Starting phenix.real_space_refine on Wed Mar 12 00:28:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iwp_35776/03_2025/8iwp_35776.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iwp_35776/03_2025/8iwp_35776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iwp_35776/03_2025/8iwp_35776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iwp_35776/03_2025/8iwp_35776.map" model { file = "/net/cci-nas-00/data/ceres_data/8iwp_35776/03_2025/8iwp_35776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iwp_35776/03_2025/8iwp_35776.cif" } resolution = 3.59 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= 0.016 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 Ca 1 9.91 5 S 52 5.16 5 C 4372 2.51 5 N 1147 2.21 5 O 1289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6861 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 896, 6860 Classifications: {'peptide': 896} Link IDs: {'PTRANS': 35, 'TRANS': 860} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.29, per 1000 atoms: 0.77 Number of scatterers: 6861 At special positions: 0 Unit cell: (86.52, 99.96, 134.4, 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) Ca 1 19.99 S 52 16.00 O 1289 8.00 N 1147 7.00 C 4372 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: 1.56 Conformation dependent library (CDL) restraints added in 901.5 milliseconds 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1670 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 54.4% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 47 through 58 Processing helix chain 'A' and resid 70 through 78 removed outlier: 3.645A pdb=" N LYS A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 97 Processing helix chain 'A' and resid 99 through 131 Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 256 through 287 removed outlier: 3.648A pdb=" N LEU A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 305 Processing helix chain 'A' and resid 309 through 328 Processing helix chain 'A' and resid 334 through 341 removed outlier: 3.601A pdb=" N ILE A 337 " --> pdb=" O LYS A 334 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 338 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU A 339 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 411 Processing helix chain 'A' and resid 424 through 437 removed outlier: 4.006A pdb=" N MET A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 5.529A pdb=" N GLY A 441 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 503 through 520 Processing helix chain 'A' and resid 551 through 563 Processing helix chain 'A' and resid 573 through 585 Processing helix chain 'A' and resid 596 through 602 Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 621 through 636 removed outlier: 3.736A pdb=" N ASN A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 683 through 723 removed outlier: 4.203A pdb=" N SER A 687 " --> pdb=" O GLN A 683 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 688 " --> pdb=" O THR A 684 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N MET A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 742 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 757 through 761 removed outlier: 3.526A pdb=" N ARG A 760 " --> pdb=" O ASP A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 798 Processing helix chain 'A' and resid 804 through 826 removed outlier: 4.279A pdb=" N THR A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 837 removed outlier: 3.709A pdb=" N ILE A 836 " --> pdb=" O SER A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 861 Processing helix chain 'A' and resid 861 through 869 Processing helix chain 'A' and resid 874 through 885 Processing helix chain 'A' and resid 888 through 910 Processing sheet with id=AA1, first strand: chain 'A' and resid 146 through 151 removed outlier: 3.550A pdb=" N THR A 150 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS A 139 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER A 182 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 226 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASP A 180 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA A 228 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 178 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N GLY A 230 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE A 176 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A 234 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 172 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU A 181 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 197 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 183 " --> pdb=" O CYS A 195 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS A 195 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 151 removed outlier: 3.550A pdb=" N THR A 150 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS A 139 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER A 182 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 226 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASP A 180 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA A 228 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 178 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N GLY A 230 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE A 176 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A 234 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 172 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 350 removed outlier: 6.629A pdb=" N GLN A 592 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A 616 " --> pdb=" O GLN A 592 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 594 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR A 618 " --> pdb=" O VAL A 594 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 392 removed outlier: 5.040A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS A 364 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE A 538 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N SER A 529 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 540 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 463 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 480 " --> pdb=" O MET A 461 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA A 462 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLU A 451 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS A 464 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 392 removed outlier: 5.040A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS A 364 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS A 490 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE A 538 " --> pdb=" O CYS A 490 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR A 492 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N GLY A 540 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 10.699A pdb=" N GLN A 494 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 14.335A pdb=" N VAL A 542 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 415 through 417 removed outlier: 4.370A pdb=" N VAL A 415 " --> pdb=" O MET A 422 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET A 422 " --> pdb=" O VAL A 415 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 660 through 661 removed outlier: 6.517A pdb=" N ALA A 660 " --> pdb=" O LEU A 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 412 hydrogen bonds defined for protein. 1194 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: 2.50 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2230 1.34 - 1.46: 1366 1.46 - 1.58: 3290 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 6970 Sorted by residual: bond pdb=" CA GLU A 62 " pdb=" CB GLU A 62 " ideal model delta sigma weight residual 1.535 1.562 -0.027 1.58e-02 4.01e+03 2.98e+00 bond pdb=" CB PRO A 744 " pdb=" CG PRO A 744 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.94e+00 bond pdb=" CA THR A 590 " pdb=" CB THR A 590 " ideal model delta sigma weight residual 1.528 1.565 -0.037 2.61e-02 1.47e+03 1.99e+00 bond pdb=" CG1 ILE A 431 " pdb=" CD1 ILE A 431 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.68e+00 bond pdb=" C THR A 804 " pdb=" N PRO A 805 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.57e+00 ... (remaining 6965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 9254 2.04 - 4.09: 134 4.09 - 6.13: 35 6.13 - 8.17: 11 8.17 - 10.21: 4 Bond angle restraints: 9438 Sorted by residual: angle pdb=" CA PRO A 744 " pdb=" N PRO A 744 " pdb=" CD PRO A 744 " ideal model delta sigma weight residual 112.00 106.71 5.29 1.40e+00 5.10e-01 1.43e+01 angle pdb=" CA GLN A 512 " pdb=" CB GLN A 512 " pdb=" CG GLN A 512 " ideal model delta sigma weight residual 114.10 121.37 -7.27 2.00e+00 2.50e-01 1.32e+01 angle pdb=" CB LYS A 756 " pdb=" CG LYS A 756 " pdb=" CD LYS A 756 " ideal model delta sigma weight residual 111.30 118.84 -7.54 2.30e+00 1.89e-01 1.08e+01 angle pdb=" CA LYS A 424 " pdb=" CB LYS A 424 " pdb=" CG LYS A 424 " ideal model delta sigma weight residual 114.10 120.66 -6.56 2.00e+00 2.50e-01 1.08e+01 angle pdb=" C VAL A 346 " pdb=" CA VAL A 346 " pdb=" CB VAL A 346 " ideal model delta sigma weight residual 111.29 116.55 -5.26 1.64e+00 3.72e-01 1.03e+01 ... (remaining 9433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3711 17.97 - 35.93: 422 35.93 - 53.90: 100 53.90 - 71.87: 21 71.87 - 89.84: 7 Dihedral angle restraints: 4261 sinusoidal: 1680 harmonic: 2581 Sorted by residual: dihedral pdb=" CA ASN A 81 " pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta harmonic sigma weight residual -180.00 -152.52 -27.48 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA MET A 602 " pdb=" C MET A 602 " pdb=" N ASP A 603 " pdb=" CA ASP A 603 " ideal model delta harmonic sigma weight residual -180.00 -156.17 -23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLY A 208 " pdb=" C GLY A 208 " pdb=" N ASP A 209 " pdb=" CA ASP A 209 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 4258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 829 0.039 - 0.078: 219 0.078 - 0.116: 78 0.116 - 0.155: 6 0.155 - 0.194: 3 Chirality restraints: 1135 Sorted by residual: chirality pdb=" CG LEU A 780 " pdb=" CB LEU A 780 " pdb=" CD1 LEU A 780 " pdb=" CD2 LEU A 780 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" CA THR A 804 " pdb=" N THR A 804 " pdb=" C THR A 804 " pdb=" CB THR A 804 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CG LEU A 29 " pdb=" CB LEU A 29 " pdb=" CD1 LEU A 29 " pdb=" CD2 LEU A 29 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 1132 not shown) Planarity restraints: 1193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 743 " -0.079 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO A 744 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO A 744 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 744 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 60 " 0.014 2.00e-02 2.50e+03 1.54e-02 5.93e+00 pdb=" CG TRP A 60 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 60 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 60 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 60 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 60 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 60 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 60 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 60 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 60 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 72 " -0.013 2.00e-02 2.50e+03 1.17e-02 3.43e+00 pdb=" CG TRP A 72 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 72 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 72 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 72 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 72 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 72 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 72 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 72 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 72 " -0.002 2.00e-02 2.50e+03 ... (remaining 1190 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2013 2.82 - 3.34: 6677 3.34 - 3.86: 11234 3.86 - 4.38: 11909 4.38 - 4.90: 21428 Nonbonded interactions: 53261 Sorted by model distance: nonbonded pdb=" OG1 THR A 570 " pdb=" OD2 ASP A 572 " model vdw 2.301 3.040 nonbonded pdb=" N GLN A 829 " pdb=" OE1 GLN A 829 " model vdw 2.351 3.120 nonbonded pdb=" NZ LYS A 333 " pdb=" O ALA A 673 " model vdw 2.351 3.120 nonbonded pdb=" ND2 ASN A 61 " pdb=" O ALA A 152 " model vdw 2.357 3.120 nonbonded pdb=" N THR A 503 " pdb=" OE1 GLN A 506 " model vdw 2.362 3.120 ... (remaining 53256 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.460 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.040 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 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 0.086 6970 Z= 0.204 Angle : 0.688 10.214 9438 Z= 0.365 Chirality : 0.041 0.194 1135 Planarity : 0.005 0.117 1193 Dihedral : 16.146 89.836 2591 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.92 % Favored : 94.97 % Rotamer: Outliers : 0.39 % Allowed : 25.03 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.30), residues: 894 helix: 2.02 (0.24), residues: 461 sheet: -0.49 (0.56), residues: 99 loop : -0.19 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 60 HIS 0.002 0.000 HIS A 149 PHE 0.020 0.001 PHE A 241 TYR 0.010 0.001 TYR A 618 ARG 0.002 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 134 time to evaluate : 0.709 Fit side-chains REVERT: A 71 LEU cc_start: 0.7714 (pp) cc_final: 0.7415 (pp) REVERT: A 797 GLU cc_start: 0.6317 (tm-30) cc_final: 0.5636 (tm-30) outliers start: 3 outliers final: 3 residues processed: 134 average time/residue: 0.1653 time to fit residues: 30.6408 Evaluate side-chains 132 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 739 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 36 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 80 optimal weight: 0.5980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.202305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.156381 restraints weight = 9048.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.157974 restraints weight = 7052.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.159942 restraints weight = 5578.607| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6970 Z= 0.229 Angle : 0.615 8.375 9438 Z= 0.309 Chirality : 0.042 0.208 1135 Planarity : 0.004 0.075 1193 Dihedral : 4.607 58.549 950 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.03 % Favored : 95.86 % Rotamer: Outliers : 2.85 % Allowed : 21.27 % Favored : 75.88 % 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: 1.44 (0.29), residues: 894 helix: 2.10 (0.24), residues: 461 sheet: 0.32 (0.61), residues: 76 loop : -0.40 (0.36), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 60 HIS 0.005 0.001 HIS A 149 PHE 0.012 0.001 PHE A 812 TYR 0.011 0.001 TYR A 483 ARG 0.003 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.756 Fit side-chains REVERT: A 306 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8444 (mt) REVERT: A 435 MET cc_start: 0.7224 (tmm) cc_final: 0.6705 (tmm) REVERT: A 780 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8490 (mm) outliers start: 22 outliers final: 11 residues processed: 146 average time/residue: 0.1648 time to fit residues: 33.4044 Evaluate side-chains 131 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 790 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 0.0030 chunk 48 optimal weight: 0.1980 chunk 3 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.201119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.156094 restraints weight = 9234.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.155593 restraints weight = 8816.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.157982 restraints weight = 7011.325| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6970 Z= 0.194 Angle : 0.597 10.054 9438 Z= 0.295 Chirality : 0.041 0.199 1135 Planarity : 0.004 0.064 1193 Dihedral : 4.025 26.728 946 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.36 % Favored : 95.41 % Rotamer: Outliers : 3.11 % Allowed : 22.18 % Favored : 74.71 % 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: 1.56 (0.29), residues: 894 helix: 2.19 (0.24), residues: 461 sheet: 0.80 (0.69), residues: 63 loop : -0.40 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 60 HIS 0.003 0.001 HIS A 149 PHE 0.008 0.001 PHE A 702 TYR 0.010 0.001 TYR A 618 ARG 0.004 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 131 LEU cc_start: 0.8171 (tt) cc_final: 0.7963 (tp) REVERT: A 435 MET cc_start: 0.7454 (tmm) cc_final: 0.6765 (tmm) REVERT: A 757 ASP cc_start: 0.7951 (t0) cc_final: 0.7573 (t70) REVERT: A 780 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8466 (mm) REVERT: A 810 MET cc_start: 0.7048 (ttm) cc_final: 0.6802 (mtp) outliers start: 24 outliers final: 18 residues processed: 145 average time/residue: 0.1801 time to fit residues: 35.4768 Evaluate side-chains 137 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 888 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 72 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 2 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.196250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.150765 restraints weight = 9354.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.148873 restraints weight = 7879.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.151063 restraints weight = 7587.986| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6970 Z= 0.222 Angle : 0.618 9.450 9438 Z= 0.308 Chirality : 0.042 0.206 1135 Planarity : 0.004 0.061 1193 Dihedral : 4.161 27.558 946 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.92 % Favored : 94.85 % Rotamer: Outliers : 4.41 % Allowed : 21.66 % Favored : 73.93 % 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: 1.48 (0.29), residues: 894 helix: 2.15 (0.24), residues: 461 sheet: 0.70 (0.70), residues: 63 loop : -0.49 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 795 HIS 0.003 0.001 HIS A 58 PHE 0.013 0.001 PHE A 702 TYR 0.013 0.001 TYR A 483 ARG 0.002 0.000 ARG A 796 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 281 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7605 (tmt) REVERT: A 306 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8611 (mt) REVERT: A 435 MET cc_start: 0.7508 (tmm) cc_final: 0.6728 (tmm) REVERT: A 757 ASP cc_start: 0.8191 (t0) cc_final: 0.7852 (t70) REVERT: A 780 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8400 (mm) outliers start: 34 outliers final: 26 residues processed: 148 average time/residue: 0.1865 time to fit residues: 37.7745 Evaluate side-chains 146 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 852 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 22 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.191505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.146818 restraints weight = 9360.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.145107 restraints weight = 9140.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.147132 restraints weight = 9255.626| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6970 Z= 0.338 Angle : 0.714 11.313 9438 Z= 0.358 Chirality : 0.045 0.221 1135 Planarity : 0.005 0.060 1193 Dihedral : 4.630 29.947 946 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.26 % Favored : 94.63 % Rotamer: Outliers : 5.19 % Allowed : 22.44 % Favored : 72.37 % 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: 1.01 (0.29), residues: 894 helix: 1.75 (0.24), residues: 462 sheet: -0.77 (0.64), residues: 79 loop : -0.37 (0.36), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 795 HIS 0.003 0.001 HIS A 58 PHE 0.018 0.002 PHE A 725 TYR 0.016 0.002 TYR A 618 ARG 0.003 0.000 ARG A 796 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 312 ILE cc_start: 0.8994 (mm) cc_final: 0.8756 (mt) REVERT: A 337 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7538 (tp) REVERT: A 435 MET cc_start: 0.7528 (tmm) cc_final: 0.6871 (tmm) REVERT: A 479 MET cc_start: 0.5084 (tpt) cc_final: 0.4573 (tmm) REVERT: A 780 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8417 (mm) outliers start: 40 outliers final: 25 residues processed: 153 average time/residue: 0.1805 time to fit residues: 37.2103 Evaluate side-chains 149 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 852 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 3 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 18 optimal weight: 20.0000 chunk 66 optimal weight: 0.0470 chunk 81 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 494 GLN A 855 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.193929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.150985 restraints weight = 9314.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149820 restraints weight = 9153.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.151978 restraints weight = 8376.428| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6970 Z= 0.214 Angle : 0.640 11.208 9438 Z= 0.317 Chirality : 0.042 0.203 1135 Planarity : 0.004 0.057 1193 Dihedral : 4.483 31.038 946 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.81 % Favored : 95.08 % Rotamer: Outliers : 4.67 % Allowed : 22.57 % Favored : 72.76 % 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: 1.29 (0.30), residues: 894 helix: 2.01 (0.24), residues: 462 sheet: -0.20 (0.67), residues: 73 loop : -0.41 (0.36), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 72 HIS 0.004 0.001 HIS A 58 PHE 0.016 0.001 PHE A 702 TYR 0.014 0.001 TYR A 618 ARG 0.004 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8782 (mt) REVERT: A 312 ILE cc_start: 0.8900 (mm) cc_final: 0.8661 (mt) REVERT: A 435 MET cc_start: 0.7656 (tmm) cc_final: 0.7002 (tmm) REVERT: A 613 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8278 (ttpp) REVERT: A 780 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8279 (mm) outliers start: 36 outliers final: 28 residues processed: 144 average time/residue: 0.1668 time to fit residues: 33.3380 Evaluate side-chains 148 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 888 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.193073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.148801 restraints weight = 9205.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.146839 restraints weight = 9791.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.148465 restraints weight = 8816.357| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6970 Z= 0.233 Angle : 0.646 10.930 9438 Z= 0.320 Chirality : 0.042 0.196 1135 Planarity : 0.004 0.055 1193 Dihedral : 4.474 32.592 946 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.47 % Favored : 95.41 % Rotamer: Outliers : 5.19 % Allowed : 22.31 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.30), residues: 894 helix: 2.02 (0.24), residues: 463 sheet: -0.83 (0.64), residues: 80 loop : -0.29 (0.37), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 72 HIS 0.004 0.001 HIS A 58 PHE 0.015 0.001 PHE A 702 TYR 0.014 0.001 TYR A 618 ARG 0.003 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 306 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8789 (mt) REVERT: A 312 ILE cc_start: 0.8910 (mm) cc_final: 0.8671 (mt) REVERT: A 337 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7112 (tp) REVERT: A 435 MET cc_start: 0.7598 (tmm) cc_final: 0.6948 (tmm) REVERT: A 594 VAL cc_start: 0.8396 (t) cc_final: 0.8187 (t) REVERT: A 613 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8268 (ttpp) REVERT: A 679 ASP cc_start: 0.8377 (t0) cc_final: 0.7876 (t70) REVERT: A 780 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8308 (mm) outliers start: 40 outliers final: 34 residues processed: 145 average time/residue: 0.1704 time to fit residues: 34.3874 Evaluate side-chains 156 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 18 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 467 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.192277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.149142 restraints weight = 9350.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.147431 restraints weight = 10025.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.149355 restraints weight = 8969.838| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6970 Z= 0.257 Angle : 0.677 11.419 9438 Z= 0.334 Chirality : 0.042 0.195 1135 Planarity : 0.004 0.054 1193 Dihedral : 4.562 36.728 946 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.15 % Favored : 94.74 % Rotamer: Outliers : 5.19 % Allowed : 23.09 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.30), residues: 894 helix: 2.01 (0.24), residues: 463 sheet: -0.83 (0.63), residues: 79 loop : -0.34 (0.37), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 72 HIS 0.003 0.001 HIS A 58 PHE 0.014 0.001 PHE A 702 TYR 0.015 0.001 TYR A 618 ARG 0.003 0.000 ARG A 796 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 306 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8767 (mt) REVERT: A 312 ILE cc_start: 0.8954 (mm) cc_final: 0.8699 (mt) REVERT: A 337 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7169 (tp) REVERT: A 435 MET cc_start: 0.7613 (tmm) cc_final: 0.6946 (tmm) REVERT: A 679 ASP cc_start: 0.8440 (t0) cc_final: 0.7950 (t70) REVERT: A 780 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8297 (mm) outliers start: 40 outliers final: 32 residues processed: 144 average time/residue: 0.1690 time to fit residues: 33.5338 Evaluate side-chains 152 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 59 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 18 optimal weight: 0.0370 chunk 82 optimal weight: 0.0040 chunk 17 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 40 optimal weight: 0.0270 overall best weight: 0.2728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.197124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.152543 restraints weight = 9393.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.149930 restraints weight = 7878.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.152324 restraints weight = 7901.410| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6970 Z= 0.182 Angle : 0.661 11.369 9438 Z= 0.318 Chirality : 0.041 0.184 1135 Planarity : 0.004 0.054 1193 Dihedral : 4.360 32.127 946 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.63 % Allowed : 24.64 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.30), residues: 894 helix: 2.20 (0.24), residues: 463 sheet: -0.29 (0.61), residues: 90 loop : -0.38 (0.37), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 72 HIS 0.002 0.000 HIS A 58 PHE 0.015 0.001 PHE A 702 TYR 0.023 0.001 TYR A 483 ARG 0.003 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 138 GLU cc_start: 0.8134 (tp30) cc_final: 0.7684 (tt0) REVERT: A 308 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7269 (pt0) REVERT: A 312 ILE cc_start: 0.8816 (mm) cc_final: 0.8575 (mt) REVERT: A 435 MET cc_start: 0.7612 (tmm) cc_final: 0.6750 (tmm) REVERT: A 594 VAL cc_start: 0.8391 (t) cc_final: 0.8167 (t) REVERT: A 679 ASP cc_start: 0.8343 (t0) cc_final: 0.7857 (t70) REVERT: A 780 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8321 (mm) outliers start: 28 outliers final: 21 residues processed: 140 average time/residue: 0.1704 time to fit residues: 33.0750 Evaluate side-chains 143 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 888 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 33 optimal weight: 0.3980 chunk 19 optimal weight: 0.0870 chunk 14 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.192861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.149678 restraints weight = 9429.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.147457 restraints weight = 9099.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.149584 restraints weight = 8330.103| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6970 Z= 0.235 Angle : 0.716 15.943 9438 Z= 0.340 Chirality : 0.042 0.190 1135 Planarity : 0.004 0.054 1193 Dihedral : 4.415 32.537 946 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.50 % Allowed : 24.77 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 1.42 (0.30), residues: 894 helix: 2.16 (0.24), residues: 463 sheet: 0.36 (0.70), residues: 63 loop : -0.55 (0.36), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 72 HIS 0.003 0.001 HIS A 58 PHE 0.013 0.001 PHE A 702 TYR 0.019 0.001 TYR A 483 ARG 0.004 0.000 ARG A 900 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 138 GLU cc_start: 0.8110 (tp30) cc_final: 0.7664 (tt0) REVERT: A 262 MET cc_start: 0.8486 (mmp) cc_final: 0.8271 (mmp) REVERT: A 308 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7306 (pt0) REVERT: A 312 ILE cc_start: 0.8883 (mm) cc_final: 0.8636 (mt) REVERT: A 435 MET cc_start: 0.7575 (tmm) cc_final: 0.6717 (tmm) REVERT: A 679 ASP cc_start: 0.8284 (t0) cc_final: 0.7902 (t70) REVERT: A 780 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8272 (mm) outliers start: 27 outliers final: 25 residues processed: 137 average time/residue: 0.1756 time to fit residues: 33.6099 Evaluate side-chains 149 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 59 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.194263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.149393 restraints weight = 9431.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.148129 restraints weight = 9108.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.149715 restraints weight = 8046.285| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6970 Z= 0.219 Angle : 0.709 15.551 9438 Z= 0.336 Chirality : 0.042 0.188 1135 Planarity : 0.004 0.054 1193 Dihedral : 4.428 33.274 946 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.63 % Allowed : 24.64 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 1.42 (0.30), residues: 894 helix: 2.18 (0.24), residues: 463 sheet: -0.38 (0.67), residues: 72 loop : -0.41 (0.36), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 72 HIS 0.003 0.001 HIS A 58 PHE 0.014 0.001 PHE A 702 TYR 0.020 0.001 TYR A 483 ARG 0.004 0.000 ARG A 900 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2433.46 seconds wall clock time: 42 minutes 52.56 seconds (2572.56 seconds total)