Starting phenix.real_space_refine
on Tue Aug  4 19:05:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yma_73100/08_2026/9yma_73100.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yma_73100/08_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_73100/08_2026/9yma_73100.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yma_73100/08_2026/9yma_73100.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yma_73100/08_2026/9yma_73100.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yma_73100/08_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-2.2rc3-6140/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: 1.34, per 1000 atoms: 0.22
  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: 0.33
  Conformation dependent library (CDL) restraints added in 282.1 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: 0.53
  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: 0.94

  Time building geometry restraints manager: 0.47 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: 8306
        1.25 -     2.50: 282
        2.50 -     3.75: 100
        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: 660
       0.033 -    0.065: 186
       0.065 -    0.098: 72
       0.098 -    0.131: 62
       0.131 -    0.163: 20
  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=" C2'   U B  15 "
            pdb=" C3'   U B  15 "
            pdb=" O2'   U B  15 "
            pdb=" C1'   U B  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.77    0.15 2.00e-01 2.50e+01 5.74e-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
  ... (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:             12.990
  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:          0.280
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.540
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.120
-------------------------------------------------------------------------------
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= 0.157
  Angle     :  0.610   6.256   8705  Z= 0.424
  Chirality :  0.048   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        0.00267 /  0.16 ( 6284)
  covalent geometry    : angle       0.61003 /  0.42 ( 8705)
  hydrogen bonds       : bond        0.20401 / 22.85 (  232)
  hydrogen bonds       : angle       7.25170 /  9.28 (  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  : 0.177 
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: 0.0639
  time to fit residues: 8.8599
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  : 0.175 
-------------------------------------------------------------------------------
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 = 0.4520 r_free = 0.4520 target = 0.162684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.132134 restraints weight = 15002.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.135965 restraints weight = 8391.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.138397 restraints weight = 5606.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.139945 restraints weight = 4268.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.141041 restraints weight = 3554.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.4228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6737
moved from start:          0.0829

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= 0.125
  Angle     :  0.596   6.980   8705  Z= 0.312
  Chirality :  0.042   0.222   1000
  Planarity :  0.005   0.044    971
  Dihedral  : 18.750 157.294   1374
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 11.87
  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: -0.25 (0.33), residues: 635
  helix:  0.72 (0.38), residues: 193
  sheet: -0.43 (0.45), residues: 134
  loop : -0.52 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 534 
 TYR   0.017   0.002   TYR A  55 
 PHE   0.013   0.001   PHE A 128 
 TRP   0.006   0.001   TRP A 435 
 HIS   0.003   0.001   HIS A 839 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.13 ( 6284)
  covalent geometry    : angle       0.59562 /  0.31 ( 8705)
  hydrogen bonds       : bond        0.05988 /  6.07 (  232)
  hydrogen bonds       : angle       5.69330 /  7.08 (  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  : 0.128 
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: 0.7697 (mmm) cc_final: 0.7308 (mmm)
REVERT: A  400 MET cc_start: 0.5219 (tpt) cc_final: 0.4604 (tpp)
REVERT: A  401 VAL cc_start: 0.7728 (p) cc_final: 0.7423 (p)
REVERT: A  448 ILE cc_start: 0.7284 (mt) cc_final: 0.6886 (mt)
REVERT: A  483 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6849 (ttm)
REVERT: A  847 GLN cc_start: 0.6741 (OUTLIER) cc_final: 0.6263 (mt0)
  outliers start: 27
  outliers final: 18
  residues processed: 99
  average time/residue: 0.0583
  time to fit residues: 7.6931
Evaluate side-chains
  94 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 7 optimal weight:   20.0000
   chunk 35 optimal weight:    3.9990
   chunk 47 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 42 optimal weight:    5.9990
   chunk 67 optimal weight:    4.9990
   chunk 3 optimal weight:   20.0000
   chunk 43 optimal weight:    0.7980
   overall best weight:    2.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 600 HIS
** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 807 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.156807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.126135 restraints weight = 15155.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.129698 restraints weight = 8567.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.131990 restraints weight = 5829.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.133391 restraints weight = 4472.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.134553 restraints weight = 3768.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6900
moved from start:          0.1289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6284  Z= 0.194
  Angle     :  0.629   6.078   8705  Z= 0.330
  Chirality :  0.044   0.221   1000
  Planarity :  0.005   0.040    971
  Dihedral  : 18.911 154.834   1371
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.41 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  6.34 %
    Allowed  : 14.79 %
    Favored  : 78.87 %
  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: -0.73 (0.33), residues: 635
  helix:  0.62 (0.38), residues: 192
  sheet: -1.17 (0.42), residues: 138
  loop : -0.77 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 534 
 TYR   0.014   0.002   TYR A 698 
 PHE   0.013   0.002   PHE A  44 
 TRP   0.014   0.002   TRP A 769 
 HIS   0.005   0.001   HIS A 839 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00413 /  0.19 ( 6284)
  covalent geometry    : angle       0.62935 /  0.33 ( 8705)
  hydrogen bonds       : bond        0.06181 /  6.19 (  232)
  hydrogen bonds       : angle       5.62467 /  6.87 (  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: 36
    poor density    : 71
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7819 (mmm) cc_final: 0.7396 (mmm)
REVERT: A  400 MET cc_start: 0.5297 (tpt) cc_final: 0.4985 (tpt)
REVERT: A  418 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7438 (pt)
REVERT: A  483 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6990 (ttm)
REVERT: A  533 LYS cc_start: 0.9233 (mmtt) cc_final: 0.8953 (tppt)
REVERT: A  847 GLN cc_start: 0.6780 (OUTLIER) cc_final: 0.6297 (mt0)
  outliers start: 36
  outliers final: 27
  residues processed: 96
  average time/residue: 0.0584
  time to fit residues: 7.6281
Evaluate side-chains
  95 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 65
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
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  219 VAL
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  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  598 VAL
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 3 optimal weight:   30.0000
   chunk 5 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 13 optimal weight:   20.0000
   chunk 53 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 44 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 4 optimal weight:    9.9990
   overall best weight:    0.9186

-------------------------------------------------------------------------------
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 = 0.4488 r_free = 0.4488 target = 0.159896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.129085 restraints weight = 15225.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.132715 restraints weight = 8596.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.135035 restraints weight = 5802.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.136574 restraints weight = 4447.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.137496 restraints weight = 3707.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6820
moved from start:          0.1398

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= 0.119
  Angle     :  0.585   5.807   8705  Z= 0.302
  Chirality :  0.042   0.226   1000
  Planarity :  0.004   0.040    971
  Dihedral  : 18.901 153.509   1371
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.62 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 18.13 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.33), residues: 635
  helix:  0.60 (0.38), residues: 193
  sheet: -1.09 (0.42), residues: 137
  loop : -0.68 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 207 
 TYR   0.017   0.001   TYR A 625 
 PHE   0.016   0.002   PHE A 388 
 TRP   0.007   0.001   TRP A 769 
 HIS   0.006   0.001   HIS A 621 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.12 ( 6284)
  covalent geometry    : angle       0.58451 /  0.30 ( 8705)
  hydrogen bonds       : bond        0.05214 /  5.14 (  232)
  hydrogen bonds       : angle       5.33657 /  6.62 (  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
  101 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 70
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7909 (mmm) cc_final: 0.7457 (mmm)
REVERT: A  400 MET cc_start: 0.5108 (tpt) cc_final: 0.4796 (tpt)
REVERT: A  533 LYS cc_start: 0.9160 (mmtt) cc_final: 0.8878 (tppt)
REVERT: A  847 GLN cc_start: 0.6833 (OUTLIER) cc_final: 0.6349 (mt0)
  outliers start: 31
  outliers final: 23
  residues processed: 93
  average time/residue: 0.0675
  time to fit residues: 8.3068
Evaluate side-chains
  91 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 67
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
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  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  429 THR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  466 HIS
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  538 THR
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  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:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.4483 r_free = 0.4483 target = 0.159425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.128564 restraints weight = 15396.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.132248 restraints weight = 8658.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.134415 restraints weight = 5827.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.136021 restraints weight = 4514.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.137013 restraints weight = 3752.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.4180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6833
moved from start:          0.1559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6284  Z= 0.128
  Angle     :  0.581   6.156   8705  Z= 0.301
  Chirality :  0.041   0.222   1000
  Planarity :  0.004   0.040    971
  Dihedral  : 18.777 152.150   1361
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 17.08 %
    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: -0.71 (0.33), residues: 635
  helix:  0.59 (0.38), residues: 193
  sheet: -1.24 (0.41), residues: 139
  loop : -0.67 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 423 
 TYR   0.015   0.001   TYR A 625 
 PHE   0.017   0.002   PHE A 388 
 TRP   0.008   0.001   TRP A 769 
 HIS   0.002   0.001   HIS A 507 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.13 ( 6284)
  covalent geometry    : angle       0.58050 /  0.30 ( 8705)
  hydrogen bonds       : bond        0.05225 /  5.15 (  232)
  hydrogen bonds       : angle       5.22134 /  6.48 (  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
  102 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 68
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 MET cc_start: 0.7966 (mmm) cc_final: 0.7456 (mmm)
REVERT: A  400 MET cc_start: 0.5026 (tpt) cc_final: 0.4703 (tpt)
REVERT: A  533 LYS cc_start: 0.9163 (mmtt) cc_final: 0.8668 (tppt)
REVERT: A  847 GLN cc_start: 0.6843 (OUTLIER) cc_final: 0.6388 (mt0)
  outliers start: 34
  outliers final: 24
  residues processed: 94
  average time/residue: 0.0647
  time to fit residues: 8.1803
Evaluate side-chains
  91 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 66
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
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  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  429 THR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  466 HIS
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  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:    7.9990
   chunk 33 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 60 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    1.3582

-------------------------------------------------------------------------------
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 = 0.4476 r_free = 0.4476 target = 0.158612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.127653 restraints weight = 15123.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.131354 restraints weight = 8475.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.133659 restraints weight = 5671.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.135271 restraints weight = 4341.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.136272 restraints weight = 3596.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6829
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6284  Z= 0.137
  Angle     :  0.604   8.657   8705  Z= 0.308
  Chirality :  0.042   0.221   1000
  Planarity :  0.004   0.052    971
  Dihedral  : 18.795 151.107   1361
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 19.19 %
    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: -0.74 (0.33), residues: 635
  helix:  0.56 (0.38), residues: 193
  sheet: -1.29 (0.42), residues: 139
  loop : -0.68 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 423 
 TYR   0.016   0.001   TYR A  55 
 PHE   0.022   0.002   PHE A 388 
 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        0.00300 /  0.14 ( 6284)
  covalent geometry    : angle       0.60390 /  0.31 ( 8705)
  hydrogen bonds       : bond        0.05186 /  5.14 (  232)
  hydrogen bonds       : angle       5.18284 /  6.41 (  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
  100 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 70
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  400 MET cc_start: 0.4990 (tpt) cc_final: 0.4688 (tpt)
REVERT: A  533 LYS cc_start: 0.9159 (mmtt) cc_final: 0.8671 (tppt)
REVERT: A  847 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.6401 (mt0)
  outliers start: 30
  outliers final: 24
  residues processed: 93
  average time/residue: 0.0596
  time to fit residues: 7.4905
Evaluate side-chains
  91 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 66
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
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  429 THR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  466 HIS
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  598 VAL
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  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:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0370
   chunk 20 optimal weight:    6.9990
   chunk 4 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    1.1462

-------------------------------------------------------------------------------
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 = 0.4479 r_free = 0.4479 target = 0.158941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.128279 restraints weight = 15358.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.131845 restraints weight = 8702.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.134186 restraints weight = 5897.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.135729 restraints weight = 4512.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.136616 restraints weight = 3768.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.4174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6828
moved from start:          0.1854

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= 0.129
  Angle     :  0.611   8.309   8705  Z= 0.310
  Chirality :  0.042   0.220   1000
  Planarity :  0.004   0.041    971
  Dihedral  : 18.808 149.775   1359
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 18.66 %
    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: -0.76 (0.33), residues: 635
  helix:  0.53 (0.37), residues: 194
  sheet: -1.29 (0.42), residues: 139
  loop : -0.69 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 658 
 TYR   0.017   0.001   TYR A 625 
 PHE   0.017   0.002   PHE A 388 
 TRP   0.010   0.001   TRP A 211 
 HIS   0.003   0.001   HIS A 507 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.13 ( 6284)
  covalent geometry    : angle       0.61126 /  0.31 ( 8705)
  hydrogen bonds       : bond        0.05101 /  5.02 (  232)
  hydrogen bonds       : angle       5.10966 /  6.33 (  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
  100 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 68
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  400 MET cc_start: 0.5061 (tpt) cc_final: 0.4760 (tpt)
REVERT: A  533 LYS cc_start: 0.9175 (mmtt) cc_final: 0.8728 (tppt)
REVERT: A  847 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.6231 (mt0)
  outliers start: 32
  outliers final: 29
  residues processed: 92
  average time/residue: 0.0608
  time to fit residues: 7.4816
Evaluate side-chains
  97 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 67
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
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  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  434 VAL
Chi-restraints excluded: chain A residue  466 HIS
Chi-restraints excluded: chain A residue  470 PHE
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  598 VAL
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 8 optimal weight:    0.1980
   chunk 27 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0670
   chunk 61 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    0.5718

-------------------------------------------------------------------------------
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 = 0.4504 r_free = 0.4504 target = 0.161029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.130539 restraints weight = 15155.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.134091 restraints weight = 8624.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.136324 restraints weight = 5871.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.137974 restraints weight = 4542.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.138784 restraints weight = 3772.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.4203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6772
moved from start:          0.1984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6284  Z= 0.108
  Angle     :  0.596   7.495   8705  Z= 0.302
  Chirality :  0.042   0.221   1000
  Planarity :  0.004   0.039    971
  Dihedral  : 18.773 148.482   1358
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 19.19 %
    Favored  : 75.00 %
  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: -0.67 (0.33), residues: 635
  helix:  0.63 (0.37), residues: 194
  sheet: -1.19 (0.42), residues: 139
  loop : -0.68 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 207 
 TYR   0.015   0.001   TYR A 625 
 PHE   0.015   0.001   PHE A 388 
 TRP   0.010   0.001   TRP A 211 
 HIS   0.002   0.001   HIS A 507 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00230 /  0.11 ( 6284)
  covalent geometry    : angle       0.59582 /  0.30 ( 8705)
  hydrogen bonds       : bond        0.04829 /  4.69 (  232)
  hydrogen bonds       : angle       4.97579 /  6.11 (  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
  102 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 69
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 MET cc_start: 0.6205 (ttm) cc_final: 0.5903 (ttm)
REVERT: A  400 MET cc_start: 0.5002 (tpt) cc_final: 0.4723 (tpt)
REVERT: A  411 ARG cc_start: 0.4356 (OUTLIER) cc_final: 0.3718 (ptp90)
REVERT: A  533 LYS cc_start: 0.9162 (mmtt) cc_final: 0.8754 (tppt)
REVERT: A  812 ARG cc_start: 0.8346 (tpp80) cc_final: 0.7884 (tpp80)
REVERT: A  847 GLN cc_start: 0.6819 (OUTLIER) cc_final: 0.6307 (mt0)
  outliers start: 33
  outliers final: 26
  residues processed: 93
  average time/residue: 0.0705
  time to fit residues: 8.5190
Evaluate side-chains
  93 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 65
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 PHE
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  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  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  501 VAL
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
Chi-restraints excluded: chain A residue  854 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 43 optimal weight:    0.4980
   chunk 18 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 25 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 = 0.160882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.130259 restraints weight = 15251.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.133809 restraints weight = 8699.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.136075 restraints weight = 5913.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.137622 restraints weight = 4563.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.138525 restraints weight = 3819.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.4199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6776
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6284  Z= 0.113
  Angle     :  0.614   8.804   8705  Z= 0.306
  Chirality :  0.042   0.220   1000
  Planarity :  0.004   0.036    971
  Dihedral  : 18.749 148.053   1358
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 19.89 %
    Favored  : 75.00 %
  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: -0.64 (0.33), residues: 635
  helix:  0.71 (0.37), residues: 194
  sheet: -1.23 (0.41), residues: 139
  loop : -0.66 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  28 
 TYR   0.021   0.002   TYR A 529 
 PHE   0.014   0.001   PHE A 388 
 TRP   0.008   0.001   TRP A 211 
 HIS   0.002   0.001   HIS A 144 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.11 ( 6284)
  covalent geometry    : angle       0.61395 /  0.31 ( 8705)
  hydrogen bonds       : bond        0.04895 /  4.84 (  232)
  hydrogen bonds       : angle       5.00927 /  6.12 (  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
  95 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 66
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  400 MET cc_start: 0.5029 (tpt) cc_final: 0.4737 (tpt)
REVERT: A  411 ARG cc_start: 0.4438 (OUTLIER) cc_final: 0.3789 (ptp90)
REVERT: A  533 LYS cc_start: 0.9126 (mmtt) cc_final: 0.8789 (tppt)
REVERT: A  549 MET cc_start: 0.6468 (tmm) cc_final: 0.6026 (tpt)
REVERT: A  847 GLN cc_start: 0.6805 (OUTLIER) cc_final: 0.6303 (mt0)
  outliers start: 29
  outliers final: 23
  residues processed: 87
  average time/residue: 0.0835
  time to fit residues: 9.5879
Evaluate side-chains
  89 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 64
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
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  501 VAL
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 61 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0030
   chunk 66 optimal weight:    8.9990
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.6190

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 652 GLN
** A 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 816 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.161125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.130646 restraints weight = 15090.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.134240 restraints weight = 8577.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.136561 restraints weight = 5841.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.137912 restraints weight = 4491.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.139103 restraints weight = 3806.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6760
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6284  Z= 0.110
  Angle     :  0.618   9.718   8705  Z= 0.310
  Chirality :  0.042   0.220   1000
  Planarity :  0.005   0.086    971
  Dihedral  : 18.730 147.962   1354
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 21.13 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.64 (0.33), residues: 635
  helix:  0.74 (0.37), residues: 194
  sheet: -1.27 (0.41), residues: 139
  loop : -0.67 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 207 
 TYR   0.017   0.002   TYR A 529 
 PHE   0.014   0.001   PHE A 388 
 TRP   0.005   0.001   TRP A 211 
 HIS   0.002   0.000   HIS A 507 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.11 ( 6284)
  covalent geometry    : angle       0.61841 /  0.31 ( 8705)
  hydrogen bonds       : bond        0.04879 /  4.81 (  232)
  hydrogen bonds       : angle       4.96216 /  6.07 (  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
  93 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 68
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  400 MET cc_start: 0.5016 (tpt) cc_final: 0.4748 (tpt)
REVERT: A  411 ARG cc_start: 0.4406 (OUTLIER) cc_final: 0.3755 (ptp90)
REVERT: A  533 LYS cc_start: 0.9121 (mmtt) cc_final: 0.8684 (tppt)
REVERT: A  549 MET cc_start: 0.6432 (tmm) cc_final: 0.6006 (tpt)
REVERT: A  749 TYR cc_start: 0.7876 (m-80) cc_final: 0.7619 (m-10)
REVERT: A  847 GLN cc_start: 0.6809 (OUTLIER) cc_final: 0.6325 (mt0)
  outliers start: 25
  outliers final: 23
  residues processed: 86
  average time/residue: 0.0685
  time to fit residues: 7.6367
Evaluate side-chains
  92 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 67
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
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  207 ARG
Chi-restraints excluded: chain A residue  215 LEU
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  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  501 VAL
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  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:   30.0000
   chunk 62 optimal weight:    0.5980
   chunk 29 optimal weight:    3.9990
   chunk 21 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4492 r_free = 0.4492 target = 0.160458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.130210 restraints weight = 15013.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.133767 restraints weight = 8565.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.136054 restraints weight = 5824.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.137445 restraints weight = 4485.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.138542 restraints weight = 3797.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.4197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6771
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6284  Z= 0.115
  Angle     :  0.624  13.989   8705  Z= 0.311
  Chirality :  0.042   0.220   1000
  Planarity :  0.005   0.069    971
  Dihedral  : 18.723 148.254   1353
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 20.42 %
    Favored  : 75.00 %
  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:  0.84 (0.38), residues: 193
  sheet: -1.32 (0.40), residues: 139
  loop : -0.70 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 207 
 TYR   0.016   0.002   TYR A 529 
 PHE   0.013   0.001   PHE A 388 
 TRP   0.011   0.001   TRP A 211 
 HIS   0.002   0.001   HIS A 507 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.11 ( 6284)
  covalent geometry    : angle       0.62404 /  0.31 ( 8705)
  hydrogen bonds       : bond        0.04854 /  4.84 (  232)
  hydrogen bonds       : angle       4.92173 /  6.00 (  613)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1298.60 seconds
wall clock time: 22 minutes 58.00 seconds (1378.00 seconds total)