Starting phenix.real_space_refine
on Thu Jul  2 03:13:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yma_73100/07_2026/9yma_73100.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yma_73100/07_2026/9yma_73100.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yma_73100/07_2026/9yma_73100.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yma_73100/07_2026/9yma_73100.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yma_73100/07_2026/9yma_73100.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yma_73100/07_2026/9yma_73100.map"
  }
  resolution = 3.87
  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=   0.002
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
     P      42      5.49       5
     S      31      5.16       5
     C    3685      2.51       5
     N    1087      2.21       5
     O    1214      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6059
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 473
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 473
          Classifications: {'RNA': 22}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 8}
          Link IDs: {'rna2p': 1, 'rna3p': 20}
    Chain: "C"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 418
          Classifications: {'RNA': 20}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 11}
          Link IDs: {'rna2p': 1, 'rna3p': 18}
    Chain: "A"
      Number of atoms: 5168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 645, 5168
          Classifications: {'peptide': 645}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 41, 'TRANS': 603}
          Chain breaks: 4
  Time building chain proxies: 1.59, per 1000 atoms: 0.26
  Number of scatterers: 6059
  At special positions: 0
  Unit cell: (76.254, 71.994, 106.5, 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)
     S      31     16.00
     P      42     15.00
     O    1214      8.00
     N    1087      7.00
     C    3685      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: 0.54
  Conformation dependent library (CDL) restraints added in 303.4 milliseconds
  

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1218

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 7 sheets defined
      38.1% alpha, 15.7% beta
      18 base pairs and 27 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 69 through 82
      removed outlier: 3.665A  pdb=" N   GLU A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   VAL A  75 " --> pdb=" O   ASN A  71 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLU A  76 " --> pdb=" O   ARG A  72 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   MET A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 87
      removed outlier: 3.632A  pdb=" N   ILE A  86 " --> pdb=" O   PHE A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 148
      removed outlier: 3.699A  pdb=" N   SER A 148 " --> pdb=" O   HIS A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 173
      removed outlier: 3.828A  pdb=" N   ILE A 159 " --> pdb=" O   PRO A 155 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   VAL A 165 " --> pdb=" O   ALA A 161 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   MET A 166 " --> pdb=" O   LEU A 162 " (cutoff:3.500A)
      Proline residue:  A 170  - end of helix
    Processing helix  chain 'A' and resid 373 through 386
    Processing helix  chain 'A' and resid 387 through 391
      removed outlier: 3.989A  pdb=" N   THR A 390 " --> pdb=" O   SER A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 398
    Processing helix  chain 'A' and resid 463 through 482
    Processing helix  chain 'A' and resid 497 through 499
      No H-bonds generated for 'chain 'A' and resid 497 through 499'
    Processing helix  chain 'A' and resid 500 through 512
      removed outlier: 3.720A  pdb=" N   MET A 504 " --> pdb=" O   SER A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 539
      removed outlier: 4.313A  pdb=" N   ALA A 530 " --> pdb=" O   THR A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 554
    Processing helix  chain 'A' and resid 556 through 572
      removed outlier: 4.660A  pdb=" N   ASN A 562 " --> pdb=" O   GLN A 558 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LEU A 565 " --> pdb=" O   SER A 561 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LYS A 566 " --> pdb=" O   ASN A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 589
      removed outlier: 3.741A  pdb=" N   GLN A 589 " --> pdb=" O   VAL A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 658
      removed outlier: 3.581A  pdb=" N   GLU A 648 " --> pdb=" O   ALA A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 674
      No H-bonds generated for 'chain 'A' and resid 672 through 674'
    Processing helix  chain 'A' and resid 675 through 695
      removed outlier: 3.691A  pdb=" N   LEU A 680 " --> pdb=" O   PHE A 676 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   HIS A 682 " --> pdb=" O   GLN A 678 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   LEU A 684 " --> pdb=" O   LEU A 680 " (cutoff:3.500A)
      removed outlier: 5.387A  pdb=" N   LEU A 685 " --> pdb=" O   HIS A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 775 through 787
      removed outlier: 4.074A  pdb=" N   CYS A 787 " --> pdb=" O   THR A 783 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 825
      removed outlier: 3.677A  pdb=" N   ARG A 814 " --> pdb=" O   ALA A 810 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   TYR A 815 " --> pdb=" O   PHE A 811 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   HIS A 816 " --> pdb=" O   ARG A 812 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU A 817 " --> pdb=" O   ALA A 813 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   VAL A 818 " --> pdb=" O   ARG A 814 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   ASP A 819 " --> pdb=" O   TYR A 815 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   LYS A 820 " --> pdb=" O   HIS A 816 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ASP A 823 " --> pdb=" O   ASP A 819 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 838 through 846
      removed outlier: 3.860A  pdb=" N   LYS A 844 " --> pdb=" O   GLN A 840 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   VAL A 846 " --> pdb=" O   LEU A 842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 849 through 853
    Processing sheet with id=AA1, first strand: chain 'A' and resid 591 through 594
      removed outlier: 6.064A  pdb=" N   ILE A 664 " --> pdb=" O   THR A 703 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   ILE A 705 " --> pdb=" O   ILE A 664 " (cutoff:3.500A)
      removed outlier: 5.834A  pdb=" N   PHE A 666 " --> pdb=" O   ILE A 705 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   VAL A 707 " --> pdb=" O   PHE A 666 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ARG A 668 " --> pdb=" O   VAL A 707 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   PHE A 704 " --> pdb=" O   LEU A 768 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LEU A 768 " --> pdb=" O   PHE A 704 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU A 750 " --> pdb=" O   SER A 763 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   THR A 734 " --> pdb=" O   CYS A 751 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 46
      removed outlier: 3.535A  pdb=" N   MET A 214 " --> pdb=" O   ARG A 207 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94
      removed outlier: 3.804A  pdb=" N   VAL A  93 " --> pdb=" O   TYR A 101 " (cutoff:3.500A)
      removed outlier: 5.686A  pdb=" N   GLU A  58 " --> pdb=" O   TRP A 134 " (cutoff:3.500A)
      removed outlier: 5.620A  pdb=" N   TRP A 134 " --> pdb=" O   GLU A  58 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ASP A  60 " --> pdb=" O   ILE A 132 " (cutoff:3.500A)
      removed outlier: 5.508A  pdb=" N   ILE A 132 " --> pdb=" O   ASP A  60 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   PHE A 128 " --> pdb=" O   VAL A 117 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   VAL A 113 " --> pdb=" O   ILE A 132 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 427 through 428
      removed outlier: 3.618A  pdb=" N   ILE A 577 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 451 through 455
      removed outlier: 3.579A  pdb=" N   LEU A 522 " --> pdb=" O   VAL A 547 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 611 through 612
    Processing sheet with id=AA7, first strand: chain 'A' and resid 615 through 617

    190 hydrogen bonds defined for protein.
    531 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      42 hydrogen bonds
      82 hydrogen bond angles
      0 basepair planarities
      18 basepair parallelities
      27 stacking parallelities
  Total time for adding SS restraints: 1.20

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1814
        1.34 -     1.45: 1159
        1.45 -     1.57: 3180
        1.57 -     1.69: 82
        1.69 -     1.81: 49
  Bond restraints: 6284
  Sorted by residual:
  bond pdb=" N9    G B  16 "
       pdb=" C4    G B  16 "
    ideal  model  delta    sigma   weight residual
    1.375  1.386 -0.011 8.00e-03 1.56e+04 2.04e+00
  bond pdb=" N   PRO A  25 "
       pdb=" CA  PRO A  25 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.016 1.31e-02 5.83e+03 1.54e+00
  bond pdb=" N1    U B  15 "
       pdb=" C2    U B  15 "
    ideal  model  delta    sigma   weight residual
    1.381  1.391 -0.010 9.00e-03 1.23e+04 1.34e+00
  bond pdb=" C   LEU A 594 "
       pdb=" N   GLY A 595 "
    ideal  model  delta    sigma   weight residual
    1.330  1.320  0.009 8.50e-03 1.38e+04 1.23e+00
  bond pdb=" N7    A B  11 "
       pdb=" C5    A B  11 "
    ideal  model  delta    sigma   weight residual
    1.388  1.383  0.005 6.00e-03 2.78e+04 7.29e-01
  ... (remaining 6279 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 8429
        1.25 -     2.50: 201
        2.50 -     3.75: 58
        3.75 -     5.01: 12
        5.01 -     6.26: 5
  Bond angle restraints: 8705
  Sorted by residual:
  angle pdb=" C1'   U B  15 "
        pdb=" N1    U B  15 "
        pdb=" C2    U B  15 "
      ideal   model   delta    sigma   weight residual
     117.70  123.81   -6.11 1.20e+00 6.94e-01 2.59e+01
  angle pdb=" N1    U B  15 "
        pdb=" C2    U B  15 "
        pdb=" O2    U B  15 "
      ideal   model   delta    sigma   weight residual
     122.80  125.55   -2.75 7.00e-01 2.04e+00 1.55e+01
  angle pdb=" N1    U B  15 "
        pdb=" C6    U B  15 "
        pdb=" C5    U B  15 "
      ideal   model   delta    sigma   weight residual
     122.70  124.61   -1.91 5.00e-01 4.00e+00 1.45e+01
  angle pdb=" C1'   U B  15 "
        pdb=" N1    U B  15 "
        pdb=" C6    U B  15 "
      ideal   model   delta    sigma   weight residual
     121.20  115.95    5.25 1.40e+00 5.10e-01 1.41e+01
  angle pdb=" C2    U B  15 "
        pdb=" N3    U B  15 "
        pdb=" C4    U B  15 "
      ideal   model   delta    sigma   weight residual
     127.00  129.12   -2.12 6.00e-01 2.78e+00 1.25e+01
  ... (remaining 8700 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.38: 3666
       31.38 -    62.77: 157
       62.77 -    94.15: 21
       94.15 -   125.54: 1
      125.54 -   156.92: 3
  Dihedral angle restraints: 3848
    sinusoidal: 1970
      harmonic: 1878
  Sorted by residual:
  dihedral pdb=" O4'   U B  15 "
           pdb=" C1'   U B  15 "
           pdb=" N1    U B  15 "
           pdb=" C2    U B  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -27.93 -132.07     1      1.50e+01 4.44e-03 7.13e+01
  dihedral pdb=" C4'   U C  23 "
           pdb=" C3'   U C  23 "
           pdb=" O3'   U C  23 "
           pdb=" P     U C  24 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   63.08  156.92     1      3.50e+01 8.16e-04 1.50e+01
  dihedral pdb=" C4'   U C  14 "
           pdb=" C3'   U C  14 "
           pdb=" O3'   U C  14 "
           pdb=" P     A C  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   73.95  146.05     1      3.50e+01 8.16e-04 1.43e+01
  ... (remaining 3845 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 705
       0.033 -    0.065: 185
       0.065 -    0.098: 67
       0.098 -    0.131: 39
       0.131 -    0.163: 4
  Chirality restraints: 1000
  Sorted by residual:
  chirality pdb=" C3'   U C  14 "
            pdb=" C4'   U C  14 "
            pdb=" O3'   U C  14 "
            pdb=" C2'   U C  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.31   -0.16 2.00e-01 2.50e+01 6.66e-01
  chirality pdb=" C3'   U C  23 "
            pdb=" C4'   U C  23 "
            pdb=" O3'   U C  23 "
            pdb=" C2'   U C  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.33   -0.15 2.00e-01 2.50e+01 5.51e-01
  chirality pdb=" CA  GLU A 502 "
            pdb=" N   GLU A 502 "
            pdb=" C   GLU A 502 "
            pdb=" CB  GLU A 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.55e-01
  ... (remaining 997 not shown)

  Planarity restraints: 971
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B   2 "    0.019 2.00e-02 2.50e+03   8.63e-03 2.05e+00
        pdb=" N9    A B   2 "   -0.020 2.00e-02 2.50e+03
        pdb=" C8    A B   2 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    A B   2 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A B   2 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    A B   2 "    0.002 2.00e-02 2.50e+03
        pdb=" N6    A B   2 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    A B   2 "    0.000 2.00e-02 2.50e+03
        pdb=" C2    A B   2 "    0.000 2.00e-02 2.50e+03
        pdb=" N3    A B   2 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    A B   2 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 154 "   -0.023 5.00e-02 4.00e+02   3.50e-02 1.96e+00
        pdb=" N   PRO A 155 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 155 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 155 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 169 "    0.020 5.00e-02 4.00e+02   3.06e-02 1.50e+00
        pdb=" N   PRO A 170 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 170 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 170 "    0.017 5.00e-02 4.00e+02
  ... (remaining 968 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 256
        2.71 -     3.25: 6115
        3.25 -     3.80: 10498
        3.80 -     4.35: 12574
        4.35 -     4.90: 20030
  Nonbonded interactions: 49473
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 209 "
            pdb=" O   LYS A 212 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" O   PRO A 661 "
            pdb=" OH  TYR A 698 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   HIS A 168 "
            pdb=" OG  SER A 171 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" NZ  LYS A 402 "
            pdb=" O   GLU A 404 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" OE1 GLN A 459 "
            pdb=" OH  TYR A 494 "
     model   vdw
     2.269 3.040
  ... (remaining 49468 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             9.810
  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:          0.300
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.240
  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:             0.010
  Load rotamer database and sin/cos tables:0.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6705
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   0.031   6284  Z= 0.148
  Angle     :  0.546   6.256   8705  Z= 0.370
  Chirality :  0.040   0.163   1000
  Planarity :  0.004   0.035    971
  Dihedral  : 16.560 156.923   2630
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.09 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 11.44 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.33), residues: 635
  helix:  0.77 (0.39), residues: 186
  sheet: -0.07 (0.49), residues: 119
  loop : -0.65 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 534 
 TYR   0.010   0.001   TYR A 698 
 PHE   0.008   0.001   PHE A 811 
 TRP   0.008   0.001   TRP A 769 
 HIS   0.003   0.001   HIS A 507 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.15 ( 6284)
  covalent geometry    : angle       0.54550 /  0.37 ( 8705)
  hydrogen bonds       : bond        0.20401 / 21.31 (  232)
  hydrogen bonds       : angle       7.25170 /  8.94 (  613)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.8004 (mmm) cc_final: 0.7445 (mmm)
REVERT: A  388 PHE cc_start: 0.7447 (m-80) cc_final: 0.7241 (m-80)
REVERT: A  400 MET cc_start: 0.5332 (tpt) cc_final: 0.4700 (tpp)
REVERT: A  401 VAL cc_start: 0.7803 (p) cc_final: 0.7451 (p)
REVERT: A  423 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7483 (tmm160)
REVERT: A  483 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.7083 (ttm)
REVERT: A  533 LYS cc_start: 0.8976 (mmtt) cc_final: 0.8594 (tppt)
REVERT: A  779 LEU cc_start: 0.9229 (tp) cc_final: 0.8972 (tt)
REVERT: A  812 ARG cc_start: 0.8371 (tpp80) cc_final: 0.8093 (tpp80)
REVERT: A  847 GLN cc_start: 0.6649 (OUTLIER) cc_final: 0.6401 (mt0)
  outliers start: 22
  outliers final: 16
  residues processed: 107
  average time/residue: 0.0925
  time to fit residues: 12.9135
Evaluate side-chains
  97 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  160 GLN
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  423 ARG
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  483 MET
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  711 HIS
Chi-restraints excluded: chain A residue  734 THR
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  797 VAL
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  847 GLN
Chi-restraints excluded: chain A residue  854 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.3980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0170
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.6418

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 216 ASN
A 551 ASN
** A 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.162648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.132155 restraints weight = 15044.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.135864 restraints weight = 8491.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.138282 restraints weight = 5713.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.139864 restraints weight = 4355.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.140803 restraints weight = 3621.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.4223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6749
moved from start:          0.0816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6284  Z= 0.122
  Angle     :  0.583   6.824   8705  Z= 0.310
  Chirality :  0.041   0.191   1000
  Planarity :  0.004   0.042    971
  Dihedral  : 18.868 161.640   1374
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.62 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 14.26 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.33), residues: 635
  helix:  0.71 (0.38), residues: 192
  sheet: -0.43 (0.45), residues: 134
  loop : -0.51 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 395 
 TYR   0.016   0.002   TYR A  55 
 PHE   0.012   0.001   PHE A 128 
 TRP   0.006   0.001   TRP A 435 
 HIS   0.003   0.001   HIS A 621 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.12 ( 6284)
  covalent geometry    : angle       0.58327 /  0.31 ( 8705)
  hydrogen bonds       : bond        0.05950 /  5.72 (  232)
  hydrogen bonds       : angle       5.68575 /  6.76 (  613)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 81
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7742 (mmm) cc_final: 0.7328 (mmm)
REVERT: A  400 MET cc_start: 0.5249 (tpt) cc_final: 0.4630 (tpp)
REVERT: A  401 VAL cc_start: 0.7748 (p) cc_final: 0.7441 (p)
REVERT: A  448 ILE cc_start: 0.7286 (mt) cc_final: 0.6896 (mt)
REVERT: A  483 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6841 (ttm)
REVERT: A  847 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.6268 (mt0)
  outliers start: 27
  outliers final: 18
  residues processed: 99
  average time/residue: 0.0848
  time to fit residues: 11.1293
Evaluate side-chains
  93 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  160 GLN
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  423 ARG
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  466 HIS
Chi-restraints excluded: chain A residue  483 MET
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  645 MET
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  711 HIS
Chi-restraints excluded: chain A residue  734 THR
Chi-restraints excluded: chain A residue  797 VAL
Chi-restraints excluded: chain A residue  847 GLN
Chi-restraints excluded: chain A residue  854 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 23 optimal weight:    0.0030
   chunk 7 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0010
   chunk 47 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 3 optimal weight:   20.0000
   chunk 43 optimal weight:    4.9990
   overall best weight:    0.9800

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.161576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.130894 restraints weight = 15049.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.134624 restraints weight = 8446.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.136893 restraints weight = 5688.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.138624 restraints weight = 4384.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.139638 restraints weight = 3607.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.4215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6770
moved from start:          0.1097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6284  Z= 0.120
  Angle     :  0.555   6.588   8705  Z= 0.291
  Chirality :  0.041   0.195   1000
  Planarity :  0.004   0.038    971
  Dihedral  : 18.896 162.284   1371
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.62 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 15.49 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.33), residues: 635
  helix:  0.77 (0.38), residues: 191
  sheet: -0.74 (0.43), residues: 131
  loop : -0.57 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 534 
 TYR   0.012   0.001   TYR A 625 
 PHE   0.013   0.001   PHE A 388 
 TRP   0.007   0.001   TRP A 769 
 HIS   0.003   0.001   HIS A 839 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.12 ( 6284)
  covalent geometry    : angle       0.55454 /  0.29 ( 8705)
  hydrogen bonds       : bond        0.05224 /  4.83 (  232)
  hydrogen bonds       : angle       5.39179 /  6.31 (  613)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 74
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7785 (mmm) cc_final: 0.7367 (mmm)
REVERT: A  400 MET cc_start: 0.5133 (tpt) cc_final: 0.4555 (tpp)
REVERT: A  401 VAL cc_start: 0.7727 (p) cc_final: 0.7421 (p)
REVERT: A  483 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6814 (ttm)
REVERT: A  533 LYS cc_start: 0.9225 (mmtt) cc_final: 0.8888 (tppt)
REVERT: A  847 GLN cc_start: 0.6781 (OUTLIER) cc_final: 0.6325 (mt0)
  outliers start: 33
  outliers final: 22
  residues processed: 98
  average time/residue: 0.0780
  time to fit residues: 10.4090
Evaluate side-chains
  96 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  466 HIS
Chi-restraints excluded: chain A residue  483 MET
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  645 MET
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  711 HIS
Chi-restraints excluded: chain A residue  734 THR
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  797 VAL
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  847 GLN
Chi-restraints excluded: chain A residue  854 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 3 optimal weight:   20.0000
   chunk 5 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 61 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 44 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.160096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.129278 restraints weight = 15142.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.133067 restraints weight = 8506.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.135443 restraints weight = 5689.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.137010 restraints weight = 4338.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.138106 restraints weight = 3603.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.4194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6807
moved from start:          0.1267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6284  Z= 0.141
  Angle     :  0.571   5.871   8705  Z= 0.301
  Chirality :  0.042   0.192   1000
  Planarity :  0.004   0.039    971
  Dihedral  : 18.838 162.527   1364
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 16.37 %
    Favored  : 78.35 %
  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 are not related in a simple way.
  whole: -0.53 (0.33), residues: 635
  helix:  0.77 (0.38), residues: 192
  sheet: -1.09 (0.42), residues: 141
  loop : -0.61 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 207 
 TYR   0.012   0.001   TYR A 698 
 PHE   0.013   0.001   PHE A 388 
 TRP   0.010   0.001   TRP A 769 
 HIS   0.003   0.001   HIS A 621 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.14 ( 6284)
  covalent geometry    : angle       0.57136 /  0.30 ( 8705)
  hydrogen bonds       : bond        0.05167 /  4.77 (  232)
  hydrogen bonds       : angle       5.29285 /  6.23 (  613)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 74
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7897 (mmm) cc_final: 0.7417 (mmm)
REVERT: A  400 MET cc_start: 0.5028 (tpt) cc_final: 0.4719 (tpt)
REVERT: A  483 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6886 (ttm)
REVERT: A  533 LYS cc_start: 0.9176 (mmtt) cc_final: 0.8671 (tppt)
REVERT: A  847 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.6348 (mt0)
  outliers start: 30
  outliers final: 23
  residues processed: 96
  average time/residue: 0.0855
  time to fit residues: 10.8804
Evaluate side-chains
  93 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 68
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  388 PHE
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  466 HIS
Chi-restraints excluded: chain A residue  483 MET
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  645 MET
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  711 HIS
Chi-restraints excluded: chain A residue  734 THR
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  797 VAL
Chi-restraints excluded: chain A residue  799 ILE
Chi-restraints excluded: chain A residue  804 TYR
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  847 GLN
Chi-restraints excluded: chain A residue  854 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   chunk 58 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 9 optimal weight:    8.9990
   chunk 61 optimal weight:    0.8980
   chunk 15 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 216 ASN
** A 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.159983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.129021 restraints weight = 15386.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.132717 restraints weight = 8703.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.135056 restraints weight = 5860.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.136598 restraints weight = 4480.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.137542 restraints weight = 3736.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6826
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6284  Z= 0.133
  Angle     :  0.572   6.705   8705  Z= 0.301
  Chirality :  0.041   0.192   1000
  Planarity :  0.004   0.042    971
  Dihedral  : 18.889 162.079   1362
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  6.51 %
    Allowed  : 16.55 %
    Favored  : 76.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.33), residues: 635
  helix:  0.70 (0.38), residues: 193
  sheet: -1.15 (0.42), residues: 141
  loop : -0.65 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 423 
 TYR   0.016   0.001   TYR A 625 
 PHE   0.013   0.002   PHE A 156 
 TRP   0.009   0.001   TRP A 769 
 HIS   0.003   0.001   HIS A 507 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.13 ( 6284)
  covalent geometry    : angle       0.57209 /  0.30 ( 8705)
  hydrogen bonds       : bond        0.04977 /  4.55 (  232)
  hydrogen bonds       : angle       5.17866 /  6.10 (  613)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 67
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7958 (mmm) cc_final: 0.7427 (mmm)
REVERT: A  400 MET cc_start: 0.4990 (tpt) cc_final: 0.4681 (tpt)
REVERT: A  418 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.7225 (pt)
REVERT: A  483 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6927 (ttm)
REVERT: A  533 LYS cc_start: 0.9176 (mmtt) cc_final: 0.8683 (tppt)
REVERT: A  847 GLN cc_start: 0.6801 (OUTLIER) cc_final: 0.6337 (mt0)
  outliers start: 37
  outliers final: 25
  residues processed: 94
  average time/residue: 0.0835
  time to fit residues: 10.3915
Evaluate side-chains
  92 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 64
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  388 PHE
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  466 HIS
Chi-restraints excluded: chain A residue  483 MET
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  645 MET
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  711 HIS
Chi-restraints excluded: chain A residue  734 THR
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  741 THR
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  797 VAL
Chi-restraints excluded: chain A residue  804 TYR
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  847 GLN
Chi-restraints excluded: chain A residue  854 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 37 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.160682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.130011 restraints weight = 15128.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.133646 restraints weight = 8526.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.135993 restraints weight = 5761.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.137618 restraints weight = 4408.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.138484 restraints weight = 3665.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6798
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6284  Z= 0.117
  Angle     :  0.575   6.959   8705  Z= 0.299
  Chirality :  0.041   0.191   1000
  Planarity :  0.004   0.039    971
  Dihedral  : 18.884 161.972   1362
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 18.84 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.33), residues: 635
  helix:  0.75 (0.38), residues: 194
  sheet: -1.14 (0.42), residues: 139
  loop : -0.62 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 207 
 TYR   0.013   0.001   TYR A 625 
 PHE   0.014   0.001   PHE A 388 
 TRP   0.007   0.001   TRP A 769 
 HIS   0.002   0.001   HIS A 507 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.12 ( 6284)
  covalent geometry    : angle       0.57478 /  0.30 ( 8705)
  hydrogen bonds       : bond        0.04819 /  4.38 (  232)
  hydrogen bonds       : angle       5.02809 /  5.92 (  613)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 67
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  400 MET cc_start: 0.4952 (tpt) cc_final: 0.4646 (tpt)
REVERT: A  483 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6893 (ttm)
REVERT: A  533 LYS cc_start: 0.9155 (mmtt) cc_final: 0.8648 (tppt)
REVERT: A  847 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.6226 (mt0)
  outliers start: 29
  outliers final: 23
  residues processed: 89
  average time/residue: 0.0895
  time to fit residues: 10.4271
Evaluate side-chains
  90 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 65
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  388 PHE
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  423 ARG
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  466 HIS
Chi-restraints excluded: chain A residue  483 MET
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  645 MET
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  711 HIS
Chi-restraints excluded: chain A residue  734 THR
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  797 VAL
Chi-restraints excluded: chain A residue  799 ILE
Chi-restraints excluded: chain A residue  804 TYR
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  847 GLN
Chi-restraints excluded: chain A residue  854 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 4 optimal weight:    8.9990
   chunk 18 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0670
   chunk 51 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.6718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 216 ASN
** A 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.161410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.130840 restraints weight = 15207.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.134507 restraints weight = 8526.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.136883 restraints weight = 5747.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.138543 restraints weight = 4394.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.139498 restraints weight = 3632.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.4216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6769
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6284  Z= 0.109
  Angle     :  0.584   8.935   8705  Z= 0.298
  Chirality :  0.041   0.191   1000
  Planarity :  0.004   0.037    971
  Dihedral  : 18.865 161.802   1362
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 18.84 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.33), residues: 635
  helix:  0.72 (0.37), residues: 194
  sheet: -1.17 (0.41), residues: 139
  loop : -0.62 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 207 
 TYR   0.013   0.001   TYR A 625 
 PHE   0.019   0.001   PHE A 388 
 TRP   0.007   0.001   TRP A 211 
 HIS   0.002   0.001   HIS A 507 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.11 ( 6284)
  covalent geometry    : angle       0.58394 /  0.30 ( 8705)
  hydrogen bonds       : bond        0.04724 /  4.25 (  232)
  hydrogen bonds       : angle       4.97099 /  5.84 (  613)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 69
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  400 MET cc_start: 0.4915 (tpt) cc_final: 0.4629 (tpt)
REVERT: A  418 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7094 (pt)
REVERT: A  483 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6956 (ttm)
REVERT: A  533 LYS cc_start: 0.9149 (mmtt) cc_final: 0.8665 (tppt)
REVERT: A  847 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.6243 (mt0)
  outliers start: 30
  outliers final: 21
  residues processed: 91
  average time/residue: 0.0637
  time to fit residues: 7.9783
Evaluate side-chains
  90 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 66
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  388 PHE
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  466 HIS
Chi-restraints excluded: chain A residue  483 MET
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  645 MET
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  711 HIS
Chi-restraints excluded: chain A residue  734 THR
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  797 VAL
Chi-restraints excluded: chain A residue  799 ILE
Chi-restraints excluded: chain A residue  804 TYR
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  847 GLN
Chi-restraints excluded: chain A residue  854 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 8 optimal weight:    0.1980
   chunk 27 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0050
   chunk 45 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 14 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9980
   chunk 19 optimal weight:    7.9990
   chunk 38 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.5394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 699 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.161939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.131270 restraints weight = 15103.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.134947 restraints weight = 8629.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.137353 restraints weight = 5854.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.138978 restraints weight = 4460.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.140166 restraints weight = 3697.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.4221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6740
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6284  Z= 0.108
  Angle     :  0.595   8.044   8705  Z= 0.302
  Chirality :  0.041   0.191   1000
  Planarity :  0.004   0.036    971
  Dihedral  : 18.838 161.659   1361
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 19.72 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.33), residues: 635
  helix:  0.83 (0.38), residues: 194
  sheet: -1.14 (0.41), residues: 139
  loop : -0.58 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 207 
 TYR   0.015   0.001   TYR A 625 
 PHE   0.015   0.001   PHE A 505 
 TRP   0.011   0.001   TRP A 211 
 HIS   0.002   0.001   HIS A 788 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.11 ( 6284)
  covalent geometry    : angle       0.59476 /  0.30 ( 8705)
  hydrogen bonds       : bond        0.04656 /  4.19 (  232)
  hydrogen bonds       : angle       4.89357 /  5.72 (  613)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 70
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  400 MET cc_start: 0.4879 (tpt) cc_final: 0.4610 (tpt)
REVERT: A  418 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7063 (pt)
REVERT: A  483 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6905 (ttm)
REVERT: A  533 LYS cc_start: 0.9147 (mmtt) cc_final: 0.8726 (tppt)
REVERT: A  749 TYR cc_start: 0.7948 (m-80) cc_final: 0.7572 (m-10)
REVERT: A  847 GLN cc_start: 0.6807 (OUTLIER) cc_final: 0.6293 (mt0)
  outliers start: 27
  outliers final: 20
  residues processed: 88
  average time/residue: 0.0796
  time to fit residues: 9.0976
Evaluate side-chains
  89 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  388 PHE
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  423 ARG
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  466 HIS
Chi-restraints excluded: chain A residue  483 MET
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  645 MET
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  711 HIS
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  797 VAL
Chi-restraints excluded: chain A residue  799 ILE
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  847 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 38 optimal weight:    0.4980
   chunk 54 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0000
   chunk 52 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.2788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 652 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.160362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.129418 restraints weight = 15155.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.133027 restraints weight = 8631.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.135343 restraints weight = 5862.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.136987 restraints weight = 4512.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.137963 restraints weight = 3751.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.4188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6803
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6284  Z= 0.133
  Angle     :  0.614   9.286   8705  Z= 0.313
  Chirality :  0.042   0.191   1000
  Planarity :  0.004   0.037    971
  Dihedral  : 18.853 161.186   1356
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 19.19 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.33), residues: 635
  helix:  0.73 (0.37), residues: 193
  sheet: -1.26 (0.41), residues: 139
  loop : -0.62 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 207 
 TYR   0.021   0.002   TYR A 529 
 PHE   0.013   0.001   PHE A 388 
 TRP   0.009   0.001   TRP A 769 
 HIS   0.004   0.001   HIS A 849 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.13 ( 6284)
  covalent geometry    : angle       0.61393 /  0.31 ( 8705)
  hydrogen bonds       : bond        0.04848 /  4.43 (  232)
  hydrogen bonds       : angle       4.94800 /  5.75 (  613)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 66
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  400 MET cc_start: 0.5061 (tpt) cc_final: 0.4741 (tpt)
REVERT: A  411 ARG cc_start: 0.4446 (OUTLIER) cc_final: 0.3790 (ptp90)
REVERT: A  483 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6860 (ttm)
REVERT: A  533 LYS cc_start: 0.9139 (mmtt) cc_final: 0.8753 (tppt)
REVERT: A  549 MET cc_start: 0.6591 (tmm) cc_final: 0.6037 (tmm)
REVERT: A  847 GLN cc_start: 0.6791 (OUTLIER) cc_final: 0.6276 (mt0)
  outliers start: 27
  outliers final: 23
  residues processed: 84
  average time/residue: 0.0833
  time to fit residues: 9.2192
Evaluate side-chains
  90 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 64
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  388 PHE
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  411 ARG
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  423 ARG
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  466 HIS
Chi-restraints excluded: chain A residue  483 MET
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  645 MET
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  711 HIS
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  797 VAL
Chi-restraints excluded: chain A residue  799 ILE
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  847 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 61 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.160402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.129397 restraints weight = 15073.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.132953 restraints weight = 8601.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.135260 restraints weight = 5873.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.136855 restraints weight = 4537.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.137762 restraints weight = 3791.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.4192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6799
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6284  Z= 0.129
  Angle     :  0.622  12.445   8705  Z= 0.315
  Chirality :  0.042   0.192   1000
  Planarity :  0.004   0.037    971
  Dihedral  : 18.872 160.637   1356
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 19.54 %
    Favored  : 75.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.33), residues: 635
  helix:  0.75 (0.37), residues: 192
  sheet: -1.24 (0.42), residues: 139
  loop : -0.61 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  28 
 TYR   0.017   0.002   TYR A 749 
 PHE   0.015   0.001   PHE A 388 
 TRP   0.009   0.001   TRP A 211 
 HIS   0.003   0.001   HIS A 849 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.13 ( 6284)
  covalent geometry    : angle       0.62192 /  0.31 ( 8705)
  hydrogen bonds       : bond        0.04823 /  4.40 (  232)
  hydrogen bonds       : angle       4.95461 /  5.73 (  613)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 65
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7538 (mmt) cc_final: 0.7270 (mmm)
REVERT: A  400 MET cc_start: 0.5052 (tpt) cc_final: 0.4776 (tpt)
REVERT: A  411 ARG cc_start: 0.4508 (OUTLIER) cc_final: 0.3852 (ptp90)
REVERT: A  483 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6817 (ttm)
REVERT: A  533 LYS cc_start: 0.9134 (mmtt) cc_final: 0.8768 (tppt)
REVERT: A  847 GLN cc_start: 0.6777 (OUTLIER) cc_final: 0.6264 (mt0)
  outliers start: 27
  outliers final: 23
  residues processed: 84
  average time/residue: 0.0886
  time to fit residues: 9.7677
Evaluate side-chains
  90 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 64
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  388 PHE
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  411 ARG
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  423 ARG
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  466 HIS
Chi-restraints excluded: chain A residue  483 MET
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  645 MET
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  711 HIS
Chi-restraints excluded: chain A residue  734 THR
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  797 VAL
Chi-restraints excluded: chain A residue  799 ILE
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  847 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 3 optimal weight:   20.0000
   chunk 62 optimal weight:    0.0470
   chunk 29 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 44 optimal weight:    8.9990
   chunk 53 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 54 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   overall best weight:    1.3480

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 600 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.159266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.128309 restraints weight = 15075.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.131881 restraints weight = 8671.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.134124 restraints weight = 5902.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.135692 restraints weight = 4579.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.136621 restraints weight = 3835.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.4172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6821
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6284  Z= 0.139
  Angle     :  0.620  11.054   8705  Z= 0.316
  Chirality :  0.042   0.193   1000
  Planarity :  0.004   0.038    971
  Dihedral  : 18.895 159.945   1356
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 15.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 19.19 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.33), residues: 635
  helix:  0.69 (0.37), residues: 192
  sheet: -1.21 (0.43), residues: 137
  loop : -0.65 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 583 
 TYR   0.015   0.002   TYR A 529 
 PHE   0.013   0.002   PHE A 505 
 TRP   0.010   0.001   TRP A 769 
 HIS   0.004   0.001   HIS A 849 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.14 ( 6284)
  covalent geometry    : angle       0.61977 /  0.32 ( 8705)
  hydrogen bonds       : bond        0.04898 /  4.52 (  232)
  hydrogen bonds       : angle       4.96886 /  5.74 (  613)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1528.43 seconds
wall clock time: 27 minutes 8.94 seconds (1628.94 seconds total)