Starting phenix.real_space_refine on Mon Jun 9 20:18:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9inh_60707/06_2025/9inh_60707.cif Found real_map, /net/cci-nas-00/data/ceres_data/9inh_60707/06_2025/9inh_60707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9inh_60707/06_2025/9inh_60707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9inh_60707/06_2025/9inh_60707.map" model { file = "/net/cci-nas-00/data/ceres_data/9inh_60707/06_2025/9inh_60707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9inh_60707/06_2025/9inh_60707.cif" } resolution = 3.68 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= -0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 5 Type Number sf(0) Gaussians P 28 5.49 5 S 42 5.16 5 C 7298 2.51 5 N 1670 2.21 5 O 1895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10933 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 5030 Classifications: {'peptide': 606} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 585} Chain breaks: 2 Chain: "D" Number of atoms: 5059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 5059 Classifications: {'peptide': 609} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 588} Chain breaks: 2 Chain: "A" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 422 Unusual residues: {'3PE': 3, 'ACD': 1, 'CLR': 6, 'IHP': 1, 'PLM': 1, 'PO4': 5} Classifications: {'undetermined': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 422 Unusual residues: {'3PE': 3, 'ACD': 1, 'CLR': 6, 'IHP': 1, 'PLM': 1, 'PO4': 5} Classifications: {'undetermined': 17} Link IDs: {None: 16} Time building chain proxies: 8.54, per 1000 atoms: 0.78 Number of scatterers: 10933 At special positions: 0 Unit cell: (109.08, 96.152, 101, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 28 15.00 O 1895 8.00 N 1670 7.00 C 7298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS D 415 " - pdb=" SG CYS D 440 " distance=2.03 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: 2.98 Conformation dependent library (CDL) restraints added in 1.3 seconds 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2332 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 79.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 Processing helix chain 'A' and resid 12 through 17 removed outlier: 4.409A pdb=" N LYS A 17 " --> pdb=" O PRO A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 34 Processing helix chain 'A' and resid 43 through 103 Processing helix chain 'A' and resid 119 through 165 Processing helix chain 'A' and resid 173 through 180 Processing helix chain 'A' and resid 183 through 188 removed outlier: 3.813A pdb=" N CYS A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 206 Processing helix chain 'A' and resid 210 through 218 removed outlier: 3.609A pdb=" N ALA A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 257 Processing helix chain 'A' and resid 265 through 296 removed outlier: 4.377A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 312 through 336 removed outlier: 3.855A pdb=" N ILE A 319 " --> pdb=" O HIS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 361 removed outlier: 3.590A pdb=" N TYR A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 384 through 387 Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.823A pdb=" N ASN A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 removed outlier: 3.706A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 446 through 471 Proline residue: A 455 - end of helix removed outlier: 3.560A pdb=" N PHE A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 removed outlier: 4.196A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 503 removed outlier: 4.582A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 524 removed outlier: 4.096A pdb=" N ILE A 520 " --> pdb=" O VAL A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 572 removed outlier: 3.868A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.650A pdb=" N GLN A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 619 Proline residue: A 598 - end of helix removed outlier: 3.732A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 10 Processing helix chain 'D' and resid 12 through 16 Processing helix chain 'D' and resid 21 through 34 removed outlier: 3.545A pdb=" N ALA D 32 " --> pdb=" O MET D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 103 removed outlier: 3.576A pdb=" N SER D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 168 removed outlier: 4.009A pdb=" N ASN D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 179 Processing helix chain 'D' and resid 183 through 188 Processing helix chain 'D' and resid 189 through 205 removed outlier: 3.557A pdb=" N GLN D 193 " --> pdb=" O LYS D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 218 Processing helix chain 'D' and resid 230 through 258 removed outlier: 3.811A pdb=" N ARG D 236 " --> pdb=" O TRP D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 296 removed outlier: 4.436A pdb=" N GLY D 274 " --> pdb=" O ARG D 270 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLY D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE D 276 " --> pdb=" O TYR D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 303 removed outlier: 4.083A pdb=" N ILE D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 337 removed outlier: 3.773A pdb=" N ILE D 319 " --> pdb=" O HIS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 346 through 360 Processing helix chain 'D' and resid 367 through 383 Processing helix chain 'D' and resid 384 through 387 removed outlier: 3.511A pdb=" N HIS D 387 " --> pdb=" O ALA D 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 384 through 387' Processing helix chain 'D' and resid 390 through 403 removed outlier: 4.091A pdb=" N ASN D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER D 402 " --> pdb=" O ASP D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 420 removed outlier: 3.739A pdb=" N LEU D 407 " --> pdb=" O LEU D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 445 No H-bonds generated for 'chain 'D' and resid 443 through 445' Processing helix chain 'D' and resid 446 through 451 Processing helix chain 'D' and resid 453 through 471 Processing helix chain 'D' and resid 472 through 477 removed outlier: 4.088A pdb=" N HIS D 476 " --> pdb=" O ARG D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 503 removed outlier: 4.569A pdb=" N THR D 486 " --> pdb=" O LYS D 482 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE D 487 " --> pdb=" O TYR D 483 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE D 488 " --> pdb=" O SER D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 522 removed outlier: 3.865A pdb=" N VAL D 509 " --> pdb=" O SER D 505 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR D 512 " --> pdb=" O MET D 508 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU D 513 " --> pdb=" O VAL D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 532 removed outlier: 3.823A pdb=" N ASP D 529 " --> pdb=" O THR D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 570 removed outlier: 3.889A pdb=" N TYR D 559 " --> pdb=" O GLN D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 580 removed outlier: 4.360A pdb=" N ILE D 575 " --> pdb=" O PHE D 571 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN D 576 " --> pdb=" O ALA D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 619 removed outlier: 3.529A pdb=" N ILE D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) Proline residue: D 598 - end of helix removed outlier: 3.588A pdb=" N PHE D 609 " --> pdb=" O PHE D 605 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE D 610 " --> pdb=" O VAL D 606 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU D 613 " --> pdb=" O PHE D 609 " (cutoff:3.500A) 695 hydrogen bonds defined for protein. 2076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.22 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1716 1.32 - 1.45: 3069 1.45 - 1.57: 6370 1.57 - 1.69: 24 1.69 - 1.82: 60 Bond restraints: 11239 Sorted by residual: bond pdb=" O3 PO4 A 814 " pdb=" P PO4 A 814 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.50e+00 bond pdb=" O3 PO4 D 805 " pdb=" P PO4 D 805 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.47e+00 bond pdb=" O3 PO4 A 812 " pdb=" P PO4 A 812 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.41e+00 bond pdb=" O3 PO4 D 804 " pdb=" P PO4 D 804 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.34e+00 bond pdb=" O3 PO4 D 807 " pdb=" P PO4 D 807 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.34e+00 ... (remaining 11234 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 14768 1.90 - 3.80: 359 3.80 - 5.71: 74 5.71 - 7.61: 20 7.61 - 9.51: 8 Bond angle restraints: 15229 Sorted by residual: angle pdb=" N VAL A 341 " pdb=" CA VAL A 341 " pdb=" C VAL A 341 " ideal model delta sigma weight residual 113.53 108.92 4.61 9.80e-01 1.04e+00 2.21e+01 angle pdb=" N ASP A 174 " pdb=" CA ASP A 174 " pdb=" C ASP A 174 " ideal model delta sigma weight residual 112.54 107.82 4.72 1.22e+00 6.72e-01 1.50e+01 angle pdb=" N ILE D 520 " pdb=" CA ILE D 520 " pdb=" C ILE D 520 " ideal model delta sigma weight residual 113.42 109.14 4.28 1.17e+00 7.31e-01 1.34e+01 angle pdb=" N LYS D 26 " pdb=" CA LYS D 26 " pdb=" C LYS D 26 " ideal model delta sigma weight residual 111.28 107.38 3.90 1.09e+00 8.42e-01 1.28e+01 angle pdb=" CA MET D 489 " pdb=" C MET D 489 " pdb=" O MET D 489 " ideal model delta sigma weight residual 120.82 117.19 3.63 1.05e+00 9.07e-01 1.20e+01 ... (remaining 15224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.80: 6846 33.80 - 67.60: 354 67.60 - 101.40: 27 101.40 - 135.21: 27 135.21 - 169.01: 9 Dihedral angle restraints: 7263 sinusoidal: 3664 harmonic: 3599 Sorted by residual: dihedral pdb=" O14 IHP D 801 " pdb=" C4 IHP D 801 " pdb=" C5 IHP D 801 " pdb=" O15 IHP D 801 " ideal model delta sinusoidal sigma weight residual -52.79 116.22 -169.01 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" O14 IHP A 801 " pdb=" C4 IHP A 801 " pdb=" C5 IHP A 801 " pdb=" O15 IHP A 801 " ideal model delta sinusoidal sigma weight residual -52.79 115.01 -167.80 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C6 IHP A 801 " pdb=" C1 IHP A 801 " pdb=" C2 IHP A 801 " pdb=" O12 IHP A 801 " ideal model delta sinusoidal sigma weight residual 61.05 -97.44 158.49 1 3.00e+01 1.11e-03 2.06e+01 ... (remaining 7260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.992: 1633 0.992 - 1.984: 0 1.984 - 2.976: 0 2.976 - 3.968: 0 3.968 - 4.961: 8 Chirality restraints: 1641 Sorted by residual: chirality pdb=" C2 IHP D 801 " pdb=" C1 IHP D 801 " pdb=" C3 IHP D 801 " pdb=" O12 IHP D 801 " both_signs ideal model delta sigma weight residual False -2.52 2.44 -4.96 2.00e-01 2.50e+01 6.15e+02 chirality pdb=" C2 IHP A 801 " pdb=" C1 IHP A 801 " pdb=" C3 IHP A 801 " pdb=" O12 IHP A 801 " both_signs ideal model delta sigma weight residual False -2.52 2.44 -4.96 2.00e-01 2.50e+01 6.14e+02 chirality pdb=" C6 IHP A 801 " pdb=" C1 IHP A 801 " pdb=" C5 IHP A 801 " pdb=" O16 IHP A 801 " both_signs ideal model delta sigma weight residual False -2.50 2.35 -4.85 2.00e-01 2.50e+01 5.88e+02 ... (remaining 1638 not shown) Planarity restraints: 1777 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 466 " 0.261 9.50e-02 1.11e+02 1.17e-01 8.43e+00 pdb=" NE ARG D 466 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG D 466 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 466 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 466 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 73 " -0.009 2.00e-02 2.50e+03 1.60e-02 5.12e+00 pdb=" CG TYR D 73 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR D 73 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR D 73 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR D 73 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 73 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR D 73 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 73 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 416 " 0.014 2.00e-02 2.50e+03 1.66e-02 4.83e+00 pdb=" CG PHE D 416 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE D 416 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE D 416 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE D 416 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE D 416 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 416 " 0.001 2.00e-02 2.50e+03 ... (remaining 1774 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1953 2.76 - 3.30: 11375 3.30 - 3.83: 18895 3.83 - 4.37: 22388 4.37 - 4.90: 36539 Nonbonded interactions: 91150 Sorted by model distance: nonbonded pdb=" OG1 THR D 545 " pdb=" OH TYR D 560 " model vdw 2.227 3.040 nonbonded pdb=" N GLU A 543 " pdb=" OE1 GLU A 543 " model vdw 2.261 3.120 nonbonded pdb=" O ASP D 43 " pdb=" OG1 THR D 46 " model vdw 2.269 3.040 nonbonded pdb=" O ARG A 122 " pdb=" ND1 HIS A 125 " model vdw 2.275 3.120 nonbonded pdb=" OG1 THR A 545 " pdb=" OH TYR A 560 " model vdw 2.283 3.040 ... (remaining 91145 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 207 or resid 211 through 625 or resid 801 or res \ id 810)) selection = (chain 'D' and (resid 1 through 165 or resid 172 through 625 or resid 801 or res \ id 810)) } 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=1.00 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: 8.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.930 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.006 0.070 11241 Z= 0.284 Angle : 0.757 9.511 15233 Z= 0.403 Chirality : 0.340 4.961 1641 Planarity : 0.005 0.117 1777 Dihedral : 20.998 169.008 4925 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.21 % Allowed : 20.13 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1203 helix: 0.83 (0.17), residues: 898 sheet: None (None), residues: 0 loop : -1.17 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 175 HIS 0.012 0.001 HIS D 163 PHE 0.038 0.002 PHE D 416 TYR 0.038 0.002 TYR D 73 ARG 0.013 0.001 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.14715 ( 695) hydrogen bonds : angle 6.55063 ( 2076) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.58570 ( 4) covalent geometry : bond 0.00565 (11239) covalent geometry : angle 0.75725 (15229) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 1.404 Fit side-chains revert: symmetry clash REVERT: A 559 TYR cc_start: 0.7589 (m-80) cc_final: 0.6917 (m-80) REVERT: D 1 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6930 (ppp) REVERT: D 25 PHE cc_start: 0.6667 (m-80) cc_final: 0.6317 (m-80) outliers start: 13 outliers final: 5 residues processed: 131 average time/residue: 0.2721 time to fit residues: 49.0404 Evaluate side-chains 117 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 609 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 0.0040 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 248 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.210358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.155007 restraints weight = 14232.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.152089 restraints weight = 13179.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.154444 restraints weight = 11210.679| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11241 Z= 0.175 Angle : 0.700 16.392 15233 Z= 0.329 Chirality : 0.046 0.426 1641 Planarity : 0.004 0.044 1777 Dihedral : 16.968 150.930 2557 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.88 % Allowed : 17.16 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.24), residues: 1203 helix: 1.03 (0.17), residues: 911 sheet: None (None), residues: 0 loop : -1.06 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 607 HIS 0.010 0.001 HIS D 163 PHE 0.029 0.002 PHE A 135 TYR 0.019 0.002 TYR A 368 ARG 0.004 0.001 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.05112 ( 695) hydrogen bonds : angle 5.09954 ( 2076) SS BOND : bond 0.00242 ( 2) SS BOND : angle 0.67435 ( 4) covalent geometry : bond 0.00384 (11239) covalent geometry : angle 0.70004 (15229) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 TYR cc_start: 0.7469 (m-10) cc_final: 0.7218 (m-10) REVERT: A 84 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.6621 (m-10) REVERT: A 451 VAL cc_start: 0.8994 (t) cc_final: 0.8746 (m) REVERT: D 176 ARG cc_start: 0.7743 (ptp-170) cc_final: 0.7145 (ptp-170) REVERT: D 508 MET cc_start: 0.5558 (tpp) cc_final: 0.5357 (tpp) outliers start: 31 outliers final: 16 residues processed: 146 average time/residue: 0.2294 time to fit residues: 47.6964 Evaluate side-chains 135 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 441 HIS Chi-restraints excluded: chain D residue 452 GLN Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 609 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 20.0000 chunk 27 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.207627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.151590 restraints weight = 14172.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.147988 restraints weight = 12915.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.150552 restraints weight = 10694.771| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11241 Z= 0.167 Angle : 0.630 11.242 15233 Z= 0.308 Chirality : 0.044 0.417 1641 Planarity : 0.004 0.050 1777 Dihedral : 15.605 146.479 2551 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.15 % Allowed : 17.81 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.24), residues: 1203 helix: 1.11 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -0.94 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 514 HIS 0.011 0.001 HIS D 163 PHE 0.018 0.002 PHE D 156 TYR 0.022 0.002 TYR D 368 ARG 0.005 0.001 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.04697 ( 695) hydrogen bonds : angle 4.87492 ( 2076) SS BOND : bond 0.00235 ( 2) SS BOND : angle 0.71726 ( 4) covalent geometry : bond 0.00374 (11239) covalent geometry : angle 0.62970 (15229) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 TYR cc_start: 0.7542 (m-10) cc_final: 0.7147 (m-10) REVERT: A 83 ARG cc_start: 0.8311 (tpp-160) cc_final: 0.7824 (mmm160) REVERT: A 84 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6558 (m-10) REVERT: D 302 ILE cc_start: 0.8496 (mt) cc_final: 0.8050 (mm) outliers start: 34 outliers final: 24 residues processed: 146 average time/residue: 0.2409 time to fit residues: 49.9722 Evaluate side-chains 142 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 441 HIS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 452 GLN Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 609 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 45 optimal weight: 0.2980 chunk 85 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 70 optimal weight: 0.0070 chunk 18 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.211429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.155882 restraints weight = 14217.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.153865 restraints weight = 13026.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.155987 restraints weight = 10956.096| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11241 Z= 0.139 Angle : 0.583 10.864 15233 Z= 0.289 Chirality : 0.043 0.406 1641 Planarity : 0.004 0.064 1777 Dihedral : 14.934 142.245 2551 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.97 % Allowed : 18.46 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.00 (0.24), residues: 1203 helix: 1.18 (0.17), residues: 919 sheet: None (None), residues: 0 loop : -0.91 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 514 HIS 0.011 0.001 HIS D 163 PHE 0.015 0.001 PHE D 156 TYR 0.024 0.002 TYR D 73 ARG 0.005 0.000 ARG D 157 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 695) hydrogen bonds : angle 4.69419 ( 2076) SS BOND : bond 0.00172 ( 2) SS BOND : angle 0.67365 ( 4) covalent geometry : bond 0.00300 (11239) covalent geometry : angle 0.58334 (15229) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 TYR cc_start: 0.7455 (m-10) cc_final: 0.7039 (m-10) REVERT: A 84 PHE cc_start: 0.6995 (OUTLIER) cc_final: 0.6587 (m-10) REVERT: A 292 TRP cc_start: 0.8591 (m-10) cc_final: 0.8344 (m-10) REVERT: A 508 MET cc_start: 0.4648 (tpp) cc_final: 0.4238 (tpp) REVERT: A 559 TYR cc_start: 0.7554 (m-80) cc_final: 0.6954 (m-80) REVERT: D 302 ILE cc_start: 0.8512 (mt) cc_final: 0.8074 (mm) REVERT: D 508 MET cc_start: 0.5656 (tpp) cc_final: 0.5450 (tpp) outliers start: 32 outliers final: 18 residues processed: 146 average time/residue: 0.2365 time to fit residues: 49.0593 Evaluate side-chains 138 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 328 CYS Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 441 HIS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 452 GLN Chi-restraints excluded: chain D residue 609 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 56 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 118 optimal weight: 0.3980 chunk 98 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.209014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.154062 restraints weight = 14213.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.151260 restraints weight = 13975.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.153263 restraints weight = 11683.806| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11241 Z= 0.167 Angle : 0.597 10.234 15233 Z= 0.296 Chirality : 0.044 0.435 1641 Planarity : 0.004 0.057 1777 Dihedral : 14.544 139.995 2550 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.53 % Allowed : 19.39 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.24), residues: 1203 helix: 1.22 (0.17), residues: 919 sheet: None (None), residues: 0 loop : -0.86 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 514 HIS 0.011 0.001 HIS D 163 PHE 0.020 0.002 PHE D 354 TYR 0.032 0.002 TYR D 19 ARG 0.004 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.04406 ( 695) hydrogen bonds : angle 4.63022 ( 2076) SS BOND : bond 0.00218 ( 2) SS BOND : angle 0.66970 ( 4) covalent geometry : bond 0.00375 (11239) covalent geometry : angle 0.59738 (15229) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 TYR cc_start: 0.7464 (m-10) cc_final: 0.7099 (m-10) REVERT: A 84 PHE cc_start: 0.6962 (OUTLIER) cc_final: 0.6638 (m-10) REVERT: A 157 ARG cc_start: 0.7480 (mmt180) cc_final: 0.7098 (mmt180) REVERT: A 508 MET cc_start: 0.4818 (tpp) cc_final: 0.4552 (tpp) REVERT: A 559 TYR cc_start: 0.7709 (m-80) cc_final: 0.7104 (m-80) REVERT: D 25 PHE cc_start: 0.7303 (m-80) cc_final: 0.6773 (m-80) REVERT: D 84 PHE cc_start: 0.7534 (m-80) cc_final: 0.7074 (m-10) REVERT: D 302 ILE cc_start: 0.8603 (mt) cc_final: 0.8119 (mm) REVERT: D 573 TRP cc_start: 0.6758 (m100) cc_final: 0.6402 (m100) outliers start: 38 outliers final: 24 residues processed: 152 average time/residue: 0.2387 time to fit residues: 51.0888 Evaluate side-chains 141 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 328 CYS Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 441 HIS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 609 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.206076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.150325 restraints weight = 14172.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.147258 restraints weight = 12447.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.149444 restraints weight = 10462.712| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11241 Z= 0.176 Angle : 0.605 8.496 15233 Z= 0.302 Chirality : 0.044 0.414 1641 Planarity : 0.004 0.079 1777 Dihedral : 14.406 139.459 2550 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.99 % Allowed : 19.48 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.24), residues: 1203 helix: 1.24 (0.17), residues: 913 sheet: None (None), residues: 0 loop : -0.91 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 514 HIS 0.011 0.001 HIS D 163 PHE 0.025 0.002 PHE A 416 TYR 0.035 0.002 TYR A 73 ARG 0.005 0.000 ARG D 157 Details of bonding type rmsd hydrogen bonds : bond 0.04441 ( 695) hydrogen bonds : angle 4.61914 ( 2076) SS BOND : bond 0.00172 ( 2) SS BOND : angle 0.66772 ( 4) covalent geometry : bond 0.00401 (11239) covalent geometry : angle 0.60483 (15229) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 TYR cc_start: 0.7585 (m-10) cc_final: 0.7170 (m-10) REVERT: A 84 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.6697 (m-10) REVERT: A 156 PHE cc_start: 0.7276 (m-80) cc_final: 0.6995 (m-80) REVERT: A 157 ARG cc_start: 0.7628 (mmt180) cc_final: 0.7181 (mmt180) REVERT: A 339 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.6405 (tt) REVERT: A 508 MET cc_start: 0.4942 (tpp) cc_final: 0.4731 (tpp) REVERT: A 559 TYR cc_start: 0.7737 (m-80) cc_final: 0.7216 (m-80) REVERT: D 84 PHE cc_start: 0.7536 (m-80) cc_final: 0.7188 (m-10) REVERT: D 508 MET cc_start: 0.5743 (tpp) cc_final: 0.5277 (tpp) REVERT: D 573 TRP cc_start: 0.6782 (m100) cc_final: 0.6348 (m100) outliers start: 43 outliers final: 29 residues processed: 153 average time/residue: 0.2398 time to fit residues: 52.2299 Evaluate side-chains 149 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 328 CYS Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 452 GLN Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 609 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.208865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.154131 restraints weight = 14551.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.150438 restraints weight = 13656.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.152742 restraints weight = 11731.701| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11241 Z= 0.162 Angle : 0.596 8.592 15233 Z= 0.299 Chirality : 0.042 0.353 1641 Planarity : 0.004 0.073 1777 Dihedral : 14.304 138.996 2550 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.62 % Allowed : 19.67 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.10 (0.24), residues: 1203 helix: 1.28 (0.17), residues: 911 sheet: None (None), residues: 0 loop : -0.93 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 514 HIS 0.013 0.001 HIS A 125 PHE 0.022 0.002 PHE A 416 TYR 0.026 0.002 TYR D 368 ARG 0.005 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.04376 ( 695) hydrogen bonds : angle 4.59448 ( 2076) SS BOND : bond 0.00172 ( 2) SS BOND : angle 0.64756 ( 4) covalent geometry : bond 0.00367 (11239) covalent geometry : angle 0.59559 (15229) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 1.147 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: A 30 TYR cc_start: 0.7527 (m-10) cc_final: 0.7121 (m-10) REVERT: A 84 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6681 (m-10) REVERT: A 157 ARG cc_start: 0.7624 (mmt180) cc_final: 0.7163 (mmt180) REVERT: D 84 PHE cc_start: 0.7483 (m-80) cc_final: 0.7098 (m-10) REVERT: D 302 ILE cc_start: 0.8639 (mt) cc_final: 0.8147 (mm) REVERT: D 408 MET cc_start: 0.7196 (ttm) cc_final: 0.6765 (mtt) REVERT: D 573 TRP cc_start: 0.6762 (m100) cc_final: 0.6303 (m100) outliers start: 39 outliers final: 29 residues processed: 150 average time/residue: 0.2396 time to fit residues: 51.0786 Evaluate side-chains 152 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 328 CYS Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 609 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 77 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.209899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.155159 restraints weight = 14351.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.152340 restraints weight = 13572.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.154574 restraints weight = 11384.266| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11241 Z= 0.150 Angle : 0.597 9.059 15233 Z= 0.300 Chirality : 0.041 0.286 1641 Planarity : 0.004 0.056 1777 Dihedral : 14.142 137.733 2550 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.53 % Allowed : 19.85 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.24), residues: 1203 helix: 1.33 (0.17), residues: 911 sheet: None (None), residues: 0 loop : -0.94 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 514 HIS 0.012 0.001 HIS A 125 PHE 0.023 0.002 PHE A 416 TYR 0.030 0.002 TYR A 73 ARG 0.004 0.000 ARG D 157 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 695) hydrogen bonds : angle 4.57329 ( 2076) SS BOND : bond 0.00180 ( 2) SS BOND : angle 0.65134 ( 4) covalent geometry : bond 0.00333 (11239) covalent geometry : angle 0.59706 (15229) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 1.200 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: A 30 TYR cc_start: 0.7378 (m-10) cc_final: 0.7013 (m-10) REVERT: A 157 ARG cc_start: 0.7544 (mmt180) cc_final: 0.7071 (mmt180) REVERT: D 84 PHE cc_start: 0.7438 (m-80) cc_final: 0.7176 (m-10) REVERT: D 302 ILE cc_start: 0.8629 (mt) cc_final: 0.8143 (mm) REVERT: D 508 MET cc_start: 0.5558 (tpp) cc_final: 0.5022 (tpp) REVERT: D 573 TRP cc_start: 0.6746 (m100) cc_final: 0.6271 (m100) outliers start: 38 outliers final: 30 residues processed: 153 average time/residue: 0.2307 time to fit residues: 50.7006 Evaluate side-chains 149 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 328 CYS Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 441 HIS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 609 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 53 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 54 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 116 optimal weight: 0.0670 chunk 107 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.208358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.152982 restraints weight = 14125.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.149983 restraints weight = 12196.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.152262 restraints weight = 10122.879| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11241 Z= 0.137 Angle : 0.591 8.672 15233 Z= 0.298 Chirality : 0.041 0.273 1641 Planarity : 0.004 0.065 1777 Dihedral : 13.876 135.820 2550 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.69 % Allowed : 20.96 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.24), residues: 1203 helix: 1.37 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -1.00 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 514 HIS 0.012 0.001 HIS A 125 PHE 0.023 0.001 PHE A 416 TYR 0.037 0.002 TYR A 73 ARG 0.005 0.000 ARG D 157 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 695) hydrogen bonds : angle 4.52271 ( 2076) SS BOND : bond 0.00202 ( 2) SS BOND : angle 0.58620 ( 4) covalent geometry : bond 0.00298 (11239) covalent geometry : angle 0.59131 (15229) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.167 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 30 TYR cc_start: 0.7436 (m-10) cc_final: 0.7074 (m-10) REVERT: D 84 PHE cc_start: 0.7456 (m-80) cc_final: 0.7190 (m-10) REVERT: D 176 ARG cc_start: 0.7242 (ptp-170) cc_final: 0.6930 (ptp-170) REVERT: D 302 ILE cc_start: 0.8578 (mt) cc_final: 0.8077 (mm) REVERT: D 508 MET cc_start: 0.5556 (tpp) cc_final: 0.5021 (tpp) REVERT: D 511 PHE cc_start: 0.7818 (t80) cc_final: 0.7329 (t80) REVERT: D 559 TYR cc_start: 0.7644 (m-80) cc_final: 0.6990 (m-80) outliers start: 29 outliers final: 29 residues processed: 151 average time/residue: 0.2447 time to fit residues: 52.5457 Evaluate side-chains 147 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 328 CYS Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 441 HIS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 609 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 26 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 17 optimal weight: 0.0870 chunk 84 optimal weight: 3.9990 chunk 38 optimal weight: 0.1980 chunk 88 optimal weight: 0.8980 chunk 63 optimal weight: 20.0000 chunk 37 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.211066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.155913 restraints weight = 14213.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.152885 restraints weight = 13682.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.155102 restraints weight = 11419.877| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11241 Z= 0.144 Angle : 0.604 9.337 15233 Z= 0.303 Chirality : 0.041 0.263 1641 Planarity : 0.004 0.048 1777 Dihedral : 13.678 134.317 2550 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.99 % Favored : 96.92 % Rotamer: Outliers : 2.78 % Allowed : 21.15 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.24), residues: 1203 helix: 1.39 (0.17), residues: 917 sheet: None (None), residues: 0 loop : -1.01 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 514 HIS 0.012 0.001 HIS A 125 PHE 0.024 0.002 PHE A 416 TYR 0.027 0.002 TYR A 412 ARG 0.004 0.000 ARG D 157 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 695) hydrogen bonds : angle 4.50981 ( 2076) SS BOND : bond 0.00142 ( 2) SS BOND : angle 0.67116 ( 4) covalent geometry : bond 0.00317 (11239) covalent geometry : angle 0.60441 (15229) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 1.068 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 30 TYR cc_start: 0.7361 (m-10) cc_final: 0.7051 (m-10) REVERT: D 84 PHE cc_start: 0.7406 (m-80) cc_final: 0.7155 (m-10) REVERT: D 176 ARG cc_start: 0.7276 (ptp-170) cc_final: 0.6840 (ptp-170) REVERT: D 302 ILE cc_start: 0.8601 (mt) cc_final: 0.8098 (mm) REVERT: D 508 MET cc_start: 0.5611 (tpp) cc_final: 0.5105 (tpp) REVERT: D 559 TYR cc_start: 0.7655 (m-80) cc_final: 0.7044 (m-80) REVERT: D 573 TRP cc_start: 0.6678 (m100) cc_final: 0.6171 (m100) outliers start: 30 outliers final: 27 residues processed: 147 average time/residue: 0.2443 time to fit residues: 50.5265 Evaluate side-chains 148 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 328 CYS Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 441 HIS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 609 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 51 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.205677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.149507 restraints weight = 14030.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.145794 restraints weight = 11893.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.148030 restraints weight = 10034.698| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11241 Z= 0.138 Angle : 0.595 8.408 15233 Z= 0.299 Chirality : 0.041 0.301 1641 Planarity : 0.004 0.050 1777 Dihedral : 13.508 133.393 2550 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.83 % Favored : 97.09 % Rotamer: Outliers : 2.60 % Allowed : 21.52 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.30 (0.24), residues: 1203 helix: 1.44 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -0.99 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 514 HIS 0.012 0.001 HIS A 125 PHE 0.024 0.002 PHE A 25 TYR 0.035 0.002 TYR A 73 ARG 0.004 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 695) hydrogen bonds : angle 4.48012 ( 2076) SS BOND : bond 0.00166 ( 2) SS BOND : angle 0.62932 ( 4) covalent geometry : bond 0.00304 (11239) covalent geometry : angle 0.59453 (15229) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3356.62 seconds wall clock time: 59 minutes 30.75 seconds (3570.75 seconds total)