Starting phenix.real_space_refine on Sat Dec 28 18:57:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7znu_14814/12_2024/7znu_14814_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7znu_14814/12_2024/7znu_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_14814/12_2024/7znu_14814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7znu_14814/12_2024/7znu_14814.map" model { file = "/net/cci-nas-00/data/ceres_data/7znu_14814/12_2024/7znu_14814_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7znu_14814/12_2024/7znu_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-5532/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: 13.58, per 1000 atoms: 1.56 Number of scatterers: 8730 At special positions: 0 Unit cell: (68.06, 91.02, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) V 2 22.97 S 44 16.00 P 4 15.00 O 1620 8.00 N 1534 7.00 C 5526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 3.2 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: 0.76 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: 2.55 Time building geometry restraints manager: 2.69 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: 0.00 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 33.660 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.620 ------------------------------------------------------------------------------- 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 : 0.990 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: 0.2351 time to fit residues: 98.2107 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 : 1.095 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 TYR cc_start: 0.8514 (m-10) cc_final: 0.8282 (m-10) REVERT: A 68 PHE cc_start: 0.6507 (m-10) cc_final: 0.6276 (m-10) REVERT: A 71 MET cc_start: 0.7979 (mtm) cc_final: 0.7650 (ptm) REVERT: A 154 MET cc_start: 0.7714 (mmp) cc_final: 0.7425 (mmp) REVERT: A 270 MET cc_start: 0.5676 (tpp) cc_final: 0.3998 (tpp) REVERT: A 297 ASN cc_start: 0.8234 (m110) cc_final: 0.7295 (m110) REVERT: A 307 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7679 (tp30) REVERT: A 482 ILE cc_start: 0.8539 (pt) cc_final: 0.8198 (mt) REVERT: A 503 ASP cc_start: 0.7691 (t70) cc_final: 0.7456 (t70) REVERT: B 1 MET cc_start: 0.6430 (mtm) cc_final: 0.4116 (tpt) REVERT: B 11 MET cc_start: 0.7914 (mmp) cc_final: 0.7670 (ttt) REVERT: B 41 LEU cc_start: 0.8749 (mt) cc_final: 0.8197 (tp) REVERT: B 102 MET cc_start: 0.8216 (tpp) cc_final: 0.7977 (mmm) REVERT: B 169 TYR cc_start: 0.8536 (m-80) cc_final: 0.7962 (m-80) REVERT: B 181 LYS cc_start: 0.8084 (ptmm) cc_final: 0.7798 (tttm) REVERT: B 239 TRP cc_start: 0.6917 (m-10) cc_final: 0.6055 (m-10) REVERT: B 288 ARG cc_start: 0.8644 (mtt-85) cc_final: 0.8009 (mtt90) REVERT: B 384 VAL cc_start: 0.7690 (OUTLIER) cc_final: 0.7276 (m) outliers start: 17 outliers final: 11 residues processed: 200 average time/residue: 0.1930 time to fit residues: 54.5792 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 : 1.083 ------------------------------------------------------------------------------- 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 55 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8886 Z= 0.239 Angle : 0.750 13.956 12060 Z= 0.380 Chirality : 0.045 0.271 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.511 100.960 1234 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.22 % Rotamer: Outliers : 2.06 % Allowed : 19.48 % Favored : 78.46 % 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: 1.20 (0.25), residues: 1112 helix: 2.02 (0.19), residues: 728 sheet: -0.94 (1.21), residues: 24 loop : -1.75 (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 0.047 0.003 PHE B 281 TYR 0.035 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 188 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 TYR cc_start: 0.8536 (m-10) cc_final: 0.8273 (m-10) REVERT: A 68 PHE cc_start: 0.6544 (m-10) cc_final: 0.6270 (m-10) REVERT: A 71 MET cc_start: 0.8112 (mtm) cc_final: 0.7785 (ptm) REVERT: A 130 TRP cc_start: 0.8056 (m-10) cc_final: 0.7594 (m-10) REVERT: A 254 MET cc_start: 0.8554 (mmm) cc_final: 0.8234 (ttp) REVERT: A 307 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7619 (tp30) REVERT: A 482 ILE cc_start: 0.8575 (pt) cc_final: 0.8264 (mt) REVERT: A 503 ASP cc_start: 0.7806 (t70) cc_final: 0.7548 (t70) REVERT: B 1 MET cc_start: 0.6548 (mtm) cc_final: 0.4230 (tpt) REVERT: B 169 TYR cc_start: 0.8682 (m-80) cc_final: 0.7969 (m-80) REVERT: B 181 LYS cc_start: 0.8143 (ptmm) cc_final: 0.7807 (tttm) REVERT: B 239 TRP cc_start: 0.6615 (m-10) cc_final: 0.5859 (m-10) REVERT: B 254 MET cc_start: 0.8390 (mtp) cc_final: 0.8103 (tpp) REVERT: B 270 MET cc_start: 0.5951 (mmp) cc_final: 0.5673 (ttm) REVERT: B 288 ARG cc_start: 0.8507 (mtt-85) cc_final: 0.7874 (mtt90) REVERT: B 297 ASN cc_start: 0.8152 (m-40) cc_final: 0.7807 (t0) outliers start: 19 outliers final: 14 residues processed: 177 average time/residue: 0.1931 time to fit residues: 49.2660 Evaluate side-chains 165 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 493 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 138 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 349 GLN A 451 HIS B 85 HIS ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8886 Z= 0.205 Angle : 0.754 13.416 12060 Z= 0.372 Chirality : 0.044 0.251 1422 Planarity : 0.004 0.037 1530 Dihedral : 7.472 102.158 1234 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.78 % Favored : 95.13 % Rotamer: Outliers : 1.95 % Allowed : 21.21 % Favored : 76.84 % 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: 1.07 (0.25), residues: 1112 helix: 1.94 (0.19), residues: 730 sheet: -1.41 (0.85), residues: 44 loop : -1.82 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.003 TRP A 239 HIS 0.003 0.001 HIS B 117 PHE 0.048 0.003 PHE B 281 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 179 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 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: 0.6497 (m-10) cc_final: 0.6214 (m-10) REVERT: A 71 MET cc_start: 0.8142 (mtm) cc_final: 0.7819 (ptm) REVERT: A 254 MET cc_start: 0.8537 (mmm) cc_final: 0.8222 (ttp) REVERT: A 307 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7549 (tp30) REVERT: A 482 ILE cc_start: 0.8540 (pt) cc_final: 0.8228 (mt) REVERT: A 503 ASP cc_start: 0.7774 (t70) cc_final: 0.7489 (t70) REVERT: B 1 MET cc_start: 0.6565 (mtm) cc_final: 0.4221 (tpt) REVERT: B 68 PHE cc_start: 0.8039 (t80) cc_final: 0.7279 (t80) REVERT: B 169 TYR cc_start: 0.8651 (m-80) cc_final: 0.7909 (m-80) REVERT: B 181 LYS cc_start: 0.8155 (ptmm) cc_final: 0.7814 (tttm) REVERT: B 239 TRP cc_start: 0.6568 (m-10) cc_final: 0.5593 (m-10) REVERT: B 297 ASN cc_start: 0.7984 (m-40) cc_final: 0.7129 (t0) outliers start: 18 outliers final: 12 residues processed: 171 average time/residue: 0.1826 time to fit residues: 45.4600 Evaluate side-chains 166 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain B residue 99 LEU 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 307 GLU Chi-restraints excluded: chain B residue 364 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 0.1980 chunk 95 optimal weight: 8.9990 chunk 26 optimal weight: 0.0870 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 451 HIS B 137 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4360 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= 0.184 Angle : 0.768 13.694 12060 Z= 0.375 Chirality : 0.044 0.346 1422 Planarity : 0.004 0.034 1530 Dihedral : 7.434 103.341 1234 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.52 % Allowed : 21.97 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.25), residues: 1112 helix: 1.94 (0.19), residues: 728 sheet: -0.87 (1.13), residues: 24 loop : -1.73 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.003 TRP A 239 HIS 0.016 0.001 HIS A 451 PHE 0.047 0.002 PHE B 281 TYR 0.028 0.001 TYR B 96 ARG 0.005 0.000 ARG B 400 *********************** 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 182 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6501 (m-10) cc_final: 0.6229 (m-10) REVERT: A 71 MET cc_start: 0.8120 (mtm) cc_final: 0.7811 (ptm) REVERT: A 130 TRP cc_start: 0.8038 (m-10) cc_final: 0.7554 (m-10) REVERT: A 254 MET cc_start: 0.8555 (mmm) cc_final: 0.8210 (ttp) REVERT: A 299 THR cc_start: 0.9232 (m) cc_final: 0.9031 (p) REVERT: A 307 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7514 (tp30) REVERT: A 482 ILE cc_start: 0.8514 (pt) cc_final: 0.8214 (mt) REVERT: A 503 ASP cc_start: 0.7752 (t70) cc_final: 0.7443 (t70) REVERT: B 1 MET cc_start: 0.6717 (mtm) cc_final: 0.4489 (tpt) REVERT: B 102 MET cc_start: 0.7877 (mmm) cc_final: 0.6859 (mmm) REVERT: B 169 TYR cc_start: 0.8491 (m-80) cc_final: 0.7889 (m-80) REVERT: B 181 LYS cc_start: 0.8113 (ptmm) cc_final: 0.7747 (tttm) REVERT: B 239 TRP cc_start: 0.6566 (m-10) cc_final: 0.5571 (m-10) REVERT: B 288 ARG cc_start: 0.8741 (mtt90) cc_final: 0.7659 (mtt90) REVERT: B 297 ASN cc_start: 0.7965 (m-40) cc_final: 0.6917 (t0) REVERT: B 525 ILE cc_start: 0.8767 (mt) cc_final: 0.8533 (mp) outliers start: 14 outliers final: 9 residues processed: 175 average time/residue: 0.1786 time to fit residues: 45.6744 Evaluate side-chains 165 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 137 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 0.0370 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS B 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8886 Z= 0.200 Angle : 0.753 13.502 12060 Z= 0.373 Chirality : 0.045 0.336 1422 Planarity : 0.004 0.032 1530 Dihedral : 7.435 103.014 1234 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.52 % Allowed : 22.51 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1112 helix: 1.97 (0.19), residues: 724 sheet: -0.70 (0.71), residues: 58 loop : -1.72 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 239 HIS 0.013 0.001 HIS A 451 PHE 0.046 0.002 PHE B 281 TYR 0.011 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 174 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6556 (m-10) cc_final: 0.6276 (m-10) REVERT: A 71 MET cc_start: 0.8156 (mtm) cc_final: 0.7821 (ptm) REVERT: A 130 TRP cc_start: 0.8070 (m-10) cc_final: 0.7590 (m-10) REVERT: A 239 TRP cc_start: 0.8575 (t-100) cc_final: 0.8360 (m100) REVERT: A 254 MET cc_start: 0.8547 (mmm) cc_final: 0.8170 (ttp) REVERT: A 307 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7522 (tp30) REVERT: A 482 ILE cc_start: 0.8527 (pt) cc_final: 0.8225 (mt) REVERT: A 503 ASP cc_start: 0.7772 (t70) cc_final: 0.7460 (t70) REVERT: A 542 MET cc_start: 0.7735 (ppp) cc_final: 0.7315 (ppp) REVERT: B 1 MET cc_start: 0.6729 (mtm) cc_final: 0.4471 (tpt) REVERT: B 11 MET cc_start: 0.7156 (ttp) cc_final: 0.6776 (tmm) REVERT: B 181 LYS cc_start: 0.8112 (ptmm) cc_final: 0.7741 (tttm) REVERT: B 239 TRP cc_start: 0.6618 (m-10) cc_final: 0.5628 (m-10) REVERT: B 288 ARG cc_start: 0.8661 (mtt90) cc_final: 0.7856 (mtt90) REVERT: B 297 ASN cc_start: 0.7985 (m-40) cc_final: 0.6843 (t0) REVERT: B 525 ILE cc_start: 0.8737 (mt) cc_final: 0.8511 (mp) outliers start: 14 outliers final: 13 residues processed: 169 average time/residue: 0.1718 time to fit residues: 43.0464 Evaluate side-chains 168 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 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 99 LEU Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 272 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 0.3980 chunk 48 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8886 Z= 0.195 Angle : 0.747 13.420 12060 Z= 0.367 Chirality : 0.044 0.259 1422 Planarity : 0.004 0.032 1530 Dihedral : 7.419 102.967 1234 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.41 % Allowed : 22.84 % 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: 1.13 (0.26), residues: 1112 helix: 1.94 (0.19), residues: 728 sheet: -0.62 (0.72), residues: 58 loop : -1.83 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 239 HIS 0.008 0.001 HIS A 451 PHE 0.050 0.002 PHE B 281 TYR 0.012 0.001 TYR B 352 ARG 0.009 0.000 ARG B 135 *********************** 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 172 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6646 (m-10) cc_final: 0.6376 (m-10) REVERT: A 71 MET cc_start: 0.8145 (mtm) cc_final: 0.7812 (ptm) REVERT: A 152 MET cc_start: 0.7518 (mmm) cc_final: 0.7197 (mmm) REVERT: A 307 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7505 (tp30) REVERT: A 482 ILE cc_start: 0.8522 (pt) cc_final: 0.8217 (mt) REVERT: A 503 ASP cc_start: 0.7754 (t70) cc_final: 0.7417 (t70) REVERT: A 542 MET cc_start: 0.7738 (ppp) cc_final: 0.7350 (ppp) REVERT: B 1 MET cc_start: 0.6768 (mtm) cc_final: 0.4469 (tpt) REVERT: B 11 MET cc_start: 0.7273 (ttp) cc_final: 0.6826 (tmm) REVERT: B 102 MET cc_start: 0.7852 (mmm) cc_final: 0.6948 (mmm) REVERT: B 181 LYS cc_start: 0.8093 (ptmm) cc_final: 0.7716 (tttm) REVERT: B 239 TRP cc_start: 0.6637 (m-10) cc_final: 0.5653 (m-10) REVERT: B 279 ILE cc_start: 0.9087 (tp) cc_final: 0.8763 (tp) REVERT: B 297 ASN cc_start: 0.8013 (m-40) cc_final: 0.6887 (t0) REVERT: B 312 MET cc_start: 0.8183 (tpt) cc_final: 0.7942 (ttp) REVERT: B 437 THR cc_start: 0.6164 (t) cc_final: 0.5775 (p) REVERT: B 525 ILE cc_start: 0.8726 (mt) cc_final: 0.8500 (mp) outliers start: 13 outliers final: 13 residues processed: 166 average time/residue: 0.1690 time to fit residues: 42.1159 Evaluate side-chains 164 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 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 36 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 272 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 0.0060 chunk 92 optimal weight: 0.7980 overall best weight: 0.9600 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4820 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= 0.201 Angle : 0.768 13.213 12060 Z= 0.381 Chirality : 0.046 0.360 1422 Planarity : 0.004 0.034 1530 Dihedral : 7.399 102.577 1234 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.73 % Allowed : 23.48 % 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 (0.26), residues: 1112 helix: 2.00 (0.19), residues: 724 sheet: -0.56 (0.72), residues: 58 loop : -1.67 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 239 HIS 0.005 0.001 HIS B 137 PHE 0.051 0.002 PHE B 281 TYR 0.014 0.001 TYR B 96 ARG 0.004 0.000 ARG B 400 *********************** 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 167 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6661 (m-10) cc_final: 0.6400 (m-10) REVERT: A 71 MET cc_start: 0.8204 (mtm) cc_final: 0.7882 (ptm) REVERT: A 152 MET cc_start: 0.7536 (mmm) cc_final: 0.7206 (mmm) REVERT: A 204 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8422 (t0) REVERT: A 254 MET cc_start: 0.8387 (mmm) cc_final: 0.8170 (ttp) REVERT: A 307 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7501 (tp30) REVERT: A 482 ILE cc_start: 0.8539 (pt) cc_final: 0.8232 (mt) REVERT: A 503 ASP cc_start: 0.7756 (t70) cc_final: 0.7398 (t70) REVERT: A 542 MET cc_start: 0.7766 (ppp) cc_final: 0.7366 (ppp) REVERT: B 1 MET cc_start: 0.6750 (mtm) cc_final: 0.4426 (tpt) REVERT: B 11 MET cc_start: 0.7322 (ttp) cc_final: 0.6839 (tmm) REVERT: B 181 LYS cc_start: 0.8072 (ptmm) cc_final: 0.7685 (tttm) REVERT: B 239 TRP cc_start: 0.6680 (m-10) cc_final: 0.5721 (m-10) REVERT: B 254 MET cc_start: 0.8421 (mtp) cc_final: 0.8102 (tpp) REVERT: B 288 ARG cc_start: 0.8584 (mtt90) cc_final: 0.7810 (mtt90) REVERT: B 297 ASN cc_start: 0.8014 (m-40) cc_final: 0.6898 (t0) REVERT: B 312 MET cc_start: 0.8209 (tpt) cc_final: 0.7962 (ttp) REVERT: B 393 MET cc_start: 0.6033 (tpp) cc_final: 0.5823 (tpp) REVERT: B 525 ILE cc_start: 0.8730 (mt) cc_final: 0.8498 (mp) outliers start: 16 outliers final: 15 residues processed: 160 average time/residue: 0.1688 time to fit residues: 40.5151 Evaluate side-chains 165 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 284 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 272 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 0.0470 chunk 43 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 chunk 93 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8886 Z= 0.209 Angle : 0.770 13.020 12060 Z= 0.382 Chirality : 0.046 0.387 1422 Planarity : 0.004 0.033 1530 Dihedral : 7.395 102.203 1234 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.62 % Allowed : 24.46 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1112 helix: 1.98 (0.19), residues: 722 sheet: -0.50 (0.72), residues: 58 loop : -1.68 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 239 HIS 0.005 0.001 HIS B 137 PHE 0.051 0.002 PHE B 281 TYR 0.039 0.002 TYR A 96 ARG 0.006 0.000 ARG B 135 *********************** 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 169 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6699 (m-10) cc_final: 0.6428 (m-10) REVERT: A 71 MET cc_start: 0.8225 (mtm) cc_final: 0.7891 (ptm) REVERT: A 152 MET cc_start: 0.7510 (mmm) cc_final: 0.7185 (mmm) REVERT: A 204 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8594 (t0) REVERT: A 254 MET cc_start: 0.8409 (mmm) cc_final: 0.8180 (ttp) REVERT: A 307 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7524 (tp30) REVERT: A 482 ILE cc_start: 0.8539 (pt) cc_final: 0.8235 (mt) REVERT: A 503 ASP cc_start: 0.7771 (t70) cc_final: 0.7408 (t70) REVERT: A 542 MET cc_start: 0.7747 (ppp) cc_final: 0.7332 (ppp) REVERT: B 1 MET cc_start: 0.6745 (mtm) cc_final: 0.4396 (tpt) REVERT: B 11 MET cc_start: 0.7255 (ttp) cc_final: 0.6819 (tmm) REVERT: B 102 MET cc_start: 0.7869 (mmm) cc_final: 0.6959 (mmm) REVERT: B 181 LYS cc_start: 0.8074 (ptmm) cc_final: 0.7688 (tttm) REVERT: B 239 TRP cc_start: 0.6607 (m-10) cc_final: 0.5675 (m-10) REVERT: B 254 MET cc_start: 0.8382 (mtp) cc_final: 0.8128 (tpt) REVERT: B 288 ARG cc_start: 0.8550 (mtt90) cc_final: 0.7808 (mtt90) REVERT: B 297 ASN cc_start: 0.8014 (m-40) cc_final: 0.6901 (t0) REVERT: B 312 MET cc_start: 0.8218 (tpt) cc_final: 0.7963 (ttp) REVERT: B 525 ILE cc_start: 0.8736 (mt) cc_final: 0.8532 (mp) outliers start: 15 outliers final: 14 residues processed: 163 average time/residue: 0.1664 time to fit residues: 40.3569 Evaluate side-chains 169 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 284 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 272 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8886 Z= 0.198 Angle : 0.797 17.602 12060 Z= 0.391 Chirality : 0.046 0.408 1422 Planarity : 0.004 0.034 1530 Dihedral : 7.397 102.169 1234 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.41 % Allowed : 24.68 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1112 helix: 2.01 (0.19), residues: 718 sheet: -0.41 (0.72), residues: 58 loop : -1.94 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 239 HIS 0.009 0.001 HIS B 137 PHE 0.052 0.002 PHE B 281 TYR 0.029 0.002 TYR A 96 ARG 0.004 0.000 ARG B 222 ********************** 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 167 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6685 (m-10) cc_final: 0.6414 (m-10) REVERT: A 71 MET cc_start: 0.8200 (mtm) cc_final: 0.7885 (ptm) REVERT: A 204 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8282 (t0) REVERT: A 254 MET cc_start: 0.8410 (mmm) cc_final: 0.8180 (ttp) REVERT: A 307 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7511 (tp30) REVERT: A 482 ILE cc_start: 0.8524 (pt) cc_final: 0.8221 (mt) REVERT: A 503 ASP cc_start: 0.7733 (t70) cc_final: 0.7362 (t70) REVERT: A 542 MET cc_start: 0.7748 (ppp) cc_final: 0.7456 (ppp) REVERT: B 1 MET cc_start: 0.6734 (mtm) cc_final: 0.4364 (tpt) REVERT: B 11 MET cc_start: 0.7255 (ttp) cc_final: 0.6796 (tmm) REVERT: B 102 MET cc_start: 0.7857 (mmm) cc_final: 0.6940 (mmm) REVERT: B 181 LYS cc_start: 0.8044 (ptmm) cc_final: 0.7654 (tttm) REVERT: B 239 TRP cc_start: 0.6619 (m-10) cc_final: 0.5678 (m-10) REVERT: B 288 ARG cc_start: 0.8564 (mtt90) cc_final: 0.7817 (mtt90) REVERT: B 297 ASN cc_start: 0.8008 (m-40) cc_final: 0.6897 (t0) REVERT: B 312 MET cc_start: 0.8190 (tpt) cc_final: 0.7940 (ttp) REVERT: B 525 ILE cc_start: 0.8744 (mt) cc_final: 0.8506 (mp) outliers start: 13 outliers final: 11 residues processed: 161 average time/residue: 0.1674 time to fit residues: 40.2146 Evaluate side-chains 163 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 204 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 36 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.099769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.079303 restraints weight = 195655.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.084593 restraints weight = 54297.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.088029 restraints weight = 25909.572| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8886 Z= 0.211 Angle : 0.816 24.351 12060 Z= 0.403 Chirality : 0.047 0.422 1422 Planarity : 0.004 0.034 1530 Dihedral : 7.414 101.769 1234 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.30 % Allowed : 24.78 % Favored : 73.92 % 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: 1.06 (0.26), residues: 1112 helix: 1.96 (0.19), residues: 718 sheet: -0.38 (0.72), residues: 58 loop : -1.98 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 239 HIS 0.014 0.001 HIS B 137 PHE 0.055 0.002 PHE B 281 TYR 0.026 0.002 TYR A 96 ARG 0.004 0.000 ARG A 288 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2090.20 seconds wall clock time: 38 minutes 58.30 seconds (2338.30 seconds total)