Starting phenix.real_space_refine on Thu Mar 13 14:29:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7znu_14814/03_2025/7znu_14814_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7znu_14814/03_2025/7znu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7znu_14814/03_2025/7znu_14814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7znu_14814/03_2025/7znu_14814.map" model { file = "/net/cci-nas-00/data/ceres_data/7znu_14814/03_2025/7znu_14814_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7znu_14814/03_2025/7znu_14814_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8730 Number of models: 1 Model: "" Number of chains: 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: 14.49, per 1000 atoms: 1.66 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: 2.42 Conformation dependent library (CDL) restraints added in 3.4 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: 0.81 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: 2.68 Time building geometry restraints manager: 2.85 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 251 or resid 253 through 556 or resid 601 throug \ h 602)) selection = (chain 'B' and (resid 1 through 251 or resid 253 through 556 or resid 601 throug \ h 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 36.000 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.850 ------------------------------------------------------------------------------- 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= 0.183 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (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 TRP 0.015 0.001 TRP A 62 HIS 0.005 0.001 HIS B 85 PHE 0.022 0.001 PHE B 278 TYR 0.012 0.001 TYR A 13 ARG 0.003 0.000 ARG A 391 *********************** 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 : 0.942 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: 0.9064 (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: 0.6956 (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: 0.4157 (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: 0.7544 (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: 0.9281 (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: 0.2328 time to fit residues: 97.4996 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 : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN A 478 GLN B 184 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 = 0.3851 r_free = 0.3851 target = 0.104366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.083072 restraints weight = 189322.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.088551 restraints weight = 57500.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.091308 restraints weight = 28165.823| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8886 Z= 0.219 Angle : 0.780 13.693 12060 Z= 0.383 Chirality : 0.046 0.195 1422 Planarity : 0.005 0.040 1530 Dihedral : 7.459 99.961 1234 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.49 % Rotamer: Outliers : 1.84 % Allowed : 16.88 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1112 helix: 2.18 (0.19), residues: 714 sheet: -1.73 (0.81), residues: 44 loop : -1.75 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 239 HIS 0.005 0.001 HIS B 546 PHE 0.037 0.002 PHE B 281 TYR 0.016 0.001 TYR B 352 ARG 0.007 0.001 ARG B 222 *********************** 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 205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 TYR cc_start: 0.8460 (m-10) cc_final: 0.8231 (m-10) REVERT: A 68 PHE cc_start: 0.6592 (m-10) cc_final: 0.6337 (m-10) REVERT: A 71 MET cc_start: 0.8055 (mtm) cc_final: 0.7689 (ptm) REVERT: A 154 MET cc_start: 0.7945 (mmp) cc_final: 0.7609 (mmp) REVERT: A 254 MET cc_start: 0.8699 (mmm) cc_final: 0.8494 (mmm) REVERT: A 270 MET cc_start: 0.5713 (tpp) cc_final: 0.3886 (tpp) REVERT: A 297 ASN cc_start: 0.8261 (m110) cc_final: 0.7367 (m110) REVERT: A 307 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7681 (tp30) REVERT: A 482 ILE cc_start: 0.8596 (pt) cc_final: 0.8209 (mt) REVERT: A 503 ASP cc_start: 0.7734 (t70) cc_final: 0.7473 (t70) REVERT: B 1 MET cc_start: 0.6437 (mtm) cc_final: 0.4126 (tpt) REVERT: B 11 MET cc_start: 0.7882 (mmp) cc_final: 0.7645 (ttt) REVERT: B 41 LEU cc_start: 0.8745 (mt) cc_final: 0.8218 (tp) REVERT: B 102 MET cc_start: 0.8245 (tpp) cc_final: 0.7904 (mmm) REVERT: B 169 TYR cc_start: 0.8467 (m-80) cc_final: 0.7956 (m-80) REVERT: B 181 LYS cc_start: 0.7910 (ptmm) cc_final: 0.7659 (tttm) REVERT: B 239 TRP cc_start: 0.6841 (m-10) cc_final: 0.5955 (m-10) REVERT: B 288 ARG cc_start: 0.8710 (mtt-85) cc_final: 0.8147 (mtt90) REVERT: B 384 VAL cc_start: 0.7795 (OUTLIER) cc_final: 0.7360 (m) outliers start: 17 outliers final: 11 residues processed: 200 average time/residue: 0.1892 time to fit residues: 53.7783 Evaluate side-chains 169 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL 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 B residue 289 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 364 VAL 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 56 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 B 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.101117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.080660 restraints weight = 166576.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.085782 restraints weight = 53329.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.089135 restraints weight = 26880.508| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8886 Z= 0.255 Angle : 0.752 13.717 12060 Z= 0.383 Chirality : 0.045 0.281 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.529 101.070 1234 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.22 % Rotamer: Outliers : 2.16 % Allowed : 19.81 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.25), residues: 1112 helix: 2.00 (0.19), residues: 728 sheet: -0.93 (1.21), residues: 24 loop : -1.76 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP A 239 HIS 0.006 0.001 HIS A 442 PHE 0.048 0.003 PHE B 133 TYR 0.036 0.002 TYR B 96 ARG 0.005 0.001 ARG B 400 *********************** 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 184 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 TYR cc_start: 0.8541 (m-10) cc_final: 0.8327 (m-10) REVERT: A 68 PHE cc_start: 0.6641 (m-10) cc_final: 0.6361 (m-10) REVERT: A 71 MET cc_start: 0.8174 (mtm) cc_final: 0.7812 (ptm) REVERT: A 130 TRP cc_start: 0.8180 (m-10) cc_final: 0.7725 (m-10) REVERT: A 307 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7721 (tp30) REVERT: A 482 ILE cc_start: 0.8621 (pt) cc_final: 0.8254 (mt) REVERT: A 503 ASP cc_start: 0.7859 (t70) cc_final: 0.7585 (t70) REVERT: B 1 MET cc_start: 0.6522 (mtm) cc_final: 0.4194 (tpt) REVERT: B 169 TYR cc_start: 0.8659 (m-80) cc_final: 0.8000 (m-80) REVERT: B 181 LYS cc_start: 0.8091 (ptmm) cc_final: 0.7751 (tttm) REVERT: B 239 TRP cc_start: 0.6695 (m-10) cc_final: 0.5855 (m-10) REVERT: B 254 MET cc_start: 0.8548 (mtp) cc_final: 0.8267 (tpp) REVERT: B 288 ARG cc_start: 0.8577 (mtt-85) cc_final: 0.7985 (mtt90) REVERT: B 297 ASN cc_start: 0.8050 (m-40) cc_final: 0.7563 (t0) outliers start: 20 outliers final: 15 residues processed: 174 average time/residue: 0.1753 time to fit residues: 44.0820 Evaluate side-chains 166 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL 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 451 HIS Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 364 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 85 HIS B 137 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.102626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.081746 restraints weight = 176212.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.088080 restraints weight = 57534.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.092075 restraints weight = 22951.375| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8886 Z= 0.188 Angle : 0.761 13.626 12060 Z= 0.373 Chirality : 0.044 0.241 1422 Planarity : 0.004 0.037 1530 Dihedral : 7.468 102.477 1234 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.23 % Favored : 94.68 % Rotamer: Outliers : 1.62 % Allowed : 20.89 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1112 helix: 2.01 (0.19), residues: 728 sheet: -0.82 (1.20), residues: 24 loop : -1.82 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.003 TRP A 239 HIS 0.003 0.001 HIS B 117 PHE 0.047 0.002 PHE B 278 TYR 0.026 0.001 TYR B 96 ARG 0.005 0.001 ARG B 400 *********************** 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 183 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6624 (m-10) cc_final: 0.6308 (m-10) REVERT: A 71 MET cc_start: 0.8135 (mtm) cc_final: 0.7779 (ptm) REVERT: A 254 MET cc_start: 0.8566 (mmm) cc_final: 0.8270 (ttp) REVERT: A 307 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7593 (tp30) REVERT: A 482 ILE cc_start: 0.8578 (pt) cc_final: 0.8217 (mt) REVERT: A 503 ASP cc_start: 0.7710 (t70) cc_final: 0.7449 (t70) REVERT: B 1 MET cc_start: 0.6454 (mtm) cc_final: 0.4077 (tpt) REVERT: B 68 PHE cc_start: 0.8152 (t80) cc_final: 0.7360 (t80) REVERT: B 169 TYR cc_start: 0.8536 (m-80) cc_final: 0.7943 (m-80) REVERT: B 181 LYS cc_start: 0.7937 (ptmm) cc_final: 0.7610 (tttm) REVERT: B 239 TRP cc_start: 0.6580 (m-10) cc_final: 0.5600 (m-10) REVERT: B 254 MET cc_start: 0.8511 (mtp) cc_final: 0.8262 (tpt) REVERT: B 270 MET cc_start: 0.7072 (ttm) cc_final: 0.6795 (mmp) REVERT: B 297 ASN cc_start: 0.7946 (m-40) cc_final: 0.7078 (t0) REVERT: B 525 ILE cc_start: 0.8852 (mt) cc_final: 0.8596 (mp) outliers start: 15 outliers final: 10 residues processed: 177 average time/residue: 0.1696 time to fit residues: 44.1201 Evaluate side-chains 165 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 137 HIS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 457 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS B 137 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.101978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.080593 restraints weight = 202648.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.086031 restraints weight = 60323.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.088946 restraints weight = 28927.594| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8886 Z= 0.195 Angle : 0.752 13.610 12060 Z= 0.374 Chirality : 0.044 0.334 1422 Planarity : 0.004 0.034 1530 Dihedral : 7.442 102.775 1234 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.62 % Allowed : 21.21 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1112 helix: 2.00 (0.19), residues: 724 sheet: -0.82 (1.16), residues: 24 loop : -1.66 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.003 TRP A 239 HIS 0.008 0.001 HIS A 451 PHE 0.049 0.002 PHE B 281 TYR 0.028 0.001 TYR B 96 ARG 0.005 0.000 ARG B 288 *********************** 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 179 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6642 (m-10) cc_final: 0.6354 (m-10) REVERT: A 71 MET cc_start: 0.8182 (mtm) cc_final: 0.7817 (ptm) REVERT: A 130 TRP cc_start: 0.8126 (m-10) cc_final: 0.7641 (m-10) REVERT: A 254 MET cc_start: 0.8507 (mmm) cc_final: 0.8245 (ttp) REVERT: A 270 MET cc_start: 0.6039 (ptp) cc_final: 0.5835 (mtt) REVERT: A 299 THR cc_start: 0.9292 (m) cc_final: 0.9088 (p) REVERT: A 307 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7609 (tp30) REVERT: A 482 ILE cc_start: 0.8557 (pt) cc_final: 0.8219 (mt) REVERT: A 503 ASP cc_start: 0.7732 (t70) cc_final: 0.7448 (t70) REVERT: B 1 MET cc_start: 0.6553 (mtm) cc_final: 0.4251 (tpt) REVERT: B 11 MET cc_start: 0.6868 (tmm) cc_final: 0.6516 (tmm) REVERT: B 102 MET cc_start: 0.7944 (mmm) cc_final: 0.6813 (mmt) REVERT: B 169 TYR cc_start: 0.8590 (m-80) cc_final: 0.7932 (m-80) REVERT: B 181 LYS cc_start: 0.7968 (ptmm) cc_final: 0.7629 (tttm) REVERT: B 239 TRP cc_start: 0.6594 (m-10) cc_final: 0.5532 (m-10) REVERT: B 270 MET cc_start: 0.7149 (ttm) cc_final: 0.6578 (mmm) REVERT: B 288 ARG cc_start: 0.8760 (mtt90) cc_final: 0.7726 (mtt90) REVERT: B 292 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9161 (mm) REVERT: B 297 ASN cc_start: 0.7951 (m-40) cc_final: 0.6766 (t0) REVERT: B 525 ILE cc_start: 0.8824 (mt) cc_final: 0.8583 (mp) outliers start: 15 outliers final: 10 residues processed: 172 average time/residue: 0.1633 time to fit residues: 41.7874 Evaluate side-chains 170 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 A residue 366 ILE Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 292 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 103 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 34 optimal weight: 0.0070 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.102114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.080946 restraints weight = 187554.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.086079 restraints weight = 54838.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.089401 restraints weight = 26749.870| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8886 Z= 0.188 Angle : 0.734 13.535 12060 Z= 0.364 Chirality : 0.044 0.279 1422 Planarity : 0.004 0.033 1530 Dihedral : 7.405 103.237 1234 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.84 % Allowed : 21.43 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1112 helix: 2.01 (0.19), residues: 728 sheet: -0.27 (0.76), residues: 48 loop : -1.90 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 239 HIS 0.009 0.001 HIS A 451 PHE 0.052 0.002 PHE B 281 TYR 0.017 0.001 TYR B 96 ARG 0.004 0.000 ARG B 400 *********************** 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 179 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6605 (m-10) cc_final: 0.6329 (m-10) REVERT: A 71 MET cc_start: 0.8153 (mtm) cc_final: 0.7822 (ptm) REVERT: A 130 TRP cc_start: 0.8110 (m-10) cc_final: 0.7628 (m-10) REVERT: A 254 MET cc_start: 0.8541 (mmm) cc_final: 0.8283 (ttp) REVERT: A 307 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7636 (tp30) REVERT: A 482 ILE cc_start: 0.8521 (pt) cc_final: 0.8184 (mt) REVERT: A 503 ASP cc_start: 0.7705 (t70) cc_final: 0.7436 (t70) REVERT: A 542 MET cc_start: 0.7731 (ppp) cc_final: 0.7378 (ppp) REVERT: B 1 MET cc_start: 0.6715 (mtm) cc_final: 0.4500 (tpt) REVERT: B 11 MET cc_start: 0.6813 (tmm) cc_final: 0.6470 (tmm) REVERT: B 169 TYR cc_start: 0.8446 (m-80) cc_final: 0.7929 (m-80) REVERT: B 181 LYS cc_start: 0.8024 (ptmm) cc_final: 0.7649 (tttm) REVERT: B 239 TRP cc_start: 0.6614 (m-10) cc_final: 0.5586 (m-10) REVERT: B 254 MET cc_start: 0.8140 (tpt) cc_final: 0.7928 (mtp) REVERT: B 288 ARG cc_start: 0.8748 (mtt90) cc_final: 0.7864 (mtt90) REVERT: B 297 ASN cc_start: 0.7951 (m-40) cc_final: 0.6795 (t0) REVERT: B 437 THR cc_start: 0.6155 (t) cc_final: 0.5766 (p) REVERT: B 457 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7215 (tmtt) REVERT: B 525 ILE cc_start: 0.8774 (mt) cc_final: 0.8532 (mp) outliers start: 17 outliers final: 13 residues processed: 172 average time/residue: 0.1636 time to fit residues: 41.7506 Evaluate side-chains 170 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 104 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 366 ILE Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 457 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.101722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.081120 restraints weight = 188628.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.087372 restraints weight = 56244.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.091457 restraints weight = 22583.702| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8886 Z= 0.192 Angle : 0.750 13.531 12060 Z= 0.369 Chirality : 0.044 0.273 1422 Planarity : 0.004 0.049 1530 Dihedral : 7.396 103.135 1234 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.62 % Allowed : 22.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.26), residues: 1112 helix: 2.00 (0.19), residues: 724 sheet: -0.61 (0.72), residues: 58 loop : -1.70 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 239 HIS 0.014 0.001 HIS A 451 PHE 0.053 0.002 PHE B 281 TYR 0.035 0.002 TYR A 96 ARG 0.008 0.000 ARG B 98 *********************** 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: 15 poor density : 156 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6689 (m-10) cc_final: 0.6412 (m-10) REVERT: A 71 MET cc_start: 0.8158 (mtm) cc_final: 0.7816 (ptm) REVERT: A 130 TRP cc_start: 0.8091 (m-10) cc_final: 0.7633 (m-10) REVERT: A 152 MET cc_start: 0.7849 (mmm) cc_final: 0.7464 (mmm) REVERT: A 254 MET cc_start: 0.8537 (mmm) cc_final: 0.8272 (ttp) REVERT: A 307 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7615 (tp30) REVERT: A 482 ILE cc_start: 0.8555 (pt) cc_final: 0.8230 (mt) REVERT: A 503 ASP cc_start: 0.7739 (t70) cc_final: 0.7380 (t70) REVERT: A 542 MET cc_start: 0.7692 (ppp) cc_final: 0.7338 (ppp) REVERT: B 1 MET cc_start: 0.6607 (mtm) cc_final: 0.4358 (tpt) REVERT: B 11 MET cc_start: 0.6852 (tmm) cc_final: 0.6439 (tmm) REVERT: B 181 LYS cc_start: 0.7927 (ptmm) cc_final: 0.7580 (tttm) REVERT: B 239 TRP cc_start: 0.6583 (m-10) cc_final: 0.5578 (m-10) REVERT: B 254 MET cc_start: 0.8161 (tpt) cc_final: 0.7928 (mtp) REVERT: B 297 ASN cc_start: 0.7915 (m-40) cc_final: 0.6750 (t0) REVERT: B 437 THR cc_start: 0.5910 (t) cc_final: 0.5551 (p) REVERT: B 525 ILE cc_start: 0.8797 (mt) cc_final: 0.8545 (mp) outliers start: 15 outliers final: 13 residues processed: 167 average time/residue: 0.1624 time to fit residues: 40.5643 Evaluate side-chains 162 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 104 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 366 ILE 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 272 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 292 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS B 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.100047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.079566 restraints weight = 167991.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.084465 restraints weight = 53710.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.087478 restraints weight = 27756.998| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8886 Z= 0.193 Angle : 0.738 13.284 12060 Z= 0.364 Chirality : 0.044 0.253 1422 Planarity : 0.004 0.034 1530 Dihedral : 7.392 102.782 1234 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.52 % Allowed : 22.94 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1112 helix: 2.12 (0.19), residues: 716 sheet: -0.51 (0.72), residues: 58 loop : -1.80 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 239 HIS 0.009 0.001 HIS A 451 PHE 0.052 0.002 PHE B 281 TYR 0.028 0.002 TYR B 96 ARG 0.005 0.000 ARG B 98 *********************** 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 168 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6678 (m-10) cc_final: 0.6421 (m-10) REVERT: A 71 MET cc_start: 0.8209 (mtm) cc_final: 0.7863 (ptm) REVERT: A 130 TRP cc_start: 0.8176 (m-10) cc_final: 0.7714 (m-10) REVERT: A 152 MET cc_start: 0.7796 (mmm) cc_final: 0.7408 (mmm) REVERT: A 254 MET cc_start: 0.8463 (mmm) cc_final: 0.8252 (ttp) REVERT: A 307 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7620 (tp30) REVERT: A 482 ILE cc_start: 0.8565 (pt) cc_final: 0.8206 (mt) REVERT: A 503 ASP cc_start: 0.7759 (t70) cc_final: 0.7451 (t70) REVERT: A 542 MET cc_start: 0.7746 (ppp) cc_final: 0.7440 (ppp) REVERT: B 1 MET cc_start: 0.6682 (mtm) cc_final: 0.4384 (tpt) REVERT: B 11 MET cc_start: 0.6950 (tmm) cc_final: 0.6534 (tmm) REVERT: B 68 PHE cc_start: 0.8104 (m-80) cc_final: 0.7565 (t80) REVERT: B 102 MET cc_start: 0.7944 (mmm) cc_final: 0.7051 (mmm) REVERT: B 181 LYS cc_start: 0.7964 (ptmm) cc_final: 0.7593 (tttm) REVERT: B 239 TRP cc_start: 0.6587 (m-10) cc_final: 0.5582 (m-10) REVERT: B 288 ARG cc_start: 0.8530 (mtt90) cc_final: 0.7814 (mtt90) REVERT: B 297 ASN cc_start: 0.7925 (m-40) cc_final: 0.6764 (t0) REVERT: B 393 MET cc_start: 0.6502 (tpp) cc_final: 0.6246 (tpp) REVERT: B 525 ILE cc_start: 0.8746 (mt) cc_final: 0.8518 (mp) outliers start: 14 outliers final: 13 residues processed: 164 average time/residue: 0.2093 time to fit residues: 52.1861 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 : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 104 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 366 ILE Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 292 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 69 optimal weight: 0.0670 chunk 86 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 90 optimal weight: 0.0040 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.3530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 298 GLN ** 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 = 0.3822 r_free = 0.3822 target = 0.102586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.082053 restraints weight = 187008.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.088281 restraints weight = 58139.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.092470 restraints weight = 23134.975| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4830 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= 0.177 Angle : 0.744 13.443 12060 Z= 0.365 Chirality : 0.044 0.247 1422 Planarity : 0.004 0.036 1530 Dihedral : 7.387 102.714 1234 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.30 % Allowed : 23.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1112 helix: 2.07 (0.19), residues: 720 sheet: 0.14 (0.79), residues: 48 loop : -1.90 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 239 HIS 0.009 0.001 HIS A 451 PHE 0.052 0.002 PHE B 281 TYR 0.030 0.002 TYR B 96 ARG 0.005 0.000 ARG B 98 *********************** 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 168 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6664 (m-10) cc_final: 0.6432 (m-10) REVERT: A 71 MET cc_start: 0.8129 (mtm) cc_final: 0.7811 (ptm) REVERT: A 130 TRP cc_start: 0.8063 (m-10) cc_final: 0.7591 (m-10) REVERT: A 204 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8375 (t0) REVERT: A 254 MET cc_start: 0.8515 (mmm) cc_final: 0.8261 (ttp) REVERT: A 307 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7620 (tp30) REVERT: A 482 ILE cc_start: 0.8534 (pt) cc_final: 0.8218 (mt) REVERT: A 503 ASP cc_start: 0.7666 (t70) cc_final: 0.7305 (t70) REVERT: B 1 MET cc_start: 0.6601 (mtm) cc_final: 0.4275 (tpt) REVERT: B 11 MET cc_start: 0.6971 (tmm) cc_final: 0.6530 (tmm) REVERT: B 102 MET cc_start: 0.7843 (mmm) cc_final: 0.6943 (mmm) REVERT: B 181 LYS cc_start: 0.7849 (ptmm) cc_final: 0.7468 (tttm) REVERT: B 239 TRP cc_start: 0.6605 (m-10) cc_final: 0.5656 (m-10) REVERT: B 254 MET cc_start: 0.8297 (mtp) cc_final: 0.8086 (tpp) REVERT: B 285 MET cc_start: 0.8840 (ptp) cc_final: 0.8621 (pmm) REVERT: B 288 ARG cc_start: 0.8558 (mtt90) cc_final: 0.7872 (mtt90) REVERT: B 297 ASN cc_start: 0.7924 (m-40) cc_final: 0.7015 (t0) REVERT: B 393 MET cc_start: 0.6294 (tpp) cc_final: 0.6065 (tpp) REVERT: B 525 ILE cc_start: 0.8805 (mt) cc_final: 0.8524 (mp) outliers start: 12 outliers final: 11 residues processed: 164 average time/residue: 0.1579 time to fit residues: 38.7561 Evaluate side-chains 165 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 104 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 204 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 72 optimal weight: 0.0170 chunk 48 optimal weight: 0.0570 chunk 100 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 91 optimal weight: 0.1980 overall best weight: 0.1936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 297 ASN A 298 GLN B 137 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.103224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.082842 restraints weight = 160793.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.089033 restraints weight = 56556.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.093314 restraints weight = 22419.745| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4879 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= 0.180 Angle : 0.747 13.637 12060 Z= 0.366 Chirality : 0.044 0.243 1422 Planarity : 0.004 0.036 1530 Dihedral : 7.361 102.658 1234 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.41 % Allowed : 23.92 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1112 helix: 2.08 (0.19), residues: 722 sheet: 0.11 (0.76), residues: 48 loop : -1.91 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 238 HIS 0.007 0.001 HIS B 190 PHE 0.053 0.002 PHE B 281 TYR 0.038 0.002 TYR B 96 ARG 0.005 0.000 ARG B 98 ********************** 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 170 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6608 (m-10) cc_final: 0.6357 (m-10) REVERT: A 71 MET cc_start: 0.8102 (mtm) cc_final: 0.7801 (ptm) REVERT: A 204 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8292 (t0) REVERT: A 254 MET cc_start: 0.8491 (mmm) cc_final: 0.8240 (ttp) REVERT: A 307 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7629 (tp30) REVERT: A 482 ILE cc_start: 0.8552 (pt) cc_final: 0.8225 (mt) REVERT: A 503 ASP cc_start: 0.7584 (t70) cc_final: 0.7220 (t70) REVERT: B 1 MET cc_start: 0.6596 (mtm) cc_final: 0.4290 (tpt) REVERT: B 11 MET cc_start: 0.6976 (tmm) cc_final: 0.6515 (tmm) REVERT: B 68 PHE cc_start: 0.7939 (t80) cc_final: 0.7232 (t80) REVERT: B 102 MET cc_start: 0.7851 (mmm) cc_final: 0.6894 (mmm) REVERT: B 181 LYS cc_start: 0.7790 (ptmm) cc_final: 0.7389 (tttm) REVERT: B 239 TRP cc_start: 0.6560 (m-10) cc_final: 0.5727 (m-10) REVERT: B 285 MET cc_start: 0.8815 (ptp) cc_final: 0.8588 (pmm) REVERT: B 288 ARG cc_start: 0.8526 (mtt90) cc_final: 0.7664 (mtt90) REVERT: B 292 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9086 (mm) REVERT: B 297 ASN cc_start: 0.7904 (m-40) cc_final: 0.7378 (t0) REVERT: B 382 GLN cc_start: 0.8626 (tt0) cc_final: 0.8230 (tm-30) REVERT: B 393 MET cc_start: 0.6274 (tpp) cc_final: 0.6040 (tpp) REVERT: B 437 THR cc_start: 0.5994 (t) cc_final: 0.5633 (p) REVERT: B 525 ILE cc_start: 0.8705 (mt) cc_final: 0.8459 (mp) outliers start: 13 outliers final: 10 residues processed: 166 average time/residue: 0.1540 time to fit residues: 38.2031 Evaluate side-chains 168 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 104 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 204 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 49 optimal weight: 0.0060 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 58 optimal weight: 0.0040 chunk 66 optimal weight: 5.9990 overall best weight: 0.5008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN B 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.102974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.082138 restraints weight = 205042.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.087953 restraints weight = 63499.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.091837 restraints weight = 26554.611| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8886 Z= 0.179 Angle : 0.749 13.539 12060 Z= 0.367 Chirality : 0.043 0.250 1422 Planarity : 0.004 0.036 1530 Dihedral : 7.337 102.456 1234 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.89 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.25), residues: 1112 helix: 2.06 (0.19), residues: 722 sheet: 0.08 (0.75), residues: 48 loop : -1.90 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 239 HIS 0.007 0.001 HIS B 190 PHE 0.053 0.002 PHE B 281 TYR 0.036 0.002 TYR B 96 ARG 0.005 0.000 ARG B 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3055.02 seconds wall clock time: 54 minutes 34.49 seconds (3274.49 seconds total)