Starting phenix.real_space_refine on Fri Dec 27 22:51:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iwp_35776/12_2024/8iwp_35776.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iwp_35776/12_2024/8iwp_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_35776/12_2024/8iwp_35776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iwp_35776/12_2024/8iwp_35776.map" model { file = "/net/cci-nas-00/data/ceres_data/8iwp_35776/12_2024/8iwp_35776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iwp_35776/12_2024/8iwp_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-5532/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: 4.99, per 1000 atoms: 0.73 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: 1.78 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.90 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: 2.54 Time building geometry restraints manager: 2.06 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: 2.110 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.740 Find NCS groups from input model: 0.080 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.190 ------------------------------------------------------------------------------- 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 : 0.780 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: 0.1737 time to fit residues: 32.0408 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 : 0.781 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 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 : 0.746 Fit side-chains REVERT: A 306 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8425 (mt) REVERT: A 435 MET cc_start: 0.7204 (tmm) cc_final: 0.6701 (tmm) REVERT: A 780 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8529 (mm) outliers start: 22 outliers final: 11 residues processed: 146 average time/residue: 0.1674 time to fit residues: 33.7210 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 : 0.827 ------------------------------------------------------------------------------- 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 44 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 80 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 79 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2114 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= 0.198 Angle : 0.604 10.297 9438 Z= 0.300 Chirality : 0.042 0.200 1135 Planarity : 0.004 0.063 1193 Dihedral : 4.059 26.851 946 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.36 % Favored : 95.41 % Rotamer: Outliers : 3.37 % Allowed : 22.18 % Favored : 74.45 % 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: 1.53 (0.29), residues: 894 helix: 2.15 (0.24), residues: 461 sheet: 0.82 (0.70), residues: 63 loop : -0.41 (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 58 PHE 0.009 0.001 PHE A 725 TYR 0.011 0.001 TYR A 618 ARG 0.005 0.000 ARG A 55 *********************** 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: 26 poor density : 128 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 435 MET cc_start: 0.7448 (tmm) cc_final: 0.6748 (tmm) REVERT: A 679 ASP cc_start: 0.7983 (t0) cc_final: 0.7707 (t0) REVERT: A 757 ASP cc_start: 0.7732 (t0) cc_final: 0.7362 (t70) REVERT: A 780 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8424 (mm) REVERT: A 810 MET cc_start: 0.7264 (ttm) cc_final: 0.6992 (mtp) outliers start: 26 outliers final: 18 residues processed: 144 average time/residue: 0.1871 time to fit residues: 36.6519 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 : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 104 VAL 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 320 LEU Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 590 THR 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 60 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 0.1980 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 58 HIS A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2898 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= 0.245 Angle : 0.637 9.489 9438 Z= 0.318 Chirality : 0.042 0.201 1135 Planarity : 0.004 0.061 1193 Dihedral : 4.275 28.306 946 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.81 % Favored : 95.08 % Rotamer: Outliers : 4.93 % Allowed : 21.92 % Favored : 73.15 % 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: 1.34 (0.29), residues: 894 helix: 2.02 (0.24), residues: 462 sheet: 0.59 (0.70), residues: 63 loop : -0.52 (0.35), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 795 HIS 0.003 0.001 HIS A 58 PHE 0.013 0.002 PHE A 725 TYR 0.013 0.001 TYR A 618 ARG 0.002 0.000 ARG A 54 *********************** 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 164 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8665 (mt) REVERT: A 435 MET cc_start: 0.7496 (tmm) cc_final: 0.6904 (tmm) REVERT: A 757 ASP cc_start: 0.7934 (t0) cc_final: 0.7627 (t70) REVERT: A 780 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8347 (mm) outliers start: 38 outliers final: 27 residues processed: 149 average time/residue: 0.1829 time to fit residues: 37.2744 Evaluate side-chains 151 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 121 GLU 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 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 569 ILE Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 590 THR 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 790 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 73 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6970 Z= 0.257 Angle : 0.644 10.646 9438 Z= 0.321 Chirality : 0.042 0.206 1135 Planarity : 0.004 0.059 1193 Dihedral : 4.350 29.250 946 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.81 % Favored : 95.08 % Rotamer: Outliers : 4.67 % Allowed : 22.83 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.30), residues: 894 helix: 1.97 (0.24), residues: 462 sheet: -0.64 (0.65), residues: 79 loop : -0.32 (0.36), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 60 HIS 0.002 0.000 HIS A 140 PHE 0.015 0.001 PHE A 702 TYR 0.013 0.001 TYR A 618 ARG 0.003 0.000 ARG A 55 *********************** 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 163 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 306 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8697 (mt) REVERT: A 337 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7336 (tp) REVERT: A 435 MET cc_start: 0.7638 (tmm) cc_final: 0.6994 (tmm) REVERT: A 679 ASP cc_start: 0.8280 (t0) cc_final: 0.8007 (t70) REVERT: A 757 ASP cc_start: 0.8037 (t0) cc_final: 0.7811 (t70) REVERT: A 780 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8309 (mm) outliers start: 36 outliers final: 28 residues processed: 151 average time/residue: 0.1838 time to fit residues: 37.7352 Evaluate side-chains 150 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 161 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 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 437 MET 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 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 740 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 798 LEU 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 50 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 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 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6970 Z= 0.240 Angle : 0.640 10.515 9438 Z= 0.318 Chirality : 0.042 0.204 1135 Planarity : 0.004 0.057 1193 Dihedral : 4.405 29.150 946 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.15 % Favored : 94.74 % Rotamer: Outliers : 5.32 % Allowed : 21.92 % 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: 463 sheet: -0.24 (0.67), residues: 73 loop : -0.42 (0.36), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 72 HIS 0.003 0.001 HIS A 58 PHE 0.015 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 163 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 306 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8741 (mt) REVERT: A 337 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7034 (tp) REVERT: A 435 MET cc_start: 0.7647 (tmm) cc_final: 0.6999 (tmm) REVERT: A 594 VAL cc_start: 0.8404 (t) cc_final: 0.8174 (t) REVERT: A 679 ASP cc_start: 0.8295 (t0) cc_final: 0.7972 (t70) REVERT: A 780 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8304 (mm) outliers start: 41 outliers final: 35 residues processed: 145 average time/residue: 0.1802 time to fit residues: 35.9442 Evaluate side-chains 159 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 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 642 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 721 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 758 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 790 THR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 0.0020 chunk 72 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6970 Z= 0.211 Angle : 0.642 11.294 9438 Z= 0.316 Chirality : 0.042 0.200 1135 Planarity : 0.004 0.056 1193 Dihedral : 4.355 29.791 946 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.92 % Favored : 94.97 % Rotamer: Outliers : 4.93 % Allowed : 23.48 % Favored : 71.60 % 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: 1.32 (0.30), residues: 894 helix: 2.08 (0.24), residues: 462 sheet: -0.77 (0.65), residues: 80 loop : -0.31 (0.36), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 72 HIS 0.002 0.001 HIS A 58 PHE 0.014 0.001 PHE A 702 TYR 0.013 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 158 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 306 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8705 (mt) REVERT: A 337 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.7003 (tp) REVERT: A 435 MET cc_start: 0.7625 (tmm) cc_final: 0.6987 (tmm) REVERT: A 613 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8258 (ttpp) REVERT: A 679 ASP cc_start: 0.8279 (t0) cc_final: 0.7958 (t70) REVERT: A 780 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8307 (mm) outliers start: 38 outliers final: 31 residues processed: 145 average time/residue: 0.1803 time to fit residues: 36.5063 Evaluate side-chains 151 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 235 THR Chi-restraints excluded: chain A residue 277 ILE 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 337 ILE 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 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 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 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 16 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 0.0670 chunk 82 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 0.0020 overall best weight: 0.2926 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3555 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= 0.172 Angle : 0.627 10.803 9438 Z= 0.309 Chirality : 0.041 0.194 1135 Planarity : 0.004 0.054 1193 Dihedral : 4.243 28.955 946 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.47 % Favored : 95.41 % Rotamer: Outliers : 4.15 % Allowed : 24.12 % 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: 1.50 (0.30), residues: 894 helix: 2.11 (0.24), residues: 468 sheet: 0.38 (0.62), residues: 84 loop : -0.40 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 72 HIS 0.002 0.000 HIS A 624 PHE 0.013 0.001 PHE A 702 TYR 0.023 0.001 TYR A 483 ARG 0.004 0.000 ARG A 900 *********************** 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 154 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7889 (tp30) cc_final: 0.7517 (tt0) REVERT: A 435 MET cc_start: 0.7652 (tmm) cc_final: 0.6767 (tmm) REVERT: A 613 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8228 (ttpp) REVERT: A 679 ASP cc_start: 0.8181 (t0) cc_final: 0.7882 (t70) REVERT: A 780 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8339 (mm) REVERT: A 810 MET cc_start: 0.7323 (ttm) cc_final: 0.7072 (mtp) outliers start: 32 outliers final: 26 residues processed: 144 average time/residue: 0.1802 time to fit residues: 35.6428 Evaluate side-chains 146 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 232 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 256 THR 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 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 716 LEU Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 739 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 852 ILE Chi-restraints excluded: chain A residue 888 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 0.1980 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 A 467 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6970 Z= 0.224 Angle : 0.693 14.877 9438 Z= 0.332 Chirality : 0.042 0.192 1135 Planarity : 0.004 0.053 1193 Dihedral : 4.276 29.376 946 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.15 % Favored : 94.74 % Rotamer: Outliers : 4.02 % Allowed : 24.51 % Favored : 71.47 % 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: 1.43 (0.30), residues: 894 helix: 2.15 (0.24), residues: 463 sheet: -0.24 (0.68), residues: 74 loop : -0.38 (0.36), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 72 HIS 0.003 0.001 HIS A 58 PHE 0.012 0.001 PHE A 702 TYR 0.022 0.001 TYR A 483 ARG 0.004 0.000 ARG A 900 *********************** 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 150 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7892 (tp30) cc_final: 0.7405 (tt0) REVERT: A 435 MET cc_start: 0.7638 (tmm) cc_final: 0.6764 (tmm) REVERT: A 780 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8317 (mm) outliers start: 31 outliers final: 26 residues processed: 139 average time/residue: 0.1990 time to fit residues: 38.2263 Evaluate side-chains 143 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 232 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 280 ILE 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 590 THR 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 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 852 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 88 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3935 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= 0.260 Angle : 0.720 15.591 9438 Z= 0.347 Chirality : 0.042 0.189 1135 Planarity : 0.004 0.053 1193 Dihedral : 4.438 30.506 946 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.15 % Allowed : 24.77 % Favored : 71.08 % 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: 1.37 (0.30), residues: 894 helix: 2.11 (0.24), residues: 463 sheet: 0.41 (0.70), residues: 63 loop : -0.55 (0.36), residues: 368 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 0.013 0.001 PHE A 702 TYR 0.020 0.001 TYR A 483 ARG 0.006 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 152 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 435 MET cc_start: 0.7623 (tmm) cc_final: 0.6744 (tmm) REVERT: A 780 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8324 (mm) outliers start: 32 outliers final: 28 residues processed: 139 average time/residue: 0.1750 time to fit residues: 33.3916 Evaluate side-chains 147 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 156 VAL 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 235 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 280 ILE 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 721 THR Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 739 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 852 ILE 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 19 optimal weight: 0.0470 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.4227 r_free = 0.4227 target = 0.195236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138900 restraints weight = 9334.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142337 restraints weight = 5716.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.144593 restraints weight = 4203.599| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6970 Z= 0.233 Angle : 0.717 14.707 9438 Z= 0.345 Chirality : 0.042 0.200 1135 Planarity : 0.004 0.053 1193 Dihedral : 4.426 31.529 946 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.76 % Allowed : 24.90 % Favored : 71.34 % 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: 1.40 (0.30), residues: 894 helix: 2.14 (0.24), residues: 463 sheet: 0.32 (0.70), residues: 61 loop : -0.54 (0.36), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 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 0.005 0.000 ARG A 900 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1828.47 seconds wall clock time: 34 minutes 40.35 seconds (2080.35 seconds total)