Starting phenix.real_space_refine
on Thu Jul  2 05:23:52 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8iwp_35776/07_2026/8iwp_35776.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iwp_35776/07_2026/8iwp_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_35776/07_2026/8iwp_35776.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iwp_35776/07_2026/8iwp_35776.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iwp_35776/07_2026/8iwp_35776.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iwp_35776/07_2026/8iwp_35776.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8iwp_35776/07_2026/8iwp_35776.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8iwp_35776/07_2026/8iwp_35776.cif"
  }
  resolution = 3.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 1.13, per 1000 atoms: 0.16
  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: 0.34
  Conformation dependent library (CDL) restraints added in 251.5 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: 0.24
  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: 1.10

  Time building geometry restraints manager: 0.46 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:             2.560
  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:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.850
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
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= 0.132
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.002   0.000   ARG A 403 
 TYR   0.010   0.001   TYR A 618 
 PHE   0.020   0.001   PHE A 241 
 TRP   0.041   0.003   TRP A  60 
 HIS   0.002   0.000   HIS A 149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 ( 6970)
  covalent geometry    : angle       0.68761 /  0.37 ( 9438)
  hydrogen bonds       : bond        0.14021 /  9.30 (  389)
  hydrogen bonds       : angle       5.38210 /  3.97 ( 1194)

*********************** 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  : 0.147 
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: 0.0532
  time to fit residues: 9.9800
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  : 0.157 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.1980
   chunk 74 optimal weight:    0.0020
   overall best weight:    0.4588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 683 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.205646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.160513 restraints weight = 9208.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.160796 restraints weight = 7271.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.162657 restraints weight = 6180.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.163336 restraints weight = 3980.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.163711 restraints weight = 3554.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.1343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6970  Z= 0.127
  Angle     :  0.598   8.501   9438  Z= 0.298
  Chirality :  0.041   0.202   1135
  Planarity :  0.004   0.075   1193
  Dihedral  :  4.548  57.683    950
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.91 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 22.05 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.30), residues: 894
  helix:  2.18 (0.25), residues: 460
  sheet:  0.41 (0.62), residues: 76
  loop : -0.41 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 213 
 TYR   0.011   0.001   TYR A 483 
 PHE   0.010   0.001   PHE A 812 
 TRP   0.019   0.002   TRP A  60 
 HIS   0.006   0.001   HIS A 149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 ( 6970)
  covalent geometry    : angle       0.59837 /  0.30 ( 9438)
  hydrogen bonds       : bond        0.03322 /  2.27 (  389)
  hydrogen bonds       : angle       3.88952 /  2.87 ( 1194)

*********************** 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
  146 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A  435 MET cc_start: 0.7234 (tmm) cc_final: 0.6708 (tmm)
REVERT: A  780 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8489 (mm)
  outliers start: 17
  outliers final: 8
  residues processed: 142
  average time/residue: 0.0550
  time to fit residues: 10.9784
Evaluate side-chains
  129 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 HIS
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  235 THR
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 31 optimal weight:    0.6980
   chunk 54 optimal weight:    0.5980
   chunk 83 optimal weight:    3.9990
   chunk 11 optimal weight:    0.2980
   chunk 5 optimal weight:    4.9990
   chunk 48 optimal weight:   10.0000
   chunk 60 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.198548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.153652 restraints weight = 9104.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.153534 restraints weight = 9772.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.155703 restraints weight = 7298.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.156079 restraints weight = 4822.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.156640 restraints weight = 4416.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.2230

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= 0.146
  Angle     :  0.625  10.779   9438  Z= 0.311
  Chirality :  0.042   0.206   1135
  Planarity :  0.004   0.066   1193
  Dihedral  :  4.106  25.699    946
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.14 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 21.53 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.30), residues: 894
  helix:  2.08 (0.24), residues: 461
  sheet: -0.38 (0.66), residues: 80
  loop : -0.23 (0.36), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 143 
 TYR   0.011   0.001   TYR A 618 
 PHE   0.011   0.001   PHE A 725 
 TRP   0.019   0.002   TRP A  60 
 HIS   0.004   0.001   HIS A 149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.15 ( 6970)
  covalent geometry    : angle       0.62459 /  0.31 ( 9438)
  hydrogen bonds       : bond        0.03676 /  2.48 (  389)
  hydrogen bonds       : angle       3.77465 /  2.78 ( 1194)

*********************** 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
  159 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
REVERT: A  281 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7473 (tmt)
REVERT: A  306 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8590 (mt)
REVERT: A  435 MET cc_start: 0.7486 (tmm) cc_final: 0.6763 (tmm)
REVERT: A  679 ASP cc_start: 0.8035 (t0) cc_final: 0.7755 (t0)
REVERT: A  757 ASP cc_start: 0.7841 (t0) cc_final: 0.7472 (t70)
REVERT: A  780 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8420 (mm)
  outliers start: 29
  outliers final: 20
  residues processed: 149
  average time/residue: 0.0537
  time to fit residues: 11.0962
Evaluate side-chains
  145 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
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  156 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  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  364 HIS
Chi-restraints excluded: chain A residue  560 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  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  888 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 79 optimal weight:    0.5980
   chunk 52 optimal weight:    9.9990
   chunk 88 optimal weight:    0.9990
   chunk 84 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0470
   chunk 21 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0870
   chunk 35 optimal weight:    8.9990
   chunk 45 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9980
   chunk 29 optimal weight:    0.1980
   overall best weight:    0.3456

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.199571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.152766 restraints weight = 9189.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.152623 restraints weight = 8669.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.155706 restraints weight = 6188.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.155771 restraints weight = 3866.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.156139 restraints weight = 3665.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.2394

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= 0.112
  Angle     :  0.589   9.976   9438  Z= 0.291
  Chirality :  0.041   0.189   1135
  Planarity :  0.004   0.059   1193
  Dihedral  :  4.059  27.843    946
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.36 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 22.05 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.30), residues: 894
  helix:  2.20 (0.24), residues: 463
  sheet:  0.95 (0.64), residues: 76
  loop : -0.48 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  55 
 TYR   0.011   0.001   TYR A 618 
 PHE   0.011   0.001   PHE A 702 
 TRP   0.018   0.002   TRP A 795 
 HIS   0.002   0.000   HIS A 149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.11 ( 6970)
  covalent geometry    : angle       0.58865 /  0.29 ( 9438)
  hydrogen bonds       : bond        0.03189 /  2.18 (  389)
  hydrogen bonds       : angle       3.58995 /  2.63 ( 1194)

*********************** 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
  152 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 123
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
REVERT: A  281 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7594 (tmt)
REVERT: A  306 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8619 (mt)
REVERT: A  435 MET cc_start: 0.7497 (tmm) cc_final: 0.6720 (tmm)
REVERT: A  479 MET cc_start: 0.4929 (tpt) cc_final: 0.4289 (tmm)
REVERT: A  757 ASP cc_start: 0.7968 (t0) cc_final: 0.7617 (t70)
REVERT: A  780 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8441 (mm)
REVERT: A  810 MET cc_start: 0.7094 (ttm) cc_final: 0.6822 (mtp)
  outliers start: 29
  outliers final: 23
  residues processed: 141
  average time/residue: 0.0564
  time to fit residues: 11.1719
Evaluate side-chains
  143 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
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  140 HIS
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  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  308 GLU
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  716 LEU
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  803 ILE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 88 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 42 optimal weight:    6.9990
   chunk 58 optimal weight:    0.3980
   chunk 61 optimal weight:    0.6980
   chunk 70 optimal weight:    0.0870
   chunk 85 optimal weight:    0.5980
   chunk 84 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 73 optimal weight:    0.4980
   overall best weight:    0.4358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.197836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.151413 restraints weight = 9279.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.150723 restraints weight = 8895.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.153041 restraints weight = 7326.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.153354 restraints weight = 4648.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.153848 restraints weight = 4296.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.2631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6970  Z= 0.119
  Angle     :  0.593   9.712   9438  Z= 0.293
  Chirality :  0.041   0.194   1135
  Planarity :  0.004   0.056   1193
  Dihedral  :  4.042  27.289    946
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.70 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 21.66 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.30), residues: 894
  helix:  2.21 (0.24), residues: 462
  sheet: -0.17 (0.61), residues: 93
  loop : -0.29 (0.36), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  55 
 TYR   0.014   0.001   TYR A 483 
 PHE   0.012   0.001   PHE A 702 
 TRP   0.023   0.002   TRP A 795 
 HIS   0.002   0.000   HIS A  58 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.12 ( 6970)
  covalent geometry    : angle       0.59250 /  0.29 ( 9438)
  hydrogen bonds       : bond        0.03248 /  2.22 (  389)
  hydrogen bonds       : angle       3.61236 /  2.64 ( 1194)

*********************** 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
  165 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 126
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
REVERT: A  281 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7598 (tmt)
REVERT: A  306 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8625 (mt)
REVERT: A  435 MET cc_start: 0.7610 (tmm) cc_final: 0.6779 (tmm)
REVERT: A  757 ASP cc_start: 0.8039 (t0) cc_final: 0.7676 (t70)
REVERT: A  780 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8452 (mm)
REVERT: A  810 MET cc_start: 0.7159 (ttm) cc_final: 0.6905 (mtp)
  outliers start: 39
  outliers final: 28
  residues processed: 151
  average time/residue: 0.0554
  time to fit residues: 11.8087
Evaluate side-chains
  147 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 116
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
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  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  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  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  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  780 LEU
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  798 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 40 optimal weight:    0.5980
   chunk 87 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 47 optimal weight:    0.0870
   chunk 75 optimal weight:    0.0000
   chunk 84 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.4162

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.196455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.152652 restraints weight = 9284.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.150481 restraints weight = 8637.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.152837 restraints weight = 8797.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.153168 restraints weight = 5155.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.153914 restraints weight = 4907.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.2824

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= 0.118
  Angle     :  0.603  10.776   9438  Z= 0.298
  Chirality :  0.041   0.191   1135
  Planarity :  0.004   0.054   1193
  Dihedral  :  4.079  28.293    946
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.03 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 22.05 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.30), residues: 894
  helix:  2.23 (0.24), residues: 462
  sheet:  0.87 (0.63), residues: 76
  loop : -0.51 (0.35), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 796 
 TYR   0.013   0.001   TYR A 380 
 PHE   0.012   0.001   PHE A 702 
 TRP   0.025   0.002   TRP A 795 
 HIS   0.003   0.001   HIS A  58 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.12 ( 6970)
  covalent geometry    : angle       0.60299 /  0.30 ( 9438)
  hydrogen bonds       : bond        0.03240 /  2.21 (  389)
  hydrogen bonds       : angle       3.58032 /  2.61 ( 1194)

*********************** 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
  149 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 118
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  281 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7633 (tmt)
REVERT: A  337 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7155 (tp)
REVERT: A  435 MET cc_start: 0.7653 (tmm) cc_final: 0.6774 (tmm)
REVERT: A  757 ASP cc_start: 0.8138 (t0) cc_final: 0.7812 (t70)
REVERT: A  780 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8393 (mm)
REVERT: A  810 MET cc_start: 0.7193 (ttm) cc_final: 0.6926 (mtp)
  outliers start: 31
  outliers final: 25
  residues processed: 138
  average time/residue: 0.0566
  time to fit residues: 11.0570
Evaluate side-chains
  141 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
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  232 VAL
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  281 MET
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  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  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  780 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  852 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 59 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 58 optimal weight:    0.3980
   chunk 22 optimal weight:    4.9990
   chunk 56 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0370
   chunk 18 optimal weight:   20.0000
   chunk 17 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.5658

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.194443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.150006 restraints weight = 9222.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.147097 restraints weight = 8440.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.148954 restraints weight = 8228.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.149949 restraints weight = 5548.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.150377 restraints weight = 5202.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.3123

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= 0.132
  Angle     :  0.619  10.282   9438  Z= 0.305
  Chirality :  0.041   0.201   1135
  Planarity :  0.004   0.053   1193
  Dihedral  :  4.117  28.226    946
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.15 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 22.05 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.30), residues: 894
  helix:  2.22 (0.24), residues: 462
  sheet: -0.55 (0.66), residues: 80
  loop : -0.30 (0.36), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 796 
 TYR   0.012   0.001   TYR A 618 
 PHE   0.013   0.001   PHE A 702 
 TRP   0.027   0.002   TRP A 795 
 HIS   0.003   0.000   HIS A  58 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.13 ( 6970)
  covalent geometry    : angle       0.61926 /  0.31 ( 9438)
  hydrogen bonds       : bond        0.03484 /  2.38 (  389)
  hydrogen bonds       : angle       3.61176 /  2.62 ( 1194)

*********************** 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
  153 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 115
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  435 MET cc_start: 0.7629 (tmm) cc_final: 0.6723 (tmm)
REVERT: A  757 ASP cc_start: 0.8225 (t0) cc_final: 0.7976 (t0)
REVERT: A  780 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8363 (mm)
REVERT: A  810 MET cc_start: 0.7203 (ttm) cc_final: 0.6914 (mtp)
  outliers start: 38
  outliers final: 30
  residues processed: 140
  average time/residue: 0.0622
  time to fit residues: 12.1770
Evaluate side-chains
  146 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
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  232 VAL
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  313 VAL
Chi-restraints excluded: chain A residue  320 LEU
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  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  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  888 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 88 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0020
   chunk 65 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0570
   chunk 51 optimal weight:    0.0570
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.2824

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  58 HIS
A 494 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 = 0.196583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.141633 restraints weight = 9369.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.145129 restraints weight = 5718.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.147498 restraints weight = 4136.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.148747 restraints weight = 3364.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.150014 restraints weight = 2959.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   6970  Z= 0.114
  Angle     :  0.625  11.450   9438  Z= 0.303
  Chirality :  0.041   0.191   1135
  Planarity :  0.004   0.052   1193
  Dihedral  :  4.077  28.586    946
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.59 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 22.70 %
    Favored  : 73.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.30), residues: 894
  helix:  2.25 (0.25), residues: 462
  sheet:  0.92 (0.64), residues: 76
  loop : -0.56 (0.36), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 900 
 TYR   0.011   0.001   TYR A 618 
 PHE   0.013   0.001   PHE A 702 
 TRP   0.021   0.002   TRP A 795 
 HIS   0.002   0.000   HIS A 149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.11 ( 6970)
  covalent geometry    : angle       0.62548 /  0.30 ( 9438)
  hydrogen bonds       : bond        0.03190 /  2.18 (  389)
  hydrogen bonds       : angle       3.55141 /  2.58 ( 1194)

*********************** 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
  153 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 123
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  337 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.6947 (tp)
REVERT: A  435 MET cc_start: 0.7572 (tmm) cc_final: 0.6702 (tmm)
REVERT: A  757 ASP cc_start: 0.8111 (t0) cc_final: 0.7853 (t0)
REVERT: A  780 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8438 (mm)
REVERT: A  810 MET cc_start: 0.7417 (ttm) cc_final: 0.7138 (mtp)
  outliers start: 30
  outliers final: 27
  residues processed: 143
  average time/residue: 0.0559
  time to fit residues: 11.0828
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  : 0.191 
-------------------------------------------------------------------------------
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  161 VAL
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  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  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  780 LEU
Chi-restraints excluded: chain A residue  798 LEU
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 24 optimal weight:    0.0370
   chunk 14 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 84 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.6258

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.193171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.147936 restraints weight = 9247.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.146466 restraints weight = 8546.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.148752 restraints weight = 8404.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.148887 restraints weight = 5036.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.149448 restraints weight = 4978.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6970  Z= 0.142
  Angle     :  0.680  15.287   9438  Z= 0.327
  Chirality :  0.042   0.197   1135
  Planarity :  0.004   0.052   1193
  Dihedral  :  4.170  28.955    946
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.03 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 22.96 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.30), residues: 894
  helix:  2.17 (0.24), residues: 462
  sheet: -0.55 (0.67), residues: 80
  loop : -0.31 (0.36), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 900 
 TYR   0.023   0.001   TYR A 483 
 PHE   0.012   0.001   PHE A 702 
 TRP   0.061   0.003   TRP A  72 
 HIS   0.004   0.001   HIS A  58 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.14 ( 6970)
  covalent geometry    : angle       0.67953 /  0.33 ( 9438)
  hydrogen bonds       : bond        0.03562 /  2.43 (  389)
  hydrogen bonds       : angle       3.64812 /  2.65 ( 1194)

*********************** 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: 33
    poor density    : 117
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  281 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7631 (tmt)
REVERT: A  337 ILE cc_start: 0.7348 (OUTLIER) cc_final: 0.6971 (tp)
REVERT: A  435 MET cc_start: 0.7638 (tmm) cc_final: 0.6765 (tmm)
REVERT: A  757 ASP cc_start: 0.8233 (t0) cc_final: 0.7993 (t70)
REVERT: A  780 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8300 (mm)
REVERT: A  810 MET cc_start: 0.7165 (ttm) cc_final: 0.6870 (mtp)
  outliers start: 33
  outliers final: 29
  residues processed: 137
  average time/residue: 0.0548
  time to fit residues: 10.5806
Evaluate side-chains
  146 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
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  161 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  225 CYS
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  281 MET
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  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  770 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  888 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 41 optimal weight:    0.3980
   chunk 16 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.4224 r_free = 0.4224 target = 0.194220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.149721 restraints weight = 9381.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.147854 restraints weight = 8791.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.149746 restraints weight = 9401.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.150391 restraints weight = 5401.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.151805 restraints weight = 4960.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.3711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   6970  Z= 0.159
  Angle     :  0.708  15.181   9438  Z= 0.341
  Chirality :  0.042   0.199   1135
  Planarity :  0.004   0.052   1193
  Dihedral  :  4.301  30.228    946
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 23.61 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.30), residues: 894
  helix:  2.11 (0.24), residues: 462
  sheet: -0.05 (0.68), residues: 73
  loop : -0.42 (0.36), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 900 
 TYR   0.020   0.001   TYR A 483 
 PHE   0.014   0.001   PHE A 702 
 TRP   0.054   0.003   TRP A  72 
 HIS   0.004   0.001   HIS A  58 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00379 /  0.16 ( 6970)
  covalent geometry    : angle       0.70793 /  0.34 ( 9438)
  hydrogen bonds       : bond        0.03837 /  2.62 (  389)
  hydrogen bonds       : angle       3.74839 /  2.71 ( 1194)

********************** 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
  153 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  281 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7710 (tmt)
REVERT: A  312 ILE cc_start: 0.8874 (mm) cc_final: 0.8636 (mt)
REVERT: A  337 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7069 (tp)
REVERT: A  435 MET cc_start: 0.7646 (tmm) cc_final: 0.6773 (tmm)
REVERT: A  780 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8308 (mm)
  outliers start: 31
  outliers final: 28
  residues processed: 140
  average time/residue: 0.0612
  time to fit residues: 12.1325
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  : 0.154 
-------------------------------------------------------------------------------
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  161 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  225 CYS
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  281 MET
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  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  770 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 2 optimal weight:    0.6980
   chunk 74 optimal weight:    4.9990
   chunk 79 optimal weight:    0.5980
   chunk 46 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0980
   chunk 30 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.194842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.150637 restraints weight = 9489.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.147379 restraints weight = 9677.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.150109 restraints weight = 9536.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.150468 restraints weight = 5572.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.151266 restraints weight = 5228.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6970  Z= 0.145
  Angle     :  0.692  15.400   9438  Z= 0.335
  Chirality :  0.042   0.197   1135
  Planarity :  0.004   0.052   1193
  Dihedral  :  4.293  30.075    946
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 23.48 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.30), residues: 894
  helix:  2.15 (0.24), residues: 462
  sheet: -0.29 (0.67), residues: 72
  loop : -0.39 (0.36), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 900 
 TYR   0.021   0.001   TYR A 483 
 PHE   0.015   0.001   PHE A 702 
 TRP   0.051   0.003   TRP A  72 
 HIS   0.003   0.001   HIS A  58 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.15 ( 6970)
  covalent geometry    : angle       0.69178 /  0.34 ( 9438)
  hydrogen bonds       : bond        0.03716 /  2.54 (  389)
  hydrogen bonds       : angle       3.71029 /  2.68 ( 1194)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1088.41 seconds
wall clock time: 19 minutes 28.03 seconds (1168.03 seconds total)