Starting phenix.real_space_refine
on Wed Feb  4 04:48:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jfs_61438/02_2026/9jfs_61438.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jfs_61438/02_2026/9jfs_61438.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jfs_61438/02_2026/9jfs_61438.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jfs_61438/02_2026/9jfs_61438.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jfs_61438/02_2026/9jfs_61438.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jfs_61438/02_2026/9jfs_61438.cif"
  }
  resolution = 2.67
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     175      5.49       5
     S      17      5.16       5
     C    4904      2.51       5
     N    1579      2.21       5
     O    2121      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8796
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4285
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 529, 4285
          Classifications: {'peptide': 529}
          Link IDs: {'PTRANS': 21, 'TRANS': 507}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 2938
          Classifications: {'RNA': 138}
          Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 64, 'rna3p_pyr': 60}
          Link IDs: {'rna2p': 14, 'rna3p': 123}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 546
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 546
          Classifications: {'DNA': 26}
          Link IDs: {'rna3p': 25}
    Chain: "D"
      Number of atoms: 225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 225
          Classifications: {'DNA': 11}
          Link IDs: {'rna3p': 10}
    Chain: "E"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 802
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99}
  Time building chain proxies: 1.94, per 1000 atoms: 0.22
  Number of scatterers: 8796
  At special positions: 0
  Unit cell: (108.992, 101.504, 123.968, 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      17     16.00
     P     175     15.00
     O    2121      8.00
     N    1579      7.00
     C    4904      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 550 " - pdb=" SG  CYS A 567 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  33 " - pdb=" SG  CYS E  36 " distance=2.03

  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: 0.73
  Conformation dependent library (CDL) restraints added in 208.5 milliseconds
  

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1198

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 5 sheets defined
      52.2% alpha, 11.4% beta
      68 base pairs and 107 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 64
      removed outlier: 4.795A  pdb=" N   CYS A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   VAL A  42 " --> pdb=" O   HIS A  38 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   THR A  43 " --> pdb=" O   ASN A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 79
      removed outlier: 3.779A  pdb=" N   GLN A  70 " --> pdb=" O   LYS A  66 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   GLN A  71 " --> pdb=" O   PRO A  67 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   LEU A  72 " --> pdb=" O   GLU A  68 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   TYR A  77 " --> pdb=" O   VAL A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 96
      removed outlier: 3.610A  pdb=" N   LEU A  92 " --> pdb=" O   LYS A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 101
    Processing helix  chain 'A' and resid 182 through 186
      removed outlier: 3.975A  pdb=" N   PHE A 185 " --> pdb=" O   GLY A 182 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   GLU A 186 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 182 through 186'
    Processing helix  chain 'A' and resid 192 through 197
    Processing helix  chain 'A' and resid 198 through 209
    Processing helix  chain 'A' and resid 217 through 237
      removed outlier: 3.554A  pdb=" N   ILE A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 295
    Processing helix  chain 'A' and resid 323 through 332
    Processing helix  chain 'A' and resid 333 through 341
    Processing helix  chain 'A' and resid 345 through 365
    Processing helix  chain 'A' and resid 396 through 428
      removed outlier: 4.311A  pdb=" N   GLU A 400 " --> pdb=" O   ASN A 396 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ARG A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL A 402 " --> pdb=" O   THR A 398 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLY A 428 " --> pdb=" O   TRP A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 472
    Processing helix  chain 'A' and resid 480 through 485
      removed outlier: 4.284A  pdb=" N   ASN A 483 " --> pdb=" O   THR A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 516
    Processing helix  chain 'A' and resid 519 through 535
    Processing helix  chain 'A' and resid 581 through 593
    Processing helix  chain 'E' and resid 12 through 18
    Processing helix  chain 'E' and resid 33 through 50
      removed outlier: 3.857A  pdb=" N   LYS E  37 " --> pdb=" O   CYS E  33 " (cutoff:3.500A)
      Proline residue:  E  41  - end of helix
      removed outlier: 3.621A  pdb=" N   ASP E  48 " --> pdb=" O   ASP E  44 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 66 through 71
      removed outlier: 3.964A  pdb=" N   LYS E  70 " --> pdb=" O   GLY E  66 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   TYR E  71 " --> pdb=" O   THR E  67 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 66 through 71'
    Processing helix  chain 'E' and resid 96 through 108
    Processing sheet with id=AA1, first strand: chain 'A' and resid 257 through 260
      removed outlier: 6.603A  pdb=" N   ALA A 320 " --> pdb=" O   PRO A 301 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   THR A 303 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   TYR A 313 " --> pdb=" O   ILE A   8 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   THR A 284 " --> pdb=" O   LYS A   9 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 128
    Processing sheet with id=AA3, first strand: chain 'A' and resid 392 through 393
      removed outlier: 3.914A  pdb=" N   VAL A 385 " --> pdb=" O   PHE A 393 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   ILE A 475 " --> pdb=" O   HIS A 539 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 564 through 565
    Processing sheet with id=AA5, first strand: chain 'E' and resid 6 through 7
      removed outlier: 6.494A  pdb=" N   ILE E   6 " --> pdb=" O   LYS E  58 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   ASN E  60 " --> pdb=" O   ILE E   6 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   LEU E  25 " --> pdb=" O   ALA E  57 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   LEU E  59 " --> pdb=" O   LEU E  25 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   ASP E  27 " --> pdb=" O   LEU E  59 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR E  78 " --> pdb=" O   PHE E  28 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   LEU E  79 " --> pdb=" O   THR E  90 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   THR E  90 " --> pdb=" O   LEU E  79 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   LEU E  81 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLU E  86 " --> pdb=" O   LYS E  83 " (cutoff:3.500A)

    266 hydrogen bonds defined for protein.
    753 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      170 hydrogen bonds
      332 hydrogen bond angles
      0 basepair planarities
      68 basepair parallelities
      107 stacking parallelities
  Total time for adding SS restraints: 1.64

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2142
        1.33 -     1.46: 2831
        1.46 -     1.58: 3998
        1.58 -     1.70: 344
        1.70 -     1.82: 22
  Bond restraints: 9337
  Sorted by residual:
  bond pdb=" N   LYS E   4 "
       pdb=" CA  LYS E   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.93e+00
  bond pdb=" N   MET A   1 "
       pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.028 1.90e-02 2.77e+03 2.19e+00
  bond pdb=" C4    C B 180 "
       pdb=" C5    C B 180 "
    ideal  model  delta    sigma   weight residual
    1.425  1.405  0.020 2.00e-02 2.50e+03 1.02e+00
  bond pdb=" C4'  DA C  12 "
       pdb=" C3'  DA C  12 "
    ideal  model  delta    sigma   weight residual
    1.523  1.503  0.020 2.00e-02 2.50e+03 9.67e-01
  bond pdb=" C2'  DT D   8 "
       pdb=" C1'  DT D   8 "
    ideal  model  delta    sigma   weight residual
    1.525  1.507  0.018 2.00e-02 2.50e+03 7.97e-01
  ... (remaining 9332 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.02: 12665
        1.02 -     2.04: 634
        2.04 -     3.06: 102
        3.06 -     4.07: 34
        4.07 -     5.09: 3
  Bond angle restraints: 13438
  Sorted by residual:
  angle pdb=" C2'   U B   8 "
        pdb=" C1'   U B   8 "
        pdb=" N1    U B   8 "
      ideal   model   delta    sigma   weight residual
     112.00  115.84   -3.84 1.50e+00 4.44e-01 6.55e+00
  angle pdb=" C2'   G B 175 "
        pdb=" C1'   G B 175 "
        pdb=" N9    G B 175 "
      ideal   model   delta    sigma   weight residual
     112.00  115.56   -3.56 1.50e+00 4.44e-01 5.64e+00
  angle pdb=" C4'   A B 105 "
        pdb=" C3'   A B 105 "
        pdb=" O3'   A B 105 "
      ideal   model   delta    sigma   weight residual
     109.40  112.72   -3.32 1.50e+00 4.44e-01 4.90e+00
  angle pdb=" C3'   A B 105 "
        pdb=" O3'   A B 105 "
        pdb=" P     U B 106 "
      ideal   model   delta    sigma   weight residual
     120.20  123.46   -3.26 1.50e+00 4.44e-01 4.71e+00
  angle pdb=" C3'  DA C  10 "
        pdb=" C2'  DA C  10 "
        pdb=" C1'  DA C  10 "
      ideal   model   delta    sigma   weight residual
     101.60  104.79   -3.19 1.50e+00 4.44e-01 4.51e+00
  ... (remaining 13433 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.41: 5207
       31.41 -    62.82: 425
       62.82 -    94.23: 79
       94.23 -   125.63: 1
      125.63 -   157.04: 2
  Dihedral angle restraints: 5714
    sinusoidal: 3871
      harmonic: 1843
  Sorted by residual:
  dihedral pdb=" C4'   A B 105 "
           pdb=" C3'   A B 105 "
           pdb=" O3'   A B 105 "
           pdb=" P     U B 106 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -110.00   47.04 -157.04     1      3.50e+01 8.16e-04 1.51e+01
  dihedral pdb=" C4'   U B 181 "
           pdb=" C3'   U B 181 "
           pdb=" O3'   U B 181 "
           pdb=" P     U B 182 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   75.72  144.28     1      3.50e+01 8.16e-04 1.42e+01
  dihedral pdb=" O4'   U B 174 "
           pdb=" C1'   U B 174 "
           pdb=" N1    U B 174 "
           pdb=" C2    U B 174 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -74.00  -54.00     1      1.70e+01 3.46e-03 1.37e+01
  ... (remaining 5711 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1104
       0.036 -    0.072: 403
       0.072 -    0.107: 73
       0.107 -    0.143: 28
       0.143 -    0.179: 5
  Chirality restraints: 1613
  Sorted by residual:
  chirality pdb=" C1'   G B 175 "
            pdb=" O4'   G B 175 "
            pdb=" C2'   G B 175 "
            pdb=" N9    G B 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.28    0.18 2.00e-01 2.50e+01 8.00e-01
  chirality pdb=" C1'   U B   8 "
            pdb=" O4'   U B   8 "
            pdb=" C2'   U B   8 "
            pdb=" N1    U B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.29    0.17 2.00e-01 2.50e+01 7.37e-01
  chirality pdb=" C3'   A B 105 "
            pdb=" C4'   A B 105 "
            pdb=" O3'   A B 105 "
            pdb=" C2'   A B 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.57   -0.17 2.00e-01 2.50e+01 7.27e-01
  ... (remaining 1610 not shown)

  Planarity restraints: 1071
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B 178 "   -0.032 2.00e-02 2.50e+03   1.59e-02 5.71e+00
        pdb=" N1    C B 178 "    0.032 2.00e-02 2.50e+03
        pdb=" C2    C B 178 "    0.003 2.00e-02 2.50e+03
        pdb=" O2    C B 178 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    C B 178 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    C B 178 "   -0.002 2.00e-02 2.50e+03
        pdb=" N4    C B 178 "   -0.011 2.00e-02 2.50e+03
        pdb=" C5    C B 178 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    C B 178 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B 175 "   -0.029 2.00e-02 2.50e+03   1.29e-02 4.98e+00
        pdb=" N9    G B 175 "    0.032 2.00e-02 2.50e+03
        pdb=" C8    G B 175 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    G B 175 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    G B 175 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G B 175 "   -0.002 2.00e-02 2.50e+03
        pdb=" O6    G B 175 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1    G B 175 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    G B 175 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G B 175 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    G B 175 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    G B 175 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B   8 "   -0.027 2.00e-02 2.50e+03   1.48e-02 4.95e+00
        pdb=" N1    U B   8 "    0.034 2.00e-02 2.50e+03
        pdb=" C2    U B   8 "   -0.003 2.00e-02 2.50e+03
        pdb=" O2    U B   8 "    0.006 2.00e-02 2.50e+03
        pdb=" N3    U B   8 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    U B   8 "   -0.003 2.00e-02 2.50e+03
        pdb=" O4    U B   8 "   -0.007 2.00e-02 2.50e+03
        pdb=" C5    U B   8 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    U B   8 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1068 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 35
        2.55 -     3.14: 6494
        3.14 -     3.72: 14522
        3.72 -     4.31: 21297
        4.31 -     4.90: 30731
  Nonbonded interactions: 73079
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 414 "
            pdb=" O2'   U B 185 "
     model   vdw
     1.960 3.040
  nonbonded pdb=" O2'   U B 181 "
            pdb=" O5'   U B 182 "
     model   vdw
     2.129 3.040
  nonbonded pdb=" OE1 GLU A 417 "
            pdb=" NH2 ARG A 433 "
     model   vdw
     2.180 3.120
  nonbonded pdb=" N   ASP E  10 "
            pdb=" OD1 ASN E  64 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" O   GLY A 201 "
            pdb=" OG1 THR A 204 "
     model   vdw
     2.212 3.040
  ... (remaining 73074 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.460
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:7.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
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      :  0.005   0.039   9339  Z= 0.231
  Angle     :  0.532   5.092  13442  Z= 0.299
  Chirality :  0.039   0.179   1613
  Planarity :  0.004   0.032   1071
  Dihedral  : 19.720 157.041   4510
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  2.84 %
    Favored  : 96.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.34), residues: 626
  helix:  2.55 (0.31), residues: 300
  sheet:  0.32 (0.55), residues: 73
  loop : -0.77 (0.36), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 293 
 TYR   0.007   0.001   TYR A 314 
 PHE   0.013   0.002   PHE E  82 
 TRP   0.011   0.002   TRP A  47 
 HIS   0.004   0.001   HIS A  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 9337)
  covalent geometry    : angle       0.53221 (13438)
  SS BOND              : bond        0.00388 (    2)
  SS BOND              : angle       0.83418 (    4)
  hydrogen bonds       : bond        0.10661 (  436)
  hydrogen bonds       : angle       4.15313 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.145 
Fit side-chains
REVERT: A  359 GLU cc_start: 0.7606 (tp30) cc_final: 0.7284 (tp30)
REVERT: A  372 ASP cc_start: 0.7612 (t0) cc_final: 0.7208 (t0)
REVERT: A  382 GLN cc_start: 0.7601 (tt0) cc_final: 0.7390 (tt0)
REVERT: E    8 LEU cc_start: 0.5697 (mp) cc_final: 0.5481 (mp)
  outliers start: 3
  outliers final: 1
  residues processed: 99
  average time/residue: 0.6532
  time to fit residues: 67.9384
Evaluate side-chains
  96 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   33 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 512 ASN
A 569 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.142584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.112299 restraints weight = 12959.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 1.49
r_work: 0.3320 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.1149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.070   9339  Z= 0.419
  Angle     :  0.686   6.753  13442  Z= 0.362
  Chirality :  0.048   0.298   1613
  Planarity :  0.005   0.039   1071
  Dihedral  : 22.344 174.786   3210
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  8.33 %
    Favored  : 90.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.33), residues: 626
  helix:  2.17 (0.30), residues: 303
  sheet:  0.24 (0.55), residues: 73
  loop : -0.75 (0.37), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 206 
 TYR   0.012   0.002   TYR A 314 
 PHE   0.020   0.003   PHE E  82 
 TRP   0.022   0.003   TRP A 424 
 HIS   0.008   0.002   HIS A 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00903 ( 9337)
  covalent geometry    : angle       0.68610 (13438)
  SS BOND              : bond        0.00284 (    2)
  SS BOND              : angle       0.92147 (    4)
  hydrogen bonds       : bond        0.07785 (  436)
  hydrogen bonds       : angle       3.56392 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.2909 (OUTLIER) cc_final: 0.2581 (tt)
REVERT: A  359 GLU cc_start: 0.7734 (tp30) cc_final: 0.7429 (tp30)
REVERT: A  372 ASP cc_start: 0.7652 (t0) cc_final: 0.7290 (t0)
REVERT: A  382 GLN cc_start: 0.7847 (tt0) cc_final: 0.7584 (tt0)
REVERT: A  414 ASP cc_start: 0.8091 (m-30) cc_final: 0.7870 (m-30)
REVERT: A  478 GLU cc_start: 0.6783 (tp30) cc_final: 0.6573 (tp30)
  outliers start: 8
  outliers final: 2
  residues processed: 102
  average time/residue: 0.5930
  time to fit residues: 63.7256
Evaluate side-chains
  102 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  425 LYS
Chi-restraints excluded: chain E residue   33 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0020
   chunk 51 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 75 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 22 optimal weight:    0.2980
   chunk 36 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0670
   overall best weight:    0.3326

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 316 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.148310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.118385 restraints weight = 12998.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.44
r_work: 0.3407 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3285 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.1312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9339  Z= 0.127
  Angle     :  0.487   6.194  13442  Z= 0.264
  Chirality :  0.035   0.211   1613
  Planarity :  0.004   0.037   1071
  Dihedral  : 22.142 163.235   3210
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 10.28 %
    Favored  : 88.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.96 (0.34), residues: 626
  helix:  2.89 (0.30), residues: 303
  sheet:  0.55 (0.58), residues: 73
  loop : -0.52 (0.37), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 267 
 TYR   0.010   0.001   TYR A  45 
 PHE   0.015   0.001   PHE E  82 
 TRP   0.017   0.002   TRP A  47 
 HIS   0.003   0.001   HIS A 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9337)
  covalent geometry    : angle       0.48693 (13438)
  SS BOND              : bond        0.00296 (    2)
  SS BOND              : angle       0.77512 (    4)
  hydrogen bonds       : bond        0.04613 (  436)
  hydrogen bonds       : angle       3.11020 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8262 (ttpp) cc_final: 0.8030 (ttpp)
REVERT: A  269 ASP cc_start: 0.8220 (t0) cc_final: 0.8016 (t70)
REVERT: A  295 ASN cc_start: 0.8477 (t0) cc_final: 0.8232 (t160)
REVERT: A  359 GLU cc_start: 0.7758 (tp30) cc_final: 0.7440 (tp30)
REVERT: A  372 ASP cc_start: 0.7675 (t0) cc_final: 0.7315 (t0)
REVERT: A  382 GLN cc_start: 0.7866 (tt0) cc_final: 0.7598 (tt0)
REVERT: E    8 LEU cc_start: 0.5932 (mp) cc_final: 0.5675 (mp)
  outliers start: 7
  outliers final: 3
  residues processed: 105
  average time/residue: 0.6093
  time to fit residues: 67.5869
Evaluate side-chains
  99 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain E residue   33 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 72 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0570
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 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 = 0.3890 r_free = 0.3890 target = 0.146323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.116196 restraints weight = 13056.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 1.44
r_work: 0.3376 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9339  Z= 0.188
  Angle     :  0.517   5.604  13442  Z= 0.279
  Chirality :  0.037   0.238   1613
  Planarity :  0.004   0.038   1071
  Dihedral  : 22.149 168.494   3210
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 11.70 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.98 (0.34), residues: 626
  helix:  2.91 (0.30), residues: 303
  sheet:  0.55 (0.58), residues: 73
  loop : -0.50 (0.37), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 206 
 TYR   0.010   0.001   TYR A 304 
 PHE   0.013   0.002   PHE E  82 
 TRP   0.014   0.002   TRP A 424 
 HIS   0.004   0.001   HIS A 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 9337)
  covalent geometry    : angle       0.51715 (13438)
  SS BOND              : bond        0.00280 (    2)
  SS BOND              : angle       0.80747 (    4)
  hydrogen bonds       : bond        0.05366 (  436)
  hydrogen bonds       : angle       3.13070 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8285 (ttpp) cc_final: 0.8039 (ttpp)
REVERT: A  359 GLU cc_start: 0.7806 (tp30) cc_final: 0.7492 (tp30)
REVERT: A  372 ASP cc_start: 0.7655 (t0) cc_final: 0.7386 (t0)
REVERT: A  382 GLN cc_start: 0.7860 (tt0) cc_final: 0.7597 (tt0)
REVERT: A  433 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8071 (ttp-110)
REVERT: E    8 LEU cc_start: 0.5980 (mp) cc_final: 0.5708 (mp)
  outliers start: 11
  outliers final: 6
  residues processed: 107
  average time/residue: 0.5579
  time to fit residues: 63.0553
Evaluate side-chains
  106 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  374 SER
Chi-restraints excluded: chain A residue  433 ARG
Chi-restraints excluded: chain E residue   33 CYS
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue  100 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 72 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 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 = 0.3880 r_free = 0.3880 target = 0.145717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.115612 restraints weight = 12989.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 1.43
r_work: 0.3372 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.1391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   9339  Z= 0.212
  Angle     :  0.528   5.656  13442  Z= 0.284
  Chirality :  0.038   0.241   1613
  Planarity :  0.004   0.038   1071
  Dihedral  : 22.144 168.276   3210
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.23 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.34), residues: 626
  helix:  2.86 (0.30), residues: 303
  sheet:  0.52 (0.59), residues: 73
  loop : -0.47 (0.38), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 206 
 TYR   0.011   0.001   TYR A 314 
 PHE   0.013   0.002   PHE E  82 
 TRP   0.018   0.002   TRP A 424 
 HIS   0.004   0.001   HIS A 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 9337)
  covalent geometry    : angle       0.52810 (13438)
  SS BOND              : bond        0.00281 (    2)
  SS BOND              : angle       0.82289 (    4)
  hydrogen bonds       : bond        0.05600 (  436)
  hydrogen bonds       : angle       3.14297 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8292 (ttpp) cc_final: 0.8051 (ttpp)
REVERT: A  359 GLU cc_start: 0.7810 (tp30) cc_final: 0.7502 (tp30)
REVERT: A  372 ASP cc_start: 0.7654 (t0) cc_final: 0.7288 (t0)
REVERT: A  382 GLN cc_start: 0.7856 (tt0) cc_final: 0.7600 (tt0)
REVERT: A  414 ASP cc_start: 0.8112 (m-30) cc_final: 0.7719 (m-30)
REVERT: A  417 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7343 (mm-30)
REVERT: A  433 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7629 (ttp-110)
  outliers start: 13
  outliers final: 8
  residues processed: 105
  average time/residue: 0.6117
  time to fit residues: 67.8899
Evaluate side-chains
  106 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ASP
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  374 SER
Chi-restraints excluded: chain A residue  433 ARG
Chi-restraints excluded: chain E residue   33 CYS
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue  100 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 25 optimal weight:    0.0870
   chunk 38 optimal weight:    0.0000
   chunk 53 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0870
   chunk 23 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 50 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.3340

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 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 = 0.3905 r_free = 0.3905 target = 0.147702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.117759 restraints weight = 13064.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 1.44
r_work: 0.3400 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9339  Z= 0.127
  Angle     :  0.488   5.694  13442  Z= 0.264
  Chirality :  0.034   0.220   1613
  Planarity :  0.004   0.037   1071
  Dihedral  : 22.140 166.424   3210
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 12.94 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  2.20 (0.34), residues: 626
  helix:  3.08 (0.30), residues: 303
  sheet:  0.52 (0.55), residues: 79
  loop : -0.35 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 267 
 TYR   0.012   0.001   TYR A  45 
 PHE   0.011   0.001   PHE A 228 
 TRP   0.013   0.001   TRP A  47 
 HIS   0.003   0.001   HIS A 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 9337)
  covalent geometry    : angle       0.48765 (13438)
  SS BOND              : bond        0.00260 (    2)
  SS BOND              : angle       0.79376 (    4)
  hydrogen bonds       : bond        0.04709 (  436)
  hydrogen bonds       : angle       3.03927 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8253 (ttpp) cc_final: 0.8015 (ttpp)
REVERT: A  295 ASN cc_start: 0.8479 (t0) cc_final: 0.8222 (t160)
REVERT: A  359 GLU cc_start: 0.7785 (tp30) cc_final: 0.7487 (tp30)
REVERT: A  372 ASP cc_start: 0.7632 (t0) cc_final: 0.7264 (t0)
REVERT: A  382 GLN cc_start: 0.7844 (tt0) cc_final: 0.7596 (tt0)
REVERT: A  414 ASP cc_start: 0.8124 (m-30) cc_final: 0.7715 (m-30)
REVERT: A  417 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7391 (mm-30)
REVERT: A  433 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7703 (ttp-110)
  outliers start: 12
  outliers final: 8
  residues processed: 102
  average time/residue: 0.5586
  time to fit residues: 60.2795
Evaluate side-chains
  102 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ASP
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain A residue  433 ARG
Chi-restraints excluded: chain E residue    6 ILE
Chi-restraints excluded: chain E residue   33 CYS
Chi-restraints excluded: chain E residue  100 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 18 optimal weight:    0.3980
   chunk 55 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 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 = 0.3857 r_free = 0.3857 target = 0.143764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.113543 restraints weight = 12975.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.45
r_work: 0.3343 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   9339  Z= 0.316
  Angle     :  0.598   6.252  13442  Z= 0.318
  Chirality :  0.042   0.266   1613
  Planarity :  0.004   0.038   1071
  Dihedral  : 22.213 170.681   3210
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 12.41 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.34), residues: 626
  helix:  2.74 (0.30), residues: 301
  sheet:  0.26 (0.56), residues: 73
  loop : -0.50 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 206 
 TYR   0.019   0.002   TYR A  45 
 PHE   0.015   0.002   PHE E  82 
 TRP   0.023   0.002   TRP A 424 
 HIS   0.006   0.002   HIS A 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00680 ( 9337)
  covalent geometry    : angle       0.59830 (13438)
  SS BOND              : bond        0.00262 (    2)
  SS BOND              : angle       0.82992 (    4)
  hydrogen bonds       : bond        0.06711 (  436)
  hydrogen bonds       : angle       3.26197 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  359 GLU cc_start: 0.7794 (tp30) cc_final: 0.7479 (tp30)
REVERT: A  372 ASP cc_start: 0.7653 (t0) cc_final: 0.7407 (t0)
REVERT: A  382 GLN cc_start: 0.7841 (tt0) cc_final: 0.7596 (tt0)
REVERT: A  414 ASP cc_start: 0.8145 (m-30) cc_final: 0.7793 (m-30)
REVERT: A  417 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7237 (mm-30)
REVERT: A  433 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7504 (ttp-110)
  outliers start: 16
  outliers final: 9
  residues processed: 107
  average time/residue: 0.6164
  time to fit residues: 69.6473
Evaluate side-chains
  108 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 THR
Chi-restraints excluded: chain A residue   13 ASP
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  374 SER
Chi-restraints excluded: chain A residue  433 ARG
Chi-restraints excluded: chain E residue   33 CYS
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue  100 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 68 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 3 optimal weight:    0.3980
   chunk 47 optimal weight:    0.0370
   chunk 24 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 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 = 0.3884 r_free = 0.3884 target = 0.145968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.116048 restraints weight = 13015.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 1.42
r_work: 0.3380 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9339  Z= 0.175
  Angle     :  0.523   7.214  13442  Z= 0.281
  Chirality :  0.036   0.233   1613
  Planarity :  0.004   0.038   1071
  Dihedral  : 22.139 167.386   3210
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 13.30 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  2.01 (0.34), residues: 626
  helix:  2.90 (0.30), residues: 303
  sheet:  0.39 (0.57), residues: 72
  loop : -0.36 (0.38), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 206 
 TYR   0.019   0.001   TYR A  45 
 PHE   0.014   0.002   PHE E  82 
 TRP   0.017   0.002   TRP A 424 
 HIS   0.004   0.001   HIS A 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 9337)
  covalent geometry    : angle       0.52316 (13438)
  SS BOND              : bond        0.00246 (    2)
  SS BOND              : angle       0.73914 (    4)
  hydrogen bonds       : bond        0.05277 (  436)
  hydrogen bonds       : angle       3.12801 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8260 (ttpp) cc_final: 0.8031 (ttpp)
REVERT: A  359 GLU cc_start: 0.7763 (tp30) cc_final: 0.7457 (tp30)
REVERT: A  372 ASP cc_start: 0.7642 (t0) cc_final: 0.7393 (t0)
REVERT: A  382 GLN cc_start: 0.7842 (tt0) cc_final: 0.7597 (tt0)
REVERT: A  414 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7732 (m-30)
REVERT: A  417 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7299 (mm-30)
REVERT: A  433 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7542 (ttp-110)
  outliers start: 13
  outliers final: 8
  residues processed: 105
  average time/residue: 0.5947
  time to fit residues: 65.8701
Evaluate side-chains
  105 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ASP
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  374 SER
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  433 ARG
Chi-restraints excluded: chain E residue   33 CYS
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue  100 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 38 optimal weight:    0.2980
   chunk 69 optimal weight:    0.0030
   chunk 57 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 36 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0470
   chunk 65 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.3890

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.147429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.117716 restraints weight = 12963.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 1.43
r_work: 0.3401 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9339  Z= 0.136
  Angle     :  0.499   7.875  13442  Z= 0.267
  Chirality :  0.035   0.220   1613
  Planarity :  0.004   0.037   1071
  Dihedral  : 22.114 166.660   3210
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.01 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  2.18 (0.34), residues: 626
  helix:  3.08 (0.30), residues: 303
  sheet:  0.34 (0.54), residues: 79
  loop : -0.31 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 206 
 TYR   0.019   0.001   TYR A  45 
 PHE   0.011   0.001   PHE E  82 
 TRP   0.015   0.002   TRP A  47 
 HIS   0.003   0.001   HIS A 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9337)
  covalent geometry    : angle       0.49904 (13438)
  SS BOND              : bond        0.00237 (    2)
  SS BOND              : angle       0.76672 (    4)
  hydrogen bonds       : bond        0.04685 (  436)
  hydrogen bonds       : angle       3.01800 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8228 (ttpp) cc_final: 0.7989 (ttpp)
REVERT: A  295 ASN cc_start: 0.8482 (t0) cc_final: 0.8229 (t160)
REVERT: A  359 GLU cc_start: 0.7778 (tp30) cc_final: 0.7489 (tp30)
REVERT: A  372 ASP cc_start: 0.7623 (t0) cc_final: 0.7382 (t0)
REVERT: A  382 GLN cc_start: 0.7841 (tt0) cc_final: 0.7602 (tt0)
REVERT: A  414 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7723 (m-30)
REVERT: A  417 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7340 (mm-30)
REVERT: A  433 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7575 (ttp-110)
  outliers start: 9
  outliers final: 6
  residues processed: 97
  average time/residue: 0.5635
  time to fit residues: 57.6355
Evaluate side-chains
  100 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ASP
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  433 ARG
Chi-restraints excluded: chain E residue   33 CYS
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue  100 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   chunk 28 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 75 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.145535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.115598 restraints weight = 12974.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 1.44
r_work: 0.3372 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.1601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   9339  Z= 0.212
  Angle     :  0.540   8.299  13442  Z= 0.286
  Chirality :  0.038   0.243   1613
  Planarity :  0.004   0.037   1071
  Dihedral  : 22.142 168.938   3210
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 14.54 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  2.08 (0.34), residues: 626
  helix:  2.96 (0.30), residues: 303
  sheet:  0.27 (0.54), residues: 78
  loop : -0.29 (0.39), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 206 
 TYR   0.018   0.001   TYR A  45 
 PHE   0.012   0.002   PHE A 228 
 TRP   0.019   0.002   TRP A 424 
 HIS   0.004   0.001   HIS A 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 9337)
  covalent geometry    : angle       0.53999 (13438)
  SS BOND              : bond        0.00251 (    2)
  SS BOND              : angle       0.80457 (    4)
  hydrogen bonds       : bond        0.05543 (  436)
  hydrogen bonds       : angle       3.08825 ( 1085)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A  359 GLU cc_start: 0.7785 (tp30) cc_final: 0.7484 (tp30)
REVERT: A  372 ASP cc_start: 0.7658 (t0) cc_final: 0.7409 (t0)
REVERT: A  382 GLN cc_start: 0.7852 (tt0) cc_final: 0.7601 (tt0)
REVERT: A  414 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7724 (m-30)
REVERT: A  417 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7296 (mm-30)
REVERT: A  433 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7537 (ttp-110)
  outliers start: 8
  outliers final: 6
  residues processed: 99
  average time/residue: 0.5632
  time to fit residues: 58.8835
Evaluate side-chains
  103 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ASP
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  433 ARG
Chi-restraints excluded: chain E residue   33 CYS
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue  100 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 49 optimal weight:    0.2980
   chunk 13 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 51 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.146148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.116389 restraints weight = 12882.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 1.42
r_work: 0.3377 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9339  Z= 0.182
  Angle     :  0.532   8.301  13442  Z= 0.283
  Chirality :  0.037   0.234   1613
  Planarity :  0.004   0.038   1071
  Dihedral  : 22.127 168.082   3210
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.89 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  2.14 (0.34), residues: 626
  helix:  3.00 (0.30), residues: 303
  sheet:  0.22 (0.53), residues: 80
  loop : -0.22 (0.39), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 206 
 TYR   0.017   0.001   TYR A  45 
 PHE   0.011   0.002   PHE E  82 
 TRP   0.019   0.002   TRP A 424 
 HIS   0.004   0.001   HIS A  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 9337)
  covalent geometry    : angle       0.53148 (13438)
  SS BOND              : bond        0.00260 (    2)
  SS BOND              : angle       0.79840 (    4)
  hydrogen bonds       : bond        0.05234 (  436)
  hydrogen bonds       : angle       3.06193 ( 1085)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3229.77 seconds
wall clock time: 55 minutes 38.18 seconds (3338.18 seconds total)