Starting phenix.real_space_refine
on Fri Aug 22 18:41:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iwu_35780/08_2025/8iwu_35780.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iwu_35780/08_2025/8iwu_35780.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iwu_35780/08_2025/8iwu_35780.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iwu_35780/08_2025/8iwu_35780.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iwu_35780/08_2025/8iwu_35780.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iwu_35780/08_2025/8iwu_35780.map"
  }
  resolution = 3.31
  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=   0.019
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: 7
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     Mg      1      5.21       5
     S      52      5.16       5
     C    4358      2.51       5
     N    1142      2.21       5
     O    1285      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 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: 6843
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 893, 6837
          Classifications: {'peptide': 893}
          Link IDs: {'PTRANS': 35, 'TRANS': 857}
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 6
          Unusual residues: {' MG': 1, 'ALF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.45, per 1000 atoms: 0.21
  Number of scatterers: 6843
  At special positions: 0
  Unit cell: (89.88, 91.56, 134.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      52     16.00
     Al      1     13.00
     Mg      1     11.99
     F       4      9.00
     O    1285      8.00
     N    1142      7.00
     C    4358      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: 0.40
  Conformation dependent library (CDL) restraints added in 340.7 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1664

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 7 sheets defined
      55.9% alpha, 19.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  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 59
    Processing helix  chain 'A' and resid 70 through 80
    Processing helix  chain 'A' and resid 81 through 96
    Processing helix  chain 'A' and resid 99 through 121
    Processing helix  chain 'A' and resid 130 through 134
      removed outlier: 3.785A  pdb=" N   LEU A 134 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
    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 209 through 213
    Processing helix  chain 'A' and resid 235 through 238
    Processing helix  chain 'A' and resid 239 through 251
    Processing helix  chain 'A' and resid 256 through 288
    Processing helix  chain 'A' and resid 290 through 306
      removed outlier: 3.904A  pdb=" N   ILE A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 328
      removed outlier: 4.393A  pdb=" N   ILE A 312 " --> pdb=" O   GLU A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 342
      removed outlier: 3.674A  pdb=" N   VAL A 338 " --> pdb=" O   LYS A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 411
    Processing helix  chain 'A' and resid 424 through 437
    Processing helix  chain 'A' and resid 442 through 444
      No H-bonds generated for 'chain 'A' and resid 442 through 444'
    Processing helix  chain 'A' and resid 482 through 489
      removed outlier: 3.973A  pdb=" N   LYS A 488 " --> pdb=" O   GLU A 484 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   TYR A 489 " --> pdb=" O   GLN A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 520
    Processing helix  chain 'A' and resid 551 through 563
      removed outlier: 4.060A  pdb=" N   SER A 562 " --> pdb=" O   THR A 558 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   GLY A 563 " --> pdb=" O   LEU A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 585
    Processing helix  chain 'A' and resid 596 through 602
    Processing helix  chain 'A' and resid 603 through 611
    Processing helix  chain 'A' and resid 621 through 635
      removed outlier: 3.959A  pdb=" N   ASN A 635 " --> pdb=" O   SER A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 645 through 655
    Processing helix  chain 'A' and resid 666 through 673
    Processing helix  chain 'A' and resid 682 through 723
    Processing helix  chain 'A' and resid 730 through 739
    Processing helix  chain 'A' and resid 742 through 751
      removed outlier: 3.535A  pdb=" N   ALA A 746 " --> pdb=" O   ASP A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 797
    Processing helix  chain 'A' and resid 804 through 826
    Processing helix  chain 'A' and resid 842 through 861
    Processing helix  chain 'A' and resid 861 through 869
    Processing helix  chain 'A' and resid 874 through 886
      removed outlier: 3.558A  pdb=" N   SER A 886 " --> pdb=" O   LEU A 882 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 886 through 907
    Processing sheet with id=AA1, first strand: chain 'A' and resid 146 through 151
      removed outlier: 4.586A  pdb=" N   HIS A 140 " --> pdb=" O   CYS A 162 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   THR A 160 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   SER A 182 " --> pdb=" O   ARG A 224 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLY A 226 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 7.397A  pdb=" N   ASP A 180 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   ALA A 228 " --> pdb=" O   ALA A 178 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ALA A 178 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   GLY A 230 " --> pdb=" O   PHE A 176 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   PHE A 176 " --> pdb=" O   GLY A 230 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   VAL A 232 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   ARG A 174 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLY A 234 " --> pdb=" O   ASP A 172 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ASP A 172 " --> pdb=" O   GLY A 234 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   LEU A 181 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 151
      removed outlier: 4.586A  pdb=" N   HIS A 140 " --> pdb=" O   CYS A 162 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   THR A 160 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   SER A 182 " --> pdb=" O   ARG A 224 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLY A 226 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 7.397A  pdb=" N   ASP A 180 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   ALA A 228 " --> pdb=" O   ALA A 178 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ALA A 178 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   GLY A 230 " --> pdb=" O   PHE A 176 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   PHE A 176 " --> pdb=" O   GLY A 230 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   VAL A 232 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   ARG A 174 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLY A 234 " --> pdb=" O   ASP A 172 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ASP A 172 " --> pdb=" O   GLY A 234 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 332
    Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 595
      removed outlier: 3.667A  pdb=" N   TYR A 618 " --> pdb=" O   VAL A 594 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ILE A 347 " --> pdb=" O   LYS A 567 " (cutoff:3.500A)
      removed outlier: 7.465A  pdb=" N   ILE A 569 " --> pdb=" O   ILE A 347 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   SER A 349 " --> pdb=" O   ILE A 569 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   VAL A 346 " --> pdb=" O   ALA A 640 " (cutoff:3.500A)
      removed outlier: 7.848A  pdb=" N   THR A 642 " --> pdb=" O   VAL A 346 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   CYS A 348 " --> pdb=" O   THR A 642 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   VAL A 639 " --> pdb=" O   ILE A 657 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   VAL A 659 " --> pdb=" O   VAL A 639 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   MET A 641 " --> pdb=" O   VAL A 659 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 392
      removed outlier: 4.911A  pdb=" N   THR A 363 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   VAL A 362 " --> pdb=" O   ILE A 545 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   ILE A 545 " --> pdb=" O   VAL A 362 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   HIS A 364 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
      removed outlier: 7.310A  pdb=" N   LEU A 527 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   LEU A 541 " --> pdb=" O   LEU A 525 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LEU A 525 " --> pdb=" O   LEU A 541 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   GLY A 543 " --> pdb=" O   ARG A 523 " (cutoff:3.500A)
      removed outlier: 5.807A  pdb=" N   ARG A 523 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   ALA A 462 " --> pdb=" O   GLU A 451 " (cutoff:3.500A)
      removed outlier: 4.937A  pdb=" N   GLU A 451 " --> pdb=" O   ALA A 462 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   LYS A 464 " --> pdb=" O   LYS A 449 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 392
      removed outlier: 4.911A  pdb=" N   THR A 363 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   VAL A 362 " --> pdb=" O   ILE A 545 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   ILE A 545 " --> pdb=" O   VAL A 362 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   HIS A 364 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   CYS A 490 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   PHE A 538 " --> pdb=" O   CYS A 490 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   THR A 492 " --> pdb=" O   PHE A 538 " (cutoff:3.500A)
      removed outlier: 8.446A  pdb=" N   GLY A 540 " --> pdb=" O   THR A 492 " (cutoff:3.500A)
      removed outlier: 10.481A  pdb=" N   GLN A 494 " --> pdb=" O   GLY A 540 " (cutoff:3.500A)
      removed outlier: 13.890A  pdb=" N   VAL A 542 " --> pdb=" O   GLN A 494 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 415 through 417

    435 hydrogen bonds defined for protein.
    1257 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: 1.33

  Time building geometry restraints manager: 0.52 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: 2224
        1.34 -     1.46: 1402
        1.46 -     1.58: 3235
        1.58 -     1.70: 1
        1.70 -     1.82: 88
  Bond restraints: 6950
  Sorted by residual:
  bond pdb=" F3  ALF A1002 "
       pdb="AL   ALF A1002 "
    ideal  model  delta    sigma   weight residual
    1.685  1.786 -0.101 2.00e-02 2.50e+03 2.54e+01
  bond pdb=" F1  ALF A1002 "
       pdb="AL   ALF A1002 "
    ideal  model  delta    sigma   weight residual
    1.684  1.785 -0.101 2.00e-02 2.50e+03 2.54e+01
  bond pdb=" F2  ALF A1002 "
       pdb="AL   ALF A1002 "
    ideal  model  delta    sigma   weight residual
    1.685  1.785 -0.100 2.00e-02 2.50e+03 2.51e+01
  bond pdb=" F4  ALF A1002 "
       pdb="AL   ALF A1002 "
    ideal  model  delta    sigma   weight residual
    1.686  1.784 -0.098 2.00e-02 2.50e+03 2.42e+01
  bond pdb=" CB  PRO A 453 "
       pdb=" CG  PRO A 453 "
    ideal  model  delta    sigma   weight residual
    1.492  1.649 -0.157 5.00e-02 4.00e+02 9.85e+00
  ... (remaining 6945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.26: 9405
       14.26 -    28.52: 4
       28.52 -    42.77: 0
       42.77 -    57.03: 0
       57.03 -    71.29: 2
  Bond angle restraints: 9411
  Sorted by residual:
  angle pdb=" F1  ALF A1002 "
        pdb="AL   ALF A1002 "
        pdb=" F2  ALF A1002 "
      ideal   model   delta    sigma   weight residual
     108.68  179.97  -71.29 3.00e+00 1.11e-01 5.65e+02
  angle pdb=" F3  ALF A1002 "
        pdb="AL   ALF A1002 "
        pdb=" F4  ALF A1002 "
      ideal   model   delta    sigma   weight residual
     109.63  179.94  -70.31 3.00e+00 1.11e-01 5.49e+02
  angle pdb=" CA  PRO A 453 "
        pdb=" N   PRO A 453 "
        pdb=" CD  PRO A 453 "
      ideal   model   delta    sigma   weight residual
     112.00  102.25    9.75 1.40e+00 5.10e-01 4.85e+01
  angle pdb=" F2  ALF A1002 "
        pdb="AL   ALF A1002 "
        pdb=" F4  ALF A1002 "
      ideal   model   delta    sigma   weight residual
     110.21   90.00   20.21 3.00e+00 1.11e-01 4.54e+01
  angle pdb=" F1  ALF A1002 "
        pdb="AL   ALF A1002 "
        pdb=" F3  ALF A1002 "
      ideal   model   delta    sigma   weight residual
     109.69   89.98   19.71 3.00e+00 1.11e-01 4.32e+01
  ... (remaining 9406 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3675
       17.95 -    35.90: 439
       35.90 -    53.85: 111
       53.85 -    71.79: 17
       71.79 -    89.74: 6
  Dihedral angle restraints: 4248
    sinusoidal: 1676
      harmonic: 2572
  Sorted by residual:
  dihedral pdb=" CA  ASN A 724 "
           pdb=" C   ASN A 724 "
           pdb=" N   PHE A 725 "
           pdb=" CA  PHE A 725 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.42   26.58     0      5.00e+00 4.00e-02 2.83e+01
  dihedral pdb=" CB  MET A 219 "
           pdb=" CG  MET A 219 "
           pdb=" SD  MET A 219 "
           pdb=" CE  MET A 219 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   -1.30  -58.70     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" CA  ILE A  65 "
           pdb=" CB  ILE A  65 "
           pdb=" CG1 ILE A  65 "
           pdb=" CD1 ILE A  65 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  116.29  -56.29     3      1.50e+01 4.44e-03 9.39e+00
  ... (remaining 4245 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 755
       0.031 -    0.062: 233
       0.062 -    0.092: 95
       0.092 -    0.123: 44
       0.123 -    0.154: 4
  Chirality restraints: 1131
  Sorted by residual:
  chirality pdb=" CA  PHE A 702 "
            pdb=" N   PHE A 702 "
            pdb=" C   PHE A 702 "
            pdb=" CB  PHE A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.93e-01
  chirality pdb=" CA  VAL A 156 "
            pdb=" N   VAL A 156 "
            pdb=" C   VAL A 156 "
            pdb=" CB  VAL A 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.70e-01
  chirality pdb=" CB  ILE A 711 "
            pdb=" CA  ILE A 711 "
            pdb=" CG1 ILE A 711 "
            pdb=" CG2 ILE A 711 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.19e-01
  ... (remaining 1128 not shown)

  Planarity restraints: 1189
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 452 "    0.053 5.00e-02 4.00e+02   7.59e-02 9.22e+00
        pdb=" N   PRO A 453 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A 453 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 453 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 135 "    0.031 5.00e-02 4.00e+02   4.66e-02 3.47e+00
        pdb=" N   PRO A 136 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 136 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 136 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 156 "   -0.029 5.00e-02 4.00e+02   4.37e-02 3.06e+00
        pdb=" N   PRO A 157 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 157 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 157 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1186 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.66: 89
        2.66 -     3.22: 6343
        3.22 -     3.78: 10777
        3.78 -     4.34: 13799
        4.34 -     4.90: 23415
  Nonbonded interactions: 54423
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 644 "
            pdb="MG    MG A1001 "
     model   vdw
     2.094 2.170
  nonbonded pdb=" O   ASP A 350 "
            pdb=" OG1 THR A 354 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" O   SER A 124 "
            pdb=" OG  SER A 124 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OD2 ASP A 350 "
            pdb="MG    MG A1001 "
     model   vdw
     2.263 2.170
  nonbonded pdb=" OD1 ASP A 603 "
            pdb=" N   VAL A 604 "
     model   vdw
     2.280 3.120
  ... (remaining 54418 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.580
  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:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.790
  Find NCS groups from input model:        0.020
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
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      :  0.004   0.157   6950  Z= 0.170
  Angle     :  1.249  71.291   9411  Z= 0.488
  Chirality :  0.039   0.154   1131
  Planarity :  0.005   0.076   1189
  Dihedral  : 16.533  89.742   2584
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.82 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 23.05 %
    Favored  : 76.82 %
  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:  1.91 (0.29), residues: 891
  helix:  2.54 (0.24), residues: 477
  sheet:  0.15 (0.49), residues: 115
  loop : -0.37 (0.38), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 473 
 TYR   0.004   0.000   TYR A 587 
 PHE   0.025   0.001   PHE A 702 
 TRP   0.011   0.001   TRP A  60 
 HIS   0.001   0.000   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 6950)
  covalent geometry    : angle       1.24912 ( 9411)
  hydrogen bonds       : bond        0.14296 (  410)
  hydrogen bonds       : angle       5.41067 ( 1257)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A  492 THR cc_start: 0.7855 (p) cc_final: 0.7548 (t)
REVERT: A  504 GLN cc_start: 0.7328 (tp40) cc_final: 0.6573 (tp40)
  outliers start: 1
  outliers final: 0
  residues processed: 116
  average time/residue: 0.0724
  time to fit residues: 11.9194
Evaluate side-chains
  107 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.0570
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:    0.0000
   overall best weight:    0.5304

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

Flipped N/Q/H residues before XYZ refinement:
A 140 HIS
A 701 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.161261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.139806 restraints weight = 10523.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3829 rms_B_bonded: 1.99
r_work: 0.3726 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3596 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.0933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   6950  Z= 0.125
  Angle     :  0.533   8.754   9411  Z= 0.276
  Chirality :  0.040   0.157   1131
  Planarity :  0.004   0.046   1189
  Dihedral  :  3.600  20.110    941
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.04 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 22.14 %
    Favored  : 76.04 %
  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:  1.87 (0.29), residues: 891
  helix:  2.52 (0.23), residues: 486
  sheet:  0.24 (0.50), residues: 109
  loop : -0.55 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 213 
 TYR   0.003   0.001   TYR A  75 
 PHE   0.023   0.001   PHE A 702 
 TRP   0.007   0.001   TRP A  72 
 HIS   0.001   0.000   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6950)
  covalent geometry    : angle       0.53324 ( 9411)
  hydrogen bonds       : bond        0.03845 (  410)
  hydrogen bonds       : angle       4.30228 ( 1257)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A   55 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7669 (mtm110)
REVERT: A  492 THR cc_start: 0.7876 (p) cc_final: 0.7621 (t)
REVERT: A  716 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8356 (tp)
  outliers start: 14
  outliers final: 9
  residues processed: 130
  average time/residue: 0.0765
  time to fit residues: 13.7981
Evaluate side-chains
  124 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  209 ASP
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  394 HIS
Chi-restraints excluded: chain A residue  435 MET
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  467 HIS
Chi-restraints excluded: chain A residue  716 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   chunk 68 optimal weight:    0.6980
   chunk 58 optimal weight:    0.1980
   chunk 71 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 82 optimal weight:    0.0270
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.148647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.126961 restraints weight = 10232.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 1.82
r_work: 0.3482 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6950  Z= 0.121
  Angle     :  0.521   7.202   9411  Z= 0.271
  Chirality :  0.041   0.156   1131
  Planarity :  0.005   0.056   1189
  Dihedral  :  3.719  16.282    941
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.82 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 20.31 %
    Favored  : 77.08 %
  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:  1.78 (0.29), residues: 891
  helix:  2.40 (0.23), residues: 488
  sheet:  0.03 (0.52), residues: 96
  loop : -0.45 (0.37), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 473 
 TYR   0.006   0.001   TYR A  75 
 PHE   0.020   0.001   PHE A 702 
 TRP   0.007   0.001   TRP A  60 
 HIS   0.001   0.001   HIS A 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6950)
  covalent geometry    : angle       0.52137 ( 9411)
  hydrogen bonds       : bond        0.03640 (  410)
  hydrogen bonds       : angle       4.02828 ( 1257)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 ARG cc_start: 0.8017 (ttm110) cc_final: 0.7697 (mtm110)
REVERT: A  492 THR cc_start: 0.7902 (OUTLIER) cc_final: 0.7676 (t)
REVERT: A  500 LEU cc_start: 0.8372 (mm) cc_final: 0.8067 (mp)
  outliers start: 20
  outliers final: 10
  residues processed: 139
  average time/residue: 0.0856
  time to fit residues: 16.1460
Evaluate side-chains
  127 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  209 ASP
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  394 HIS
Chi-restraints excluded: chain A residue  435 MET
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  467 HIS
Chi-restraints excluded: chain A residue  492 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 82 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0970
   chunk 83 optimal weight:    0.2980
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.147185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.125017 restraints weight = 10286.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 1.86
r_work: 0.3465 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   6950  Z= 0.110
  Angle     :  0.513   7.998   9411  Z= 0.266
  Chirality :  0.040   0.149   1131
  Planarity :  0.004   0.050   1189
  Dihedral  :  3.692  15.488    941
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.04 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 21.61 %
    Favored  : 75.13 %
  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:  1.80 (0.29), residues: 891
  helix:  2.42 (0.24), residues: 488
  sheet:  0.09 (0.53), residues: 96
  loop : -0.45 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 473 
 TYR   0.005   0.001   TYR A  75 
 PHE   0.023   0.001   PHE A 702 
 TRP   0.008   0.001   TRP A  72 
 HIS   0.004   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 6950)
  covalent geometry    : angle       0.51306 ( 9411)
  hydrogen bonds       : bond        0.03485 (  410)
  hydrogen bonds       : angle       3.95068 ( 1257)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A   55 ARG cc_start: 0.8010 (ttm110) cc_final: 0.7762 (mtm110)
REVERT: A   81 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8529 (t0)
REVERT: A  492 THR cc_start: 0.7917 (OUTLIER) cc_final: 0.7690 (t)
REVERT: A  500 LEU cc_start: 0.8387 (mm) cc_final: 0.8069 (mp)
REVERT: A  742 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7138 (t0)
  outliers start: 25
  outliers final: 15
  residues processed: 139
  average time/residue: 0.0847
  time to fit residues: 16.0397
Evaluate side-chains
  130 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 GLN
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  394 HIS
Chi-restraints excluded: chain A residue  435 MET
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  467 HIS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  742 ASP
Chi-restraints excluded: chain A residue  857 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0670
   chunk 64 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 82 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS
A 605 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.147002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.122873 restraints weight = 10559.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 2.03
r_work: 0.3487 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6950  Z= 0.130
  Angle     :  0.534   9.551   9411  Z= 0.277
  Chirality :  0.041   0.154   1131
  Planarity :  0.005   0.048   1189
  Dihedral  :  3.723  17.272    941
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.59 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 22.01 %
    Favored  : 74.35 %
  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:  1.69 (0.29), residues: 891
  helix:  2.29 (0.23), residues: 488
  sheet:  0.07 (0.54), residues: 96
  loop : -0.44 (0.37), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 900 
 TYR   0.005   0.001   TYR A  75 
 PHE   0.025   0.002   PHE A 702 
 TRP   0.009   0.001   TRP A  60 
 HIS   0.005   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6950)
  covalent geometry    : angle       0.53385 ( 9411)
  hydrogen bonds       : bond        0.03795 (  410)
  hydrogen bonds       : angle       3.98439 ( 1257)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 125
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A   81 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8463 (t0)
REVERT: A  167 ASP cc_start: 0.7480 (t0) cc_final: 0.7159 (t0)
REVERT: A  461 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.7855 (ttp)
REVERT: A  492 THR cc_start: 0.7960 (OUTLIER) cc_final: 0.7695 (t)
REVERT: A  500 LEU cc_start: 0.8371 (mm) cc_final: 0.7985 (mp)
REVERT: A  568 MET cc_start: 0.8457 (tpp) cc_final: 0.8244 (ttt)
  outliers start: 28
  outliers final: 17
  residues processed: 142
  average time/residue: 0.0879
  time to fit residues: 16.7399
Evaluate side-chains
  133 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 GLN
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  382 GLN
Chi-restraints excluded: chain A residue  394 HIS
Chi-restraints excluded: chain A residue  435 MET
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  467 HIS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  721 THR
Chi-restraints excluded: chain A residue  804 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0770
   chunk 82 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 13 optimal weight:    0.2980
   chunk 49 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0770
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.147507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.123453 restraints weight = 10529.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 2.02
r_work: 0.3497 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3359 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6950  Z= 0.109
  Angle     :  0.525  10.327   9411  Z= 0.272
  Chirality :  0.040   0.150   1131
  Planarity :  0.005   0.050   1189
  Dihedral  :  3.711  17.248    941
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 21.88 %
    Favored  : 74.48 %
  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:  1.74 (0.29), residues: 891
  helix:  2.31 (0.23), residues: 487
  sheet:  0.06 (0.54), residues: 96
  loop : -0.36 (0.37), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 473 
 TYR   0.005   0.001   TYR A  75 
 PHE   0.024   0.001   PHE A 702 
 TRP   0.020   0.001   TRP A 795 
 HIS   0.005   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 6950)
  covalent geometry    : angle       0.52509 ( 9411)
  hydrogen bonds       : bond        0.03593 (  410)
  hydrogen bonds       : angle       3.91517 ( 1257)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 118
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A   81 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8466 (t0)
REVERT: A  167 ASP cc_start: 0.7516 (t0) cc_final: 0.7165 (t0)
REVERT: A  382 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8768 (pt0)
REVERT: A  461 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.7853 (ttp)
REVERT: A  492 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7678 (t)
REVERT: A  500 LEU cc_start: 0.8374 (mm) cc_final: 0.8005 (mp)
REVERT: A  742 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7188 (t0)
  outliers start: 28
  outliers final: 17
  residues processed: 138
  average time/residue: 0.0825
  time to fit residues: 15.4826
Evaluate side-chains
  132 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 GLN
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  209 ASP
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  382 GLN
Chi-restraints excluded: chain A residue  394 HIS
Chi-restraints excluded: chain A residue  435 MET
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  467 HIS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  721 THR
Chi-restraints excluded: chain A residue  742 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 42 optimal weight:    0.2980
   chunk 36 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS
A 822 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.140140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.115255 restraints weight = 10467.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 2.00
r_work: 0.3375 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6950  Z= 0.178
  Angle     :  0.606  11.472   9411  Z= 0.313
  Chirality :  0.043   0.167   1131
  Planarity :  0.005   0.053   1189
  Dihedral  :  4.030  17.088    941
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 21.09 %
    Favored  : 74.35 %
  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 (0.29), residues: 891
  helix:  1.95 (0.23), residues: 493
  sheet: -0.05 (0.53), residues: 103
  loop : -0.41 (0.38), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 174 
 TYR   0.008   0.001   TYR A 587 
 PHE   0.022   0.002   PHE A 702 
 TRP   0.025   0.002   TRP A 795 
 HIS   0.005   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 6950)
  covalent geometry    : angle       0.60633 ( 9411)
  hydrogen bonds       : bond        0.04689 (  410)
  hydrogen bonds       : angle       4.18510 ( 1257)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 115
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A   81 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8559 (t0)
REVERT: A  123 ARG cc_start: 0.8477 (tpp80) cc_final: 0.8182 (tpp-160)
REVERT: A  382 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8738 (pt0)
REVERT: A  461 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8014 (ttp)
REVERT: A  742 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7416 (t0)
  outliers start: 35
  outliers final: 22
  residues processed: 136
  average time/residue: 0.0776
  time to fit residues: 14.3766
Evaluate side-chains
  132 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 106
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 GLN
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  382 GLN
Chi-restraints excluded: chain A residue  394 HIS
Chi-restraints excluded: chain A residue  435 MET
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  467 HIS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  721 THR
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  742 ASP
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  804 THR
Chi-restraints excluded: chain A residue  833 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 63 optimal weight:    0.5980
   chunk 73 optimal weight:    0.4980
   chunk 30 optimal weight:    0.9990
   chunk 5 optimal weight:    0.1980
   chunk 11 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.142659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.117903 restraints weight = 10482.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 2.01
r_work: 0.3416 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.3263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6950  Z= 0.124
  Angle     :  0.551   9.161   9411  Z= 0.286
  Chirality :  0.041   0.175   1131
  Planarity :  0.005   0.053   1189
  Dihedral  :  3.921  16.577    941
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 21.61 %
    Favored  : 74.48 %
  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:  1.55 (0.29), residues: 891
  helix:  2.14 (0.23), residues: 488
  sheet:  0.06 (0.54), residues: 97
  loop : -0.44 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 473 
 TYR   0.006   0.001   TYR A 587 
 PHE   0.021   0.001   PHE A 702 
 TRP   0.027   0.002   TRP A 795 
 HIS   0.005   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6950)
  covalent geometry    : angle       0.55054 ( 9411)
  hydrogen bonds       : bond        0.04023 (  410)
  hydrogen bonds       : angle       4.04925 ( 1257)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A   81 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8401 (t0)
REVERT: A  123 ARG cc_start: 0.8448 (tpp80) cc_final: 0.8178 (tpp-160)
REVERT: A  382 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8686 (pt0)
REVERT: A  461 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.7986 (ttp)
REVERT: A  492 THR cc_start: 0.8025 (OUTLIER) cc_final: 0.7728 (t)
REVERT: A  742 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7426 (t0)
  outliers start: 30
  outliers final: 21
  residues processed: 132
  average time/residue: 0.0755
  time to fit residues: 13.6012
Evaluate side-chains
  135 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 GLN
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  382 GLN
Chi-restraints excluded: chain A residue  394 HIS
Chi-restraints excluded: chain A residue  435 MET
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  467 HIS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain A residue  679 ASP
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  721 THR
Chi-restraints excluded: chain A residue  742 ASP
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  804 THR
Chi-restraints excluded: chain A residue  876 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 85 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 42 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9990
   chunk 68 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0070
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.139120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.112539 restraints weight = 10595.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 2.27
r_work: 0.3388 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.3381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6950  Z= 0.128
  Angle     :  0.570  12.403   9411  Z= 0.291
  Chirality :  0.041   0.172   1131
  Planarity :  0.005   0.053   1189
  Dihedral  :  3.915  16.236    941
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 22.40 %
    Favored  : 73.96 %
  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:  1.56 (0.29), residues: 891
  helix:  2.16 (0.23), residues: 488
  sheet: -0.03 (0.54), residues: 97
  loop : -0.44 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 473 
 TYR   0.007   0.001   TYR A 587 
 PHE   0.022   0.002   PHE A 702 
 TRP   0.026   0.002   TRP A 795 
 HIS   0.006   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6950)
  covalent geometry    : angle       0.56986 ( 9411)
  hydrogen bonds       : bond        0.04038 (  410)
  hydrogen bonds       : angle       4.03556 ( 1257)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8431 (t0)
REVERT: A  123 ARG cc_start: 0.8517 (tpp80) cc_final: 0.8241 (tpp-160)
REVERT: A  382 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8749 (pt0)
REVERT: A  492 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7736 (t)
REVERT: A  742 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7477 (t0)
  outliers start: 28
  outliers final: 21
  residues processed: 131
  average time/residue: 0.0760
  time to fit residues: 13.7112
Evaluate side-chains
  136 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 GLN
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  382 GLN
Chi-restraints excluded: chain A residue  394 HIS
Chi-restraints excluded: chain A residue  435 MET
Chi-restraints excluded: chain A residue  467 HIS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  721 THR
Chi-restraints excluded: chain A residue  742 ASP
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  804 THR
Chi-restraints excluded: chain A residue  876 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 72 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 16 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 21 optimal weight:    0.3980
   chunk 85 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.142118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.117439 restraints weight = 10350.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 1.99
r_work: 0.3410 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3275 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.3468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6950  Z= 0.132
  Angle     :  0.560   8.571   9411  Z= 0.290
  Chirality :  0.041   0.176   1131
  Planarity :  0.005   0.053   1189
  Dihedral  :  3.930  16.216    941
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 22.40 %
    Favored  : 73.83 %
  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:  1.57 (0.29), residues: 891
  helix:  2.18 (0.23), residues: 488
  sheet: -0.07 (0.54), residues: 97
  loop : -0.44 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 473 
 TYR   0.007   0.001   TYR A 587 
 PHE   0.022   0.002   PHE A 702 
 TRP   0.025   0.002   TRP A 795 
 HIS   0.007   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6950)
  covalent geometry    : angle       0.55996 ( 9411)
  hydrogen bonds       : bond        0.04050 (  410)
  hydrogen bonds       : angle       4.04081 ( 1257)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8464 (t0)
REVERT: A  123 ARG cc_start: 0.8472 (tpp80) cc_final: 0.8196 (tpp-160)
REVERT: A  461 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8071 (ttp)
REVERT: A  492 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7742 (t)
REVERT: A  742 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7518 (t0)
  outliers start: 29
  outliers final: 19
  residues processed: 134
  average time/residue: 0.0712
  time to fit residues: 13.1265
Evaluate side-chains
  134 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 GLN
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  435 MET
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  467 HIS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  657 ILE
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  721 THR
Chi-restraints excluded: chain A residue  742 ASP
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  804 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 88 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0370
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.8860

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.141249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.116487 restraints weight = 10414.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 2.00
r_work: 0.3395 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3257 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.3578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6950  Z= 0.146
  Angle     :  0.581   8.948   9411  Z= 0.299
  Chirality :  0.042   0.176   1131
  Planarity :  0.005   0.050   1189
  Dihedral  :  3.976  16.066    941
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 23.31 %
    Favored  : 73.44 %
  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:  1.52 (0.29), residues: 891
  helix:  2.14 (0.23), residues: 488
  sheet: -0.07 (0.54), residues: 97
  loop : -0.47 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 473 
 TYR   0.007   0.001   TYR A 587 
 PHE   0.024   0.002   PHE A 818 
 TRP   0.024   0.002   TRP A 795 
 HIS   0.007   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6950)
  covalent geometry    : angle       0.58052 ( 9411)
  hydrogen bonds       : bond        0.04216 (  410)
  hydrogen bonds       : angle       4.07937 ( 1257)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1993.74 seconds
wall clock time: 34 minutes 49.74 seconds (2089.74 seconds total)