Starting phenix.real_space_refine
on Fri Aug 22 18:40:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iwp_35776/08_2025/8iwp_35776.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iwp_35776/08_2025/8iwp_35776.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iwp_35776/08_2025/8iwp_35776.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iwp_35776/08_2025/8iwp_35776.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iwp_35776/08_2025/8iwp_35776.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iwp_35776/08_2025/8iwp_35776.map"
  }
  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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 1.82, per 1000 atoms: 0.27
  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: 0.57
  Conformation dependent library (CDL) restraints added in 381.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.30
  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: 1.30

  Time building geometry restraints manager: 0.75 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.34: 2230
        1.34 -     1.46: 1366
        1.46 -     1.58: 3290
        1.58 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 6970
  Sorted by residual:
  bond pdb=" CA  GLU A  62 "
       pdb=" CB  GLU A  62 "
    ideal  model  delta    sigma   weight residual
    1.535  1.562 -0.027 1.58e-02 4.01e+03 2.98e+00
  bond pdb=" CB  PRO A 744 "
       pdb=" CG  PRO A 744 "
    ideal  model  delta    sigma   weight residual
    1.492  1.578 -0.086 5.00e-02 4.00e+02 2.94e+00
  bond pdb=" CA  THR A 590 "
       pdb=" CB  THR A 590 "
    ideal  model  delta    sigma   weight residual
    1.528  1.565 -0.037 2.61e-02 1.47e+03 1.99e+00
  bond pdb=" CG1 ILE A 431 "
       pdb=" CD1 ILE A 431 "
    ideal  model  delta    sigma   weight residual
    1.513  1.462  0.051 3.90e-02 6.57e+02 1.68e+00
  bond pdb=" C   THR A 804 "
       pdb=" N   PRO A 805 "
    ideal  model  delta    sigma   weight residual
    1.334  1.363 -0.029 2.34e-02 1.83e+03 1.57e+00
  ... (remaining 6965 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 9254
        2.04 -     4.09: 134
        4.09 -     6.13: 35
        6.13 -     8.17: 11
        8.17 -    10.21: 4
  Bond angle restraints: 9438
  Sorted by residual:
  angle pdb=" CA  PRO A 744 "
        pdb=" N   PRO A 744 "
        pdb=" CD  PRO A 744 "
      ideal   model   delta    sigma   weight residual
     112.00  106.71    5.29 1.40e+00 5.10e-01 1.43e+01
  angle pdb=" CA  GLN A 512 "
        pdb=" CB  GLN A 512 "
        pdb=" CG  GLN A 512 "
      ideal   model   delta    sigma   weight residual
     114.10  121.37   -7.27 2.00e+00 2.50e-01 1.32e+01
  angle pdb=" CB  LYS A 756 "
        pdb=" CG  LYS A 756 "
        pdb=" CD  LYS A 756 "
      ideal   model   delta    sigma   weight residual
     111.30  118.84   -7.54 2.30e+00 1.89e-01 1.08e+01
  angle pdb=" CA  LYS A 424 "
        pdb=" CB  LYS A 424 "
        pdb=" CG  LYS A 424 "
      ideal   model   delta    sigma   weight residual
     114.10  120.66   -6.56 2.00e+00 2.50e-01 1.08e+01
  angle pdb=" C   VAL A 346 "
        pdb=" CA  VAL A 346 "
        pdb=" CB  VAL A 346 "
      ideal   model   delta    sigma   weight residual
     111.29  116.55   -5.26 1.64e+00 3.72e-01 1.03e+01
  ... (remaining 9433 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 3711
       17.97 -    35.93: 422
       35.93 -    53.90: 100
       53.90 -    71.87: 21
       71.87 -    89.84: 7
  Dihedral angle restraints: 4261
    sinusoidal: 1680
      harmonic: 2581
  Sorted by residual:
  dihedral pdb=" CA  ASN A  81 "
           pdb=" C   ASN A  81 "
           pdb=" N   PRO A  82 "
           pdb=" CA  PRO A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.52  -27.48     0      5.00e+00 4.00e-02 3.02e+01
  dihedral pdb=" CA  MET A 602 "
           pdb=" C   MET A 602 "
           pdb=" N   ASP A 603 "
           pdb=" CA  ASP A 603 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.17  -23.83     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  GLY A 208 "
           pdb=" C   GLY A 208 "
           pdb=" N   ASP A 209 "
           pdb=" CA  ASP A 209 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.72   22.28     0      5.00e+00 4.00e-02 1.98e+01
  ... (remaining 4258 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 829
       0.039 -    0.078: 219
       0.078 -    0.116: 78
       0.116 -    0.155: 6
       0.155 -    0.194: 3
  Chirality restraints: 1135
  Sorted by residual:
  chirality pdb=" CG  LEU A 780 "
            pdb=" CB  LEU A 780 "
            pdb=" CD1 LEU A 780 "
            pdb=" CD2 LEU A 780 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.40e-01
  chirality pdb=" CA  THR A 804 "
            pdb=" N   THR A 804 "
            pdb=" C   THR A 804 "
            pdb=" CB  THR A 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.19 2.00e-01 2.50e+01 9.01e-01
  chirality pdb=" CG  LEU A  29 "
            pdb=" CB  LEU A  29 "
            pdb=" CD1 LEU A  29 "
            pdb=" CD2 LEU A  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 8.18e-01
  ... (remaining 1132 not shown)

  Planarity restraints: 1193
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 743 "   -0.079 5.00e-02 4.00e+02   1.17e-01 2.20e+01
        pdb=" N   PRO A 744 "    0.203 5.00e-02 4.00e+02
        pdb=" CA  PRO A 744 "   -0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO A 744 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  60 "    0.014 2.00e-02 2.50e+03   1.54e-02 5.93e+00
        pdb=" CG  TRP A  60 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  60 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  60 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  60 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  60 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  60 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  60 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  60 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  60 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  72 "   -0.013 2.00e-02 2.50e+03   1.17e-02 3.43e+00
        pdb=" CG  TRP A  72 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  72 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  72 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  72 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  72 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  72 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  72 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  72 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  72 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1190 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2013
        2.82 -     3.34: 6677
        3.34 -     3.86: 11234
        3.86 -     4.38: 11909
        4.38 -     4.90: 21428
  Nonbonded interactions: 53261
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 570 "
            pdb=" OD2 ASP A 572 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" N   GLN A 829 "
            pdb=" OE1 GLN A 829 "
     model   vdw
     2.351 3.120
  nonbonded pdb=" NZ  LYS A 333 "
            pdb=" O   ALA A 673 "
     model   vdw
     2.351 3.120
  nonbonded pdb=" ND2 ASN A  61 "
            pdb=" O   ALA A 152 "
     model   vdw
     2.357 3.120
  nonbonded pdb=" N   THR A 503 "
            pdb=" OE1 GLN A 506 "
     model   vdw
     2.362 3.120
  ... (remaining 53256 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.620
  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:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.086   6970  Z= 0.132
  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 aren 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
  covalent geometry    : bond        0.00294 ( 6970)
  covalent geometry    : angle       0.68761 ( 9438)
  hydrogen bonds       : bond        0.14021 (  389)
  hydrogen bonds       : angle       5.38210 ( 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  : 0.325 
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: 0.0727
  time to fit residues: 13.6880
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  : 0.229 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
A 683 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 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: 0.7271
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 aren 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
  covalent geometry    : bond        0.00294 ( 6970)
  covalent geometry    : angle       0.59837 ( 9438)
  hydrogen bonds       : bond        0.03322 (  389)
  hydrogen bonds       : angle       3.88952 ( 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  : 0.328 
Fit side-chains
REVERT: A  435 MET cc_start: 0.7234 (tmm) cc_final: 0.6709 (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: 0.0749
  time to fit residues: 14.9409
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  : 0.263 
-------------------------------------------------------------------------------
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...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.198299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.153714 restraints weight = 9097.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.150080 restraints weight = 8579.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.152138 restraints weight = 8224.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.153788 restraints weight = 5717.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.153894 restraints weight = 4869.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   6970  Z= 0.145
  Angle     :  0.621  10.945   9438  Z= 0.309
  Chirality :  0.042   0.206   1135
  Planarity :  0.004   0.065   1193
  Dihedral  :  4.107  25.803    946
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.36 %
    Favored  : 95.41 %
  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 aren not related in a simple way.
  whole:  1.46 (0.29), residues: 894
  helix:  2.07 (0.24), residues: 461
  sheet:  0.86 (0.72), residues: 63
  loop : -0.42 (0.35), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 796 
 TYR   0.012   0.001   TYR A 618 
 PHE   0.011   0.001   PHE A 725 
 TRP   0.018   0.002   TRP A  60 
 HIS   0.004   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 6970)
  covalent geometry    : angle       0.62110 ( 9438)
  hydrogen bonds       : bond        0.03708 (  389)
  hydrogen bonds       : angle       3.76364 ( 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  : 0.468 
Fit side-chains
   revert: symmetry clash
REVERT: A  281 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7481 (tmt)
REVERT: A  306 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8583 (mt)
REVERT: A  435 MET cc_start: 0.7490 (tmm) cc_final: 0.7248 (tmm)
REVERT: A  607 LEU cc_start: 0.7495 (tt) cc_final: 0.7165 (tt)
REVERT: A  679 ASP cc_start: 0.8057 (t0) cc_final: 0.7768 (t0)
REVERT: A  757 ASP cc_start: 0.7868 (t0) cc_final: 0.7507 (t70)
REVERT: A  780 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8436 (mm)
  outliers start: 29
  outliers final: 19
  residues processed: 149
  average time/residue: 0.0790
  time to fit residues: 16.3978
Evaluate side-chains
  145 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
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  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:    0.9980
   chunk 88 optimal weight:    0.7980
   chunk 84 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 42 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 45 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
A 855 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.192999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.149904 restraints weight = 9313.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.148064 restraints weight = 9773.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.150249 restraints weight = 8768.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.150601 restraints weight = 5588.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.151440 restraints weight = 5584.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.2864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6970  Z= 0.159
  Angle     :  0.634  10.294   9438  Z= 0.316
  Chirality :  0.042   0.200   1135
  Planarity :  0.004   0.062   1193
  Dihedral  :  4.255  28.844    946
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 8.18
  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 aren not related in a simple way.
  whole:  1.34 (0.29), residues: 894
  helix:  2.03 (0.24), residues: 462
  sheet:  0.62 (0.70), residues: 63
  loop : -0.53 (0.35), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 796 
 TYR   0.012   0.001   TYR A 618 
 PHE   0.013   0.001   PHE A 702 
 TRP   0.018   0.002   TRP A 795 
 HIS   0.003   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 6970)
  covalent geometry    : angle       0.63377 ( 9438)
  hydrogen bonds       : bond        0.03889 (  389)
  hydrogen bonds       : angle       3.77546 ( 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
  164 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 125
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  281 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7683 (tmt)
REVERT: A  306 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8661 (mt)
REVERT: A  435 MET cc_start: 0.7495 (tmm) cc_final: 0.6902 (tmm)
REVERT: A  757 ASP cc_start: 0.8149 (t0) cc_final: 0.7870 (t70)
REVERT: A  780 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8302 (mm)
  outliers start: 39
  outliers final: 31
  residues processed: 149
  average time/residue: 0.0876
  time to fit residues: 17.7672
Evaluate side-chains
  149 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 115
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
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   76 ILE
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  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  716 LEU
Chi-restraints excluded: chain A residue  725 PHE
Chi-restraints excluded: chain A residue  739 ILE
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  790 THR
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain A residue  852 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 88 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0020
   chunk 58 optimal weight:    0.1980
   chunk 61 optimal weight:    0.3980
   chunk 70 optimal weight:    0.5980
   chunk 85 optimal weight:    0.6980
   chunk 84 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   overall best weight:    0.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
A 494 GLN
A 855 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.196749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.152057 restraints weight = 9201.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.152036 restraints weight = 8734.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.154116 restraints weight = 7356.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.154152 restraints weight = 4711.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.154440 restraints weight = 4974.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   6970  Z= 0.119
  Angle     :  0.606  10.019   9438  Z= 0.299
  Chirality :  0.041   0.194   1135
  Planarity :  0.004   0.058   1193
  Dihedral  :  4.167  28.145    946
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.47 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 22.05 %
    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 aren not related in a simple way.
  whole:  1.40 (0.30), residues: 894
  helix:  2.13 (0.24), residues: 462
  sheet: -0.60 (0.65), residues: 80
  loop : -0.27 (0.36), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  55 
 TYR   0.014   0.001   TYR A 380 
 PHE   0.014   0.001   PHE A 702 
 TRP   0.020   0.002   TRP A 795 
 HIS   0.004   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6970)
  covalent geometry    : angle       0.60565 ( 9438)
  hydrogen bonds       : bond        0.03454 (  389)
  hydrogen bonds       : angle       3.65350 ( 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
  160 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 124
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: A  281 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7699 (tmt)
REVERT: A  435 MET cc_start: 0.7615 (tmm) cc_final: 0.6768 (tmm)
REVERT: A  757 ASP cc_start: 0.8129 (t0) cc_final: 0.7844 (t70)
REVERT: A  780 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8327 (mm)
REVERT: A  810 MET cc_start: 0.7253 (ttm) cc_final: 0.7014 (mtp)
  outliers start: 36
  outliers final: 25
  residues processed: 145
  average time/residue: 0.0772
  time to fit residues: 15.4336
Evaluate side-chains
  144 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
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  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  308 GLU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  725 PHE
Chi-restraints excluded: chain A residue  739 ILE
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  798 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 40 optimal weight:    0.1980
   chunk 87 optimal weight:    0.3980
   chunk 88 optimal weight:    0.7980
   chunk 68 optimal weight:    0.4980
   chunk 47 optimal weight:    9.9990
   chunk 75 optimal weight:    0.3980
   chunk 84 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.196231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.153382 restraints weight = 9383.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.152325 restraints weight = 11658.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.155001 restraints weight = 8865.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.154521 restraints weight = 5386.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.155515 restraints weight = 5740.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.3073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6970  Z= 0.122
  Angle     :  0.612  10.710   9438  Z= 0.302
  Chirality :  0.041   0.192   1135
  Planarity :  0.004   0.055   1193
  Dihedral  :  4.180  28.703    946
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.81 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 22.83 %
    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 aren not related in a simple way.
  whole:  1.45 (0.30), residues: 894
  helix:  2.13 (0.24), residues: 462
  sheet:  0.79 (0.63), residues: 76
  loop : -0.56 (0.36), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 174 
 TYR   0.015   0.001   TYR A 483 
 PHE   0.013   0.001   PHE A 702 
 TRP   0.026   0.002   TRP A 795 
 HIS   0.003   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6970)
  covalent geometry    : angle       0.61227 ( 9438)
  hydrogen bonds       : bond        0.03416 (  389)
  hydrogen bonds       : angle       3.62842 ( 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
  152 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 120
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: A  337 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7160 (tp)
REVERT: A  435 MET cc_start: 0.7586 (tmm) cc_final: 0.6741 (tmm)
REVERT: A  757 ASP cc_start: 0.8139 (t0) cc_final: 0.7872 (t0)
REVERT: A  780 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8346 (mm)
REVERT: A  810 MET cc_start: 0.7189 (ttm) cc_final: 0.6924 (mtp)
  outliers start: 32
  outliers final: 26
  residues processed: 142
  average time/residue: 0.0664
  time to fit residues: 13.1257
Evaluate side-chains
  142 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
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  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  308 GLU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  611 VAL
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  836 ILE
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  888 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 38 optimal weight:    9.9990
   chunk 59 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0020
   chunk 22 optimal weight:    0.0770
   chunk 56 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0770
   chunk 18 optimal weight:   20.0000
   chunk 17 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 70 optimal weight:    0.4980
   overall best weight:    0.2704

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.197508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.152160 restraints weight = 9210.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.150586 restraints weight = 8617.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.153113 restraints weight = 8071.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.153199 restraints weight = 4990.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.153710 restraints weight = 5093.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.3061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6970  Z= 0.112
  Angle     :  0.615  10.673   9438  Z= 0.301
  Chirality :  0.041   0.186   1135
  Planarity :  0.004   0.054   1193
  Dihedral  :  4.124  28.322    946
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.59 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 22.44 %
    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 aren not related in a simple way.
  whole:  1.49 (0.30), residues: 894
  helix:  2.19 (0.25), residues: 462
  sheet: -0.19 (0.60), residues: 93
  loop : -0.33 (0.37), residues: 339

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   0.013   0.001   PHE A 702 
 TRP   0.047   0.003   TRP A  72 
 HIS   0.002   0.000   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6970)
  covalent geometry    : angle       0.61481 ( 9438)
  hydrogen bonds       : bond        0.03168 (  389)
  hydrogen bonds       : angle       3.53579 ( 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
  148 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: A  281 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7607 (tmt)
REVERT: A  337 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.7067 (tp)
REVERT: A  435 MET cc_start: 0.7594 (tmm) cc_final: 0.6712 (tmm)
REVERT: A  679 ASP cc_start: 0.8148 (t0) cc_final: 0.7860 (t0)
REVERT: A  757 ASP cc_start: 0.8178 (t0) cc_final: 0.7934 (t0)
REVERT: A  780 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8427 (mm)
REVERT: A  810 MET cc_start: 0.7176 (ttm) cc_final: 0.6933 (mtp)
  outliers start: 32
  outliers final: 26
  residues processed: 138
  average time/residue: 0.0754
  time to fit residues: 14.5853
Evaluate side-chains
  141 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 112
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
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  149 HIS
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  281 MET
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  337 ILE
Chi-restraints excluded: chain A residue  364 HIS
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  716 LEU
Chi-restraints excluded: chain A residue  725 PHE
Chi-restraints excluded: chain A residue  739 ILE
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  836 ILE
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:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0040
   chunk 88 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0870
   chunk 66 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.4770

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.197990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.154543 restraints weight = 9472.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.151951 restraints weight = 8674.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.154080 restraints weight = 8426.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.154618 restraints weight = 5052.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.154735 restraints weight = 5363.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.3208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   6970  Z= 0.126
  Angle     :  0.627  11.241   9438  Z= 0.309
  Chirality :  0.041   0.188   1135
  Planarity :  0.004   0.053   1193
  Dihedral  :  4.167  29.017    946
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.92 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 22.96 %
    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 aren not related in a simple way.
  whole:  1.37 (0.30), residues: 894
  helix:  2.13 (0.24), residues: 462
  sheet:  0.61 (0.60), residues: 84
  loop : -0.69 (0.36), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 900 
 TYR   0.012   0.001   TYR A 618 
 PHE   0.012   0.001   PHE A 702 
 TRP   0.039   0.003   TRP A  72 
 HIS   0.003   0.000   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6970)
  covalent geometry    : angle       0.62747 ( 9438)
  hydrogen bonds       : bond        0.03390 (  389)
  hydrogen bonds       : angle       3.62346 ( 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
  144 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
REVERT: A  281 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7655 (tmt)
REVERT: A  337 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.7085 (tp)
REVERT: A  435 MET cc_start: 0.7642 (tmm) cc_final: 0.6769 (tmm)
REVERT: A  679 ASP cc_start: 0.8185 (t0) cc_final: 0.7946 (t70)
REVERT: A  757 ASP cc_start: 0.8208 (t0) cc_final: 0.7960 (t0)
REVERT: A  780 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8382 (mm)
REVERT: A  810 MET cc_start: 0.7200 (ttm) cc_final: 0.6935 (mtp)
  outliers start: 31
  outliers final: 28
  residues processed: 132
  average time/residue: 0.0723
  time to fit residues: 13.4046
Evaluate side-chains
  144 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
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  149 HIS
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  281 MET
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  337 ILE
Chi-restraints excluded: chain A residue  364 HIS
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  716 LEU
Chi-restraints excluded: chain A residue  725 PHE
Chi-restraints excluded: chain A residue  739 ILE
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 24 optimal weight:    0.1980
   chunk 14 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   chunk 49 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 8 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0770
   chunk 5 optimal weight:    0.4980
   overall best weight:    0.3938

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.199004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.154361 restraints weight = 9460.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.152360 restraints weight = 9225.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.154100 restraints weight = 8486.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.155481 restraints weight = 5435.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.155909 restraints weight = 4877.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.3286

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= 0.121
  Angle     :  0.640  11.234   9438  Z= 0.313
  Chirality :  0.041   0.188   1135
  Planarity :  0.004   0.052   1193
  Dihedral  :  4.142  28.617    946
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.81 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 22.70 %
    Favored  : 73.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.46 (0.30), residues: 894
  helix:  2.16 (0.24), residues: 462
  sheet: -0.11 (0.61), residues: 92
  loop : -0.36 (0.37), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  55 
 TYR   0.012   0.001   TYR A 618 
 PHE   0.012   0.001   PHE A 702 
 TRP   0.037   0.003   TRP A  72 
 HIS   0.002   0.000   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6970)
  covalent geometry    : angle       0.64019 ( 9438)
  hydrogen bonds       : bond        0.03264 (  389)
  hydrogen bonds       : angle       3.60476 ( 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
  147 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 115
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  281 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7628 (tmt)
REVERT: A  337 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.6980 (tp)
REVERT: A  435 MET cc_start: 0.7658 (tmm) cc_final: 0.6790 (tmm)
REVERT: A  757 ASP cc_start: 0.8241 (t0) cc_final: 0.7997 (t0)
REVERT: A  780 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8417 (mm)
REVERT: A  810 MET cc_start: 0.7217 (ttm) cc_final: 0.6954 (mtp)
  outliers start: 32
  outliers final: 27
  residues processed: 136
  average time/residue: 0.0670
  time to fit residues: 12.7859
Evaluate side-chains
  141 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 111
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
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  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  281 MET
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  337 ILE
Chi-restraints excluded: chain A residue  364 HIS
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  716 LEU
Chi-restraints excluded: chain A residue  725 PHE
Chi-restraints excluded: chain A residue  739 ILE
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  888 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0970
   chunk 81 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0010
   chunk 23 optimal weight:    6.9990
   chunk 42 optimal weight:    0.0470
   chunk 24 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0870
   chunk 16 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    0.1660

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.197535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.151952 restraints weight = 9212.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.151903 restraints weight = 8872.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.153925 restraints weight = 7821.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.154289 restraints weight = 5156.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.154466 restraints weight = 4561.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.3258

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= 0.114
  Angle     :  0.672  16.136   9438  Z= 0.320
  Chirality :  0.041   0.183   1135
  Planarity :  0.004   0.052   1193
  Dihedral  :  4.123  28.730    946
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 23.74 %
    Favored  : 72.89 %
  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 aren not related in a simple way.
  whole:  1.46 (0.30), residues: 894
  helix:  2.20 (0.24), residues: 462
  sheet:  0.70 (0.61), residues: 84
  loop : -0.66 (0.37), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  55 
 TYR   0.023   0.001   TYR A 483 
 PHE   0.012   0.001   PHE A 702 
 TRP   0.035   0.002   TRP A  72 
 HIS   0.002   0.000   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 6970)
  covalent geometry    : angle       0.67238 ( 9438)
  hydrogen bonds       : bond        0.03033 (  389)
  hydrogen bonds       : angle       3.51604 ( 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
  143 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.7964 (tp30) cc_final: 0.7563 (tt0)
REVERT: A  262 MET cc_start: 0.8388 (mmp) cc_final: 0.8184 (mmp)
REVERT: A  281 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7600 (tmt)
REVERT: A  435 MET cc_start: 0.7679 (tmm) cc_final: 0.6805 (tmm)
REVERT: A  709 THR cc_start: 0.8460 (t) cc_final: 0.7312 (p)
REVERT: A  757 ASP cc_start: 0.8210 (t0) cc_final: 0.7923 (t70)
REVERT: A  780 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8341 (mm)
REVERT: A  810 MET cc_start: 0.7121 (ttm) cc_final: 0.6874 (mtp)
  outliers start: 26
  outliers final: 21
  residues processed: 134
  average time/residue: 0.0713
  time to fit residues: 13.2897
Evaluate side-chains
  138 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
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  281 MET
Chi-restraints excluded: chain A residue  364 HIS
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  725 PHE
Chi-restraints excluded: chain A residue  739 ILE
Chi-restraints excluded: chain A residue  770 ILE
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  888 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 18 optimal weight:    0.0470
   chunk 2 optimal weight:    5.9990
   chunk 74 optimal weight:    0.0370
   chunk 79 optimal weight:    0.0980
   chunk 46 optimal weight:    8.9990
   chunk 27 optimal weight:    0.0000
   chunk 30 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 41 optimal weight:   10.0000
   chunk 29 optimal weight:    0.7980
   chunk 64 optimal weight:    0.5980
   overall best weight:    0.1560

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.199667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.154684 restraints weight = 9228.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.153650 restraints weight = 8388.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.155736 restraints weight = 7390.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.156274 restraints weight = 4572.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.156431 restraints weight = 4703.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.3246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6970  Z= 0.112
  Angle     :  0.669  14.414   9438  Z= 0.318
  Chirality :  0.041   0.182   1135
  Planarity :  0.004   0.051   1193
  Dihedral  :  4.052  28.110    946
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 23.99 %
    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 aren not related in a simple way.
  whole:  1.54 (0.30), residues: 894
  helix:  2.24 (0.24), residues: 462
  sheet: -0.05 (0.61), residues: 91
  loop : -0.37 (0.37), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 900 
 TYR   0.023   0.001   TYR A 483 
 PHE   0.011   0.001   PHE A 702 
 TRP   0.035   0.002   TRP A  72 
 HIS   0.002   0.000   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 6970)
  covalent geometry    : angle       0.66909 ( 9438)
  hydrogen bonds       : bond        0.02904 (  389)
  hydrogen bonds       : angle       3.46670 ( 1194)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1341.42 seconds
wall clock time: 23 minutes 50.87 seconds (1430.87 seconds total)