| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8886 Z= 0.140 Angle : 0.734 13.604 12060 Z= 0.361 Chirality : 0.044 0.193 1422 Planarity : 0.004 0.037 1530 Dihedral : 7.285 102.832 1234 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.52 % Allowed : 23.27 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.25), residues: 1112 helix: 2.03 (0.19), residues: 730 sheet: -0.79 (1.10), residues: 24 loop : -1.55 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 271 TYR 0.022 0.002 TYR A 96 PHE 0.046 0.002 PHE B 281 TRP 0.038 0.002 TRP B 239 HIS 0.002 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8886) covalent geometry : angle 0.73417 (12060) hydrogen bonds : bond 0.04644 ( 592) hydrogen bonds : angle 4.22491 ( 1741) *********************** 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 171 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8022 (mtm) cc_final: 0.7765 (ptm) REVERT: A 130 TRP cc_start: 0.8069 (m-10) cc_final: 0.7544 (m-10) REVERT: A 254 MET cc_start: 0.8575 (mmm) cc_final: 0.8071 (ttp) REVERT: A 482 ILE cc_start: 0.8507 (pt) cc_final: 0.8192 (mt) REVERT: A 503 ASP cc_start: 0.7602 (t70) cc_final: 0.7332 (t70) REVERT: A 542 MET cc_start: 0.7695 (ppp) cc_final: 0.7376 (ppp) REVERT: B 1 MET cc_start: 0.6518 (mtm) cc_final: 0.4293 (tpt) REVERT: B 24 MET cc_start: 0.8205 (tpt) cc_final: 0.7974 (tpt) REVERT: B 169 TYR cc_start: 0.8418 (m-80) cc_final: 0.8016 (m-80) REVERT: B 181 LYS cc_start: 0.7746 (ptmm) cc_final: 0.7381 (tttm) REVERT: B 288 ARG cc_start: 0.8834 (mmt90) cc_final: 0.8087 (mtt90) REVERT: B 457 LYS cc_start: 0.7520 (tmtt) cc_final: 0.7263 (tmtt) REVERT: B 525 ILE cc_start: 0.8709 (mt) cc_final: 0.8417 (mp) outliers start: 14 outliers final: 14 residues processed: 167 average time/residue: 0.0658 time to fit residues: 16.7935 Evaluate side-chains 168 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 464 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 61 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.097931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.077233 restraints weight = 184922.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.082641 restraints weight = 54890.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.085584 restraints weight = 25972.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.088722 restraints weight = 15998.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.089676 restraints weight = 9785.336| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3568 r_free = 0.3568 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3568 r_free = 0.3568 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8886 Z= 0.182 Angle : 0.764 13.978 12060 Z= 0.384 Chirality : 0.045 0.197 1422 Planarity : 0.004 0.034 1530 Dihedral : 7.382 102.580 1234 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.73 % Allowed : 23.16 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.25), residues: 1112 helix: 1.92 (0.19), residues: 724 sheet: -1.28 (0.81), residues: 44 loop : -1.53 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 135 TYR 0.021 0.002 TYR A 96 PHE 0.052 0.002 PHE B 281 TRP 0.020 0.002 TRP B 239 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 8886) covalent geometry : angle 0.76447 (12060) hydrogen bonds : bond 0.04993 ( 592) hydrogen bonds : angle 4.37276 ( 1741) *********************** 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 172 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8184 (mtm) cc_final: 0.7885 (ptm) REVERT: A 130 TRP cc_start: 0.8273 (m-10) cc_final: 0.7701 (m-10) REVERT: A 482 ILE cc_start: 0.8576 (pt) cc_final: 0.8217 (mt) REVERT: A 503 ASP cc_start: 0.7755 (t70) cc_final: 0.7439 (t70) REVERT: B 1 MET cc_start: 0.6619 (mtm) cc_final: 0.4694 (tpt) REVERT: B 102 MET cc_start: 0.7914 (mmm) cc_final: 0.6752 (mmt) REVERT: B 181 LYS cc_start: 0.7901 (ptmm) cc_final: 0.7639 (tttt) REVERT: B 285 MET cc_start: 0.8765 (ptm) cc_final: 0.8464 (ptp) REVERT: B 525 ILE cc_start: 0.8785 (mt) cc_final: 0.8489 (mp) outliers start: 16 outliers final: 13 residues processed: 167 average time/residue: 0.0713 time to fit residues: 17.8100 Evaluate side-chains 163 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 464 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 97 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 0.0270 chunk 69 optimal weight: 0.9980 chunk 60 optimal weight: 0.0670 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.100122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.079952 restraints weight = 157220.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.085257 restraints weight = 49435.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.088269 restraints weight = 23716.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.090785 restraints weight = 14184.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.092375 restraints weight = 9460.302| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4961 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= 0.143 Angle : 0.774 15.174 12060 Z= 0.374 Chirality : 0.044 0.188 1422 Planarity : 0.004 0.036 1530 Dihedral : 7.345 103.439 1234 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.30 % Allowed : 23.92 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.25), residues: 1112 helix: 1.90 (0.19), residues: 732 sheet: -0.70 (1.08), residues: 24 loop : -1.53 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 288 TYR 0.027 0.002 TYR A 96 PHE 0.052 0.002 PHE B 281 TRP 0.017 0.002 TRP B 239 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8886) covalent geometry : angle 0.77398 (12060) hydrogen bonds : bond 0.04843 ( 592) hydrogen bonds : angle 4.27236 ( 1741) *********************** 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 166 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8066 (mtm) cc_final: 0.7846 (ptm) REVERT: A 130 TRP cc_start: 0.8240 (m-10) cc_final: 0.7734 (m-10) REVERT: A 476 GLU cc_start: 0.7256 (pm20) cc_final: 0.6819 (pm20) REVERT: A 482 ILE cc_start: 0.8476 (pt) cc_final: 0.8128 (mt) REVERT: A 503 ASP cc_start: 0.7706 (t70) cc_final: 0.7437 (t70) REVERT: A 542 MET cc_start: 0.7664 (ppp) cc_final: 0.7294 (ppp) REVERT: B 1 MET cc_start: 0.6572 (mtm) cc_final: 0.4645 (tpt) REVERT: B 102 MET cc_start: 0.7847 (mmm) cc_final: 0.6625 (mmt) REVERT: B 169 TYR cc_start: 0.8440 (m-80) cc_final: 0.7960 (m-80) REVERT: B 181 LYS cc_start: 0.7818 (ptmm) cc_final: 0.7532 (tttt) REVERT: B 285 MET cc_start: 0.8758 (ptm) cc_final: 0.8479 (ptp) REVERT: B 393 MET cc_start: 0.6150 (tpp) cc_final: 0.5941 (tpp) REVERT: B 525 ILE cc_start: 0.8729 (mt) cc_final: 0.8469 (mp) outliers start: 12 outliers final: 12 residues processed: 162 average time/residue: 0.0647 time to fit residues: 16.1729 Evaluate side-chains 164 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 464 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 53 optimal weight: 0.0070 chunk 31 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 40 optimal weight: 0.0070 chunk 70 optimal weight: 0.6980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.100956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.079859 restraints weight = 203772.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.085079 restraints weight = 55582.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.088595 restraints weight = 26326.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.090857 restraints weight = 15403.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.092377 restraints weight = 10302.678| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8886 Z= 0.141 Angle : 0.764 14.797 12060 Z= 0.371 Chirality : 0.043 0.184 1422 Planarity : 0.004 0.036 1530 Dihedral : 7.314 102.362 1234 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.30 % Allowed : 24.13 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.25), residues: 1112 helix: 1.94 (0.19), residues: 728 sheet: -0.57 (1.07), residues: 24 loop : -1.56 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 288 TYR 0.027 0.002 TYR A 96 PHE 0.054 0.002 PHE B 281 TRP 0.021 0.002 TRP B 239 HIS 0.008 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8886) covalent geometry : angle 0.76358 (12060) hydrogen bonds : bond 0.04785 ( 592) hydrogen bonds : angle 4.25629 ( 1741) ********************** 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 164 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TRP cc_start: 0.8226 (m-10) cc_final: 0.7726 (m-10) REVERT: A 482 ILE cc_start: 0.8464 (pt) cc_final: 0.8103 (mt) REVERT: A 503 ASP cc_start: 0.7627 (t70) cc_final: 0.7353 (t70) REVERT: B 1 MET cc_start: 0.6555 (mtm) cc_final: 0.4633 (tpt) REVERT: B 169 TYR cc_start: 0.8391 (m-80) cc_final: 0.7964 (m-80) REVERT: B 181 LYS cc_start: 0.7793 (ptmm) cc_final: 0.7457 (tttt) REVERT: B 288 ARG cc_start: 0.8739 (mmt90) cc_final: 0.8457 (tpp-160) REVERT: B 393 MET cc_start: 0.6221 (tpp) cc_final: 0.6017 (tpp) REVERT: B 457 LYS cc_start: 0.7584 (tmtt) cc_final: 0.7319 (tmtt) REVERT: B 525 ILE cc_start: 0.8736 (mt) cc_final: 0.8437 (mp) outliers start: 12 outliers final: 10 residues processed: 159 average time/residue: 0.0666 time to fit residues: 16.0661 Evaluate side-chains 158 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 298 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 0.9990 chunk 97 optimal weight: 0.0270 chunk 92 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 53 optimal weight: 0.0170 chunk 43 optimal weight: 0.0000 chunk 0 optimal weight: 4.9990 overall best weight: 0.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.101960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.081380 restraints weight = 190196.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.087448 restraints weight = 57152.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.091398 restraints weight = 22420.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.093451 restraints weight = 11397.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.094053 restraints weight = 7841.534| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8886 Z= 0.141 Angle : 0.782 14.725 12060 Z= 0.376 Chirality : 0.043 0.178 1422 Planarity : 0.004 0.036 1530 Dihedral : 7.268 101.916 1234 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.30 % Allowed : 24.57 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.25), residues: 1112 helix: 1.97 (0.19), residues: 726 sheet: -0.00 (0.76), residues: 48 loop : -1.83 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 288 TYR 0.024 0.002 TYR A 96 PHE 0.051 0.002 PHE B 281 TRP 0.022 0.002 TRP B 239 HIS 0.004 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8886) covalent geometry : angle 0.78159 (12060) hydrogen bonds : bond 0.04679 ( 592) hydrogen bonds : angle 4.22708 ( 1741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1528.13 seconds wall clock time: 27 minutes 2.53 seconds (1622.53 seconds total)