Starting phenix.real_space_refine
on Thu Feb  5 00:05:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v52_64784/02_2026/9v52_64784.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v52_64784/02_2026/9v52_64784.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9v52_64784/02_2026/9v52_64784.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v52_64784/02_2026/9v52_64784.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9v52_64784/02_2026/9v52_64784.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v52_64784/02_2026/9v52_64784.cif"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    8328      2.51       5
     N    2427      2.21       5
     O    2757      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 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: 13539
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C1"
      Number of atoms: 3331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 432, 3331
          Classifications: {'peptide': 432}
          Link IDs: {'PTRANS': 11, 'TRANS': 420}
    Chain: "P1"
      Number of atoms: 1182
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 1182
          Classifications: {'peptide': 152}
          Link IDs: {'PTRANS': 8, 'TRANS': 143}
    Chain: "C3"
      Number of atoms: 3331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 432, 3331
          Classifications: {'peptide': 432}
          Link IDs: {'PTRANS': 11, 'TRANS': 420}
    Chain: "P3"
      Number of atoms: 1182
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 1182
          Classifications: {'peptide': 152}
          Link IDs: {'PTRANS': 8, 'TRANS': 143}
    Chain: "C2"
      Number of atoms: 3331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 432, 3331
          Classifications: {'peptide': 432}
          Link IDs: {'PTRANS': 11, 'TRANS': 420}
    Chain: "P2"
      Number of atoms: 1182
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 1182
          Classifications: {'peptide': 152}
          Link IDs: {'PTRANS': 8, 'TRANS': 143}
  Time building chain proxies: 3.04, per 1000 atoms: 0.22
  Number of scatterers: 13539
  At special positions: 0
  Unit cell: (108, 110.7, 160.65, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O    2757      8.00
     N    2427      7.00
     C    8328      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYSP1  36 " - pdb=" SG  CYSP1 144 " distance=2.03
    Simple disulfide: pdb=" SG  CYSP3  36 " - pdb=" SG  CYSP3 144 " distance=2.03
    Simple disulfide: pdb=" SG  CYSP2  36 " - pdb=" SG  CYSP2 144 " 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: 1.14
  Conformation dependent library (CDL) restraints added in 501.4 milliseconds
  

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3324

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 10 sheets defined
      61.4% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'C1' and resid 24 through 35
    Processing helix  chain 'C1' and resid 36 through 58
      removed outlier: 4.401A  pdb=" N   ILEC1  53 " --> pdb=" O   ALAC1  49 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   ASNC1  54 " --> pdb=" O   PHEC1  50 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   GLUC1  55 " --> pdb=" O   GLUC1  51 " (cutoff:3.500A)
    Processing helix  chain 'C1' and resid 59 through 61
      No H-bonds generated for 'chain 'C1' and resid 59 through 61'
    Processing helix  chain 'C1' and resid 99 through 169
      removed outlier: 3.986A  pdb=" N   TRPC1 103 " --> pdb=" O   ASPC1  99 " (cutoff:3.500A)
    Processing helix  chain 'C1' and resid 173 through 209
    Processing helix  chain 'C1' and resid 230 through 242
    Processing helix  chain 'C1' and resid 242 through 263
      removed outlier: 4.340A  pdb=" N   GLNC1 263 " --> pdb=" O   ILEC1 259 " (cutoff:3.500A)
    Processing helix  chain 'C1' and resid 286 through 290
      removed outlier: 3.730A  pdb=" N   ARGC1 289 " --> pdb=" O   SERC1 286 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLYC1 290 " --> pdb=" O   LYSC1 287 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C1' and resid 286 through 290'
    Processing helix  chain 'C1' and resid 318 through 387
      removed outlier: 3.902A  pdb=" N   ASNC1 364 " --> pdb=" O   ILEC1 360 " (cutoff:3.500A)
    Processing helix  chain 'C1' and resid 390 through 427
    Processing helix  chain 'C1' and resid 430 through 439
      removed outlier: 3.781A  pdb=" N   LEUC1 434 " --> pdb=" O   ASNC1 430 " (cutoff:3.500A)
    Processing helix  chain 'C1' and resid 448 through 453
    Processing helix  chain 'P1' and resid 40 through 55
    Processing helix  chain 'P1' and resid 63 through 67
    Processing helix  chain 'P1' and resid 70 through 82
      removed outlier: 3.574A  pdb=" N   ASNP1  82 " --> pdb=" O   ALAP1  78 " (cutoff:3.500A)
    Processing helix  chain 'P1' and resid 84 through 91
      removed outlier: 3.506A  pdb=" N   ASPP1  91 " --> pdb=" O   LEUP1  87 " (cutoff:3.500A)
    Processing helix  chain 'P1' and resid 163 through 168
    Processing helix  chain 'C3' and resid 24 through 35
    Processing helix  chain 'C3' and resid 36 through 58
      removed outlier: 4.188A  pdb=" N   ILEC3  53 " --> pdb=" O   ALAC3  49 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   ASNC3  54 " --> pdb=" O   PHEC3  50 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   GLUC3  55 " --> pdb=" O   GLUC3  51 " (cutoff:3.500A)
    Processing helix  chain 'C3' and resid 59 through 61
      No H-bonds generated for 'chain 'C3' and resid 59 through 61'
    Processing helix  chain 'C3' and resid 99 through 169
      removed outlier: 3.997A  pdb=" N   TRPC3 103 " --> pdb=" O   ASPC3  99 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEUC3 139 " --> pdb=" O   TYRC3 135 " (cutoff:3.500A)
    Processing helix  chain 'C3' and resid 173 through 209
    Processing helix  chain 'C3' and resid 230 through 242
    Processing helix  chain 'C3' and resid 242 through 263
      removed outlier: 4.227A  pdb=" N   GLNC3 263 " --> pdb=" O   ILEC3 259 " (cutoff:3.500A)
    Processing helix  chain 'C3' and resid 286 through 290
      removed outlier: 3.800A  pdb=" N   ARGC3 289 " --> pdb=" O   SERC3 286 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLYC3 290 " --> pdb=" O   LYSC3 287 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C3' and resid 286 through 290'
    Processing helix  chain 'C3' and resid 318 through 387
      removed outlier: 3.702A  pdb=" N   ASNC3 364 " --> pdb=" O   ILEC3 360 " (cutoff:3.500A)
    Processing helix  chain 'C3' and resid 390 through 427
      removed outlier: 3.623A  pdb=" N   GLYC3 427 " --> pdb=" O   LYSC3 423 " (cutoff:3.500A)
    Processing helix  chain 'C3' and resid 430 through 439
      removed outlier: 3.769A  pdb=" N   LEUC3 434 " --> pdb=" O   ASNC3 430 " (cutoff:3.500A)
    Processing helix  chain 'C3' and resid 448 through 453
      removed outlier: 3.602A  pdb=" N   ALAC3 453 " --> pdb=" O   PROC3 449 " (cutoff:3.500A)
    Processing helix  chain 'P3' and resid 40 through 55
    Processing helix  chain 'P3' and resid 59 through 64
    Processing helix  chain 'P3' and resid 65 through 67
      No H-bonds generated for 'chain 'P3' and resid 65 through 67'
    Processing helix  chain 'P3' and resid 70 through 82
      removed outlier: 3.863A  pdb=" N   ASNP3  82 " --> pdb=" O   ALAP3  78 " (cutoff:3.500A)
    Processing helix  chain 'P3' and resid 84 through 91
      removed outlier: 3.729A  pdb=" N   ASPP3  91 " --> pdb=" O   LEUP3  87 " (cutoff:3.500A)
    Processing helix  chain 'P3' and resid 163 through 169
    Processing helix  chain 'C2' and resid 24 through 35
    Processing helix  chain 'C2' and resid 36 through 58
      removed outlier: 4.431A  pdb=" N   ILEC2  53 " --> pdb=" O   ALAC2  49 " (cutoff:3.500A)
      removed outlier: 5.097A  pdb=" N   ASNC2  54 " --> pdb=" O   PHEC2  50 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   GLUC2  55 " --> pdb=" O   GLUC2  51 " (cutoff:3.500A)
    Processing helix  chain 'C2' and resid 59 through 61
      No H-bonds generated for 'chain 'C2' and resid 59 through 61'
    Processing helix  chain 'C2' and resid 99 through 169
      removed outlier: 4.008A  pdb=" N   TRPC2 103 " --> pdb=" O   ASPC2  99 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEUC2 139 " --> pdb=" O   TYRC2 135 " (cutoff:3.500A)
    Processing helix  chain 'C2' and resid 173 through 209
    Processing helix  chain 'C2' and resid 230 through 242
    Processing helix  chain 'C2' and resid 242 through 263
      removed outlier: 4.275A  pdb=" N   GLNC2 263 " --> pdb=" O   ILEC2 259 " (cutoff:3.500A)
    Processing helix  chain 'C2' and resid 286 through 290
      removed outlier: 3.836A  pdb=" N   ARGC2 289 " --> pdb=" O   SERC2 286 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLYC2 290 " --> pdb=" O   LYSC2 287 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C2' and resid 286 through 290'
    Processing helix  chain 'C2' and resid 318 through 387
      removed outlier: 3.706A  pdb=" N   ASNC2 364 " --> pdb=" O   ILEC2 360 " (cutoff:3.500A)
    Processing helix  chain 'C2' and resid 390 through 427
      removed outlier: 3.568A  pdb=" N   GLYC2 427 " --> pdb=" O   LYSC2 423 " (cutoff:3.500A)
    Processing helix  chain 'C2' and resid 430 through 439
      removed outlier: 3.753A  pdb=" N   LEUC2 434 " --> pdb=" O   ASNC2 430 " (cutoff:3.500A)
    Processing helix  chain 'C2' and resid 448 through 453
      removed outlier: 3.558A  pdb=" N   ALAC2 453 " --> pdb=" O   PROC2 449 " (cutoff:3.500A)
    Processing helix  chain 'P2' and resid 40 through 55
    Processing helix  chain 'P2' and resid 70 through 82
      removed outlier: 3.641A  pdb=" N   ASNP2  82 " --> pdb=" O   ALAP2  78 " (cutoff:3.500A)
    Processing helix  chain 'P2' and resid 84 through 91
      removed outlier: 3.921A  pdb=" N   ASNP2  90 " --> pdb=" O   GLUP2  86 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ASPP2  91 " --> pdb=" O   LEUP2  87 " (cutoff:3.500A)
    Processing helix  chain 'P2' and resid 163 through 169
    Processing sheet with id=AA1, first strand: chain 'C1' and resid 63 through 77
      removed outlier: 6.751A  pdb=" N   LEUC1 270 " --> pdb=" O   ILEC1  97 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ILEC1 314 " --> pdb=" O   LEUC3  64 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   LEUC3  64 " --> pdb=" O   ILEC1 314 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   LEUC3 270 " --> pdb=" O   ILEC3  97 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ILEC3 314 " --> pdb=" O   LEUC2  64 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   LEUC2  64 " --> pdb=" O   ILEC3 314 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   LEUC2 270 " --> pdb=" O   ILEC2  97 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ILEC2 314 " --> pdb=" O   LEUC1  64 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   LEUC1  64 " --> pdb=" O   ILEC2 314 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C1' and resid 214 through 216
    Processing sheet with id=AA3, first strand: chain 'P1' and resid 102 through 105
    Processing sheet with id=AA4, first strand: chain 'P1' and resid 102 through 105
    Processing sheet with id=AA5, first strand: chain 'C3' and resid 214 through 216
    Processing sheet with id=AA6, first strand: chain 'P3' and resid 102 through 105
    Processing sheet with id=AA7, first strand: chain 'P3' and resid 102 through 105
    Processing sheet with id=AA8, first strand: chain 'C2' and resid 214 through 216
    Processing sheet with id=AA9, first strand: chain 'P2' and resid 102 through 105
    Processing sheet with id=AB1, first strand: chain 'P2' and resid 102 through 105

    1064 hydrogen bonds defined for protein.
    3096 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.18

  Time building geometry restraints manager: 1.48 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: 4756
        1.34 -     1.46: 1634
        1.46 -     1.57: 7296
        1.57 -     1.69: 0
        1.69 -     1.81: 45
  Bond restraints: 13731
  Sorted by residual:
  bond pdb=" CB  ILEC2 422 "
       pdb=" CG2 ILEC2 422 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.52e+00
  bond pdb=" CB  PROP2  92 "
       pdb=" CG  PROP2  92 "
    ideal  model  delta    sigma   weight residual
    1.492  1.552 -0.060 5.00e-02 4.00e+02 1.46e+00
  bond pdb=" CB  ASNP3  82 "
       pdb=" CG  ASNP3  82 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 2.50e-02 1.60e+03 1.33e+00
  bond pdb=" CG1 ILEC2 356 "
       pdb=" CD1 ILEC2 356 "
    ideal  model  delta    sigma   weight residual
    1.513  1.472  0.041 3.90e-02 6.57e+02 1.08e+00
  bond pdb=" CB  GLUC3 221 "
       pdb=" CG  GLUC3 221 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.05e+00
  ... (remaining 13726 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 18123
        1.45 -     2.90: 445
        2.90 -     4.34: 84
        4.34 -     5.79: 15
        5.79 -     7.24: 5
  Bond angle restraints: 18672
  Sorted by residual:
  angle pdb=" N   PROP2  92 "
        pdb=" CD  PROP2  92 "
        pdb=" CG  PROP2  92 "
      ideal   model   delta    sigma   weight residual
     103.20   98.61    4.59 1.50e+00 4.44e-01 9.36e+00
  angle pdb=" CA  PROP2  92 "
        pdb=" N   PROP2  92 "
        pdb=" CD  PROP2  92 "
      ideal   model   delta    sigma   weight residual
     112.00  108.28    3.72 1.40e+00 5.10e-01 7.08e+00
  angle pdb=" C   THRP3 160 "
        pdb=" CA  THRP3 160 "
        pdb=" CB  THRP3 160 "
      ideal   model   delta    sigma   weight residual
     110.42  115.65   -5.23 1.99e+00 2.53e-01 6.90e+00
  angle pdb=" N   SERP1  68 "
        pdb=" CA  SERP1  68 "
        pdb=" C   SERP1  68 "
      ideal   model   delta    sigma   weight residual
     110.80  116.14   -5.34 2.13e+00 2.20e-01 6.28e+00
  angle pdb=" N   SERP2  68 "
        pdb=" CA  SERP2  68 "
        pdb=" C   SERP2  68 "
      ideal   model   delta    sigma   weight residual
     110.80  115.84   -5.04 2.13e+00 2.20e-01 5.61e+00
  ... (remaining 18667 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 7037
       17.80 -    35.60: 983
       35.60 -    53.40: 293
       53.40 -    71.20: 81
       71.20 -    89.00: 15
  Dihedral angle restraints: 8409
    sinusoidal: 3264
      harmonic: 5145
  Sorted by residual:
  dihedral pdb=" CB  CYSP2  36 "
           pdb=" SG  CYSP2  36 "
           pdb=" SG  CYSP2 144 "
           pdb=" CB  CYSP2 144 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  139.97  -46.97     1      1.00e+01 1.00e-02 3.05e+01
  dihedral pdb=" CB  CYSP1  36 "
           pdb=" SG  CYSP1  36 "
           pdb=" SG  CYSP1 144 "
           pdb=" CB  CYSP1 144 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.88  -45.88     1      1.00e+01 1.00e-02 2.92e+01
  dihedral pdb=" CB  CYSP3  36 "
           pdb=" SG  CYSP3  36 "
           pdb=" SG  CYSP3 144 "
           pdb=" CB  CYSP3 144 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.47  -45.47     1      1.00e+01 1.00e-02 2.87e+01
  ... (remaining 8406 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1458
       0.032 -    0.064: 513
       0.064 -    0.096: 129
       0.096 -    0.128: 42
       0.128 -    0.160: 12
  Chirality restraints: 2154
  Sorted by residual:
  chirality pdb=" CA  ILEP3 147 "
            pdb=" N   ILEP3 147 "
            pdb=" C   ILEP3 147 "
            pdb=" CB  ILEP3 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.43e-01
  chirality pdb=" CB  THRP3  20 "
            pdb=" CA  THRP3  20 "
            pdb=" OG1 THRP3  20 "
            pdb=" CG2 THRP3  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.16 2.00e-01 2.50e+01 6.05e-01
  chirality pdb=" CA  THRP3  20 "
            pdb=" N   THRP3  20 "
            pdb=" C   THRP3  20 "
            pdb=" CB  THRP3  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.14 2.00e-01 2.50e+01 4.81e-01
  ... (remaining 2151 not shown)

  Planarity restraints: 2502
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASNP3  82 "   -0.011 2.00e-02 2.50e+03   2.31e-02 5.32e+00
        pdb=" C   ASNP3  82 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ASNP3  82 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ASNP3  83 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASNC1 448 "    0.037 5.00e-02 4.00e+02   5.63e-02 5.08e+00
        pdb=" N   PROC1 449 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PROC1 449 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PROC1 449 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASNC2 448 "   -0.037 5.00e-02 4.00e+02   5.62e-02 5.05e+00
        pdb=" N   PROC2 449 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PROC2 449 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PROC2 449 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 2499 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 349
        2.69 -     3.25: 13701
        3.25 -     3.80: 21968
        3.80 -     4.35: 25290
        4.35 -     4.90: 44077
  Nonbonded interactions: 105385
  Sorted by model distance:
  nonbonded pdb=" O   PROP2  92 "
            pdb=" OH  TYRP2 152 "
     model   vdw
     2.143 3.040
  nonbonded pdb=" O   SERP2 109 "
            pdb=" OG  SERP2 109 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" OG1 THRP2 163 "
            pdb=" OE1 GLNP2 166 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" O   PROP1  92 "
            pdb=" OH  TYRP1 152 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" O   THRP3  23 "
            pdb=" OG1 THRP3  23 "
     model   vdw
     2.245 3.040
  ... (remaining 105380 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'C1'
  selection = chain 'C2'
  selection = chain 'C3'
}
ncs_group {
  reference = chain 'P1'
  selection = chain 'P2'
  selection = chain 'P3'
}

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:             1.050
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.730
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  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:   15.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
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   0.060  13734  Z= 0.154
  Angle     :  0.559   7.238  18678  Z= 0.298
  Chirality :  0.037   0.160   2154
  Planarity :  0.004   0.056   2502
  Dihedral  : 18.446  89.002   5076
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.13 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  : 30.96 %
    Favored  : 68.70 %
  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:  1.98 (0.21), residues: 1740
  helix:  3.42 (0.16), residues: 984
  sheet:  0.82 (0.32), residues: 225
  loop : -2.90 (0.23), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARGC3  40 
 TYR   0.017   0.001   TYRP1  26 
 PHE   0.013   0.002   PHEC3  98 
 TRP   0.011   0.001   TRPP3 132 
 HIS   0.008   0.001   HISP1 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (13731)
  covalent geometry    : angle       0.55866 (18672)
  SS BOND              : bond        0.00249 (    3)
  SS BOND              : angle       0.80243 (    6)
  hydrogen bonds       : bond        0.10603 ( 1052)
  hydrogen bonds       : angle       4.81777 ( 3096)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 118
  time to evaluate  : 0.572 
Fit side-chains
REVERT: P3   96 ARG cc_start: 0.6896 (mtp180) cc_final: 0.6607 (mtt180)
REVERT: P2  149 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6806 (t0)
  outliers start: 5
  outliers final: 3
  residues processed: 121
  average time/residue: 0.1009
  time to fit residues: 19.0301
Evaluate side-chains
  115 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 111
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C1 residue  422 ILE
Chi-restraints excluded: chain P1 residue   77 ASP
Chi-restraints excluded: chain C3 residue  259 ILE
Chi-restraints excluded: chain P2 residue  149 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.0370
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    0.6980
   chunk 149 optimal weight:    1.9990
   overall best weight:    0.9060

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

Flipped N/Q/H residues before XYZ refinement:
C1 178 ASN
** C1 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P1 113 ASN
** P1 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P3 113 ASN
** P3 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C2 328 GLN
P2  29 ASN
P2 140 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.132238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.112068 restraints weight = 19181.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.115666 restraints weight = 10517.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.118179 restraints weight = 6904.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.119865 restraints weight = 5111.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.120980 restraints weight = 4145.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.0594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13734  Z= 0.158
  Angle     :  0.554   6.924  18678  Z= 0.297
  Chirality :  0.038   0.156   2154
  Planarity :  0.004   0.050   2502
  Dihedral  :  4.196  53.523   1925
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.49 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 28.25 %
    Favored  : 68.09 %
  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:  1.96 (0.21), residues: 1740
  helix:  3.37 (0.15), residues: 999
  sheet:  1.18 (0.32), residues: 219
  loop : -3.19 (0.23), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARGC3  40 
 TYR   0.016   0.001   TYRC1 135 
 PHE   0.014   0.002   PHEP3  48 
 TRP   0.009   0.001   TRPP3 132 
 HIS   0.007   0.001   HISP1 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (13731)
  covalent geometry    : angle       0.55364 (18672)
  SS BOND              : bond        0.00429 (    3)
  SS BOND              : angle       0.77178 (    6)
  hydrogen bonds       : bond        0.05773 ( 1052)
  hydrogen bonds       : angle       4.31334 ( 3096)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 123
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
REVERT: C1  263 GLN cc_start: 0.5035 (OUTLIER) cc_final: 0.4713 (pm20)
REVERT: P1   91 ASP cc_start: 0.8690 (t0) cc_final: 0.8198 (t0)
REVERT: P1  113 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7895 (p0)
REVERT: P1  138 MET cc_start: 0.8679 (mmt) cc_final: 0.8475 (mmt)
REVERT: C3  428 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8259 (m)
REVERT: C2   76 TYR cc_start: 0.4552 (OUTLIER) cc_final: 0.2544 (t80)
REVERT: C2  123 ASP cc_start: 0.8352 (t70) cc_final: 0.8121 (t0)
REVERT: P2   96 ARG cc_start: 0.7025 (mtp180) cc_final: 0.6693 (mtp180)
REVERT: P2  149 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6681 (t0)
REVERT: P2  166 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7957 (mp10)
  outliers start: 54
  outliers final: 25
  residues processed: 164
  average time/residue: 0.0919
  time to fit residues: 23.4703
Evaluate side-chains
  146 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C1 residue   50 PHE
Chi-restraints excluded: chain C1 residue  263 GLN
Chi-restraints excluded: chain C1 residue  422 ILE
Chi-restraints excluded: chain C1 residue  434 LEU
Chi-restraints excluded: chain P1 residue   22 VAL
Chi-restraints excluded: chain P1 residue   77 ASP
Chi-restraints excluded: chain P1 residue   88 LEU
Chi-restraints excluded: chain P1 residue  113 ASN
Chi-restraints excluded: chain P1 residue  123 VAL
Chi-restraints excluded: chain P1 residue  147 ILE
Chi-restraints excluded: chain C3 residue   50 PHE
Chi-restraints excluded: chain C3 residue  259 ILE
Chi-restraints excluded: chain C3 residue  350 ARG
Chi-restraints excluded: chain C3 residue  428 THR
Chi-restraints excluded: chain P3 residue   22 VAL
Chi-restraints excluded: chain P3 residue  123 VAL
Chi-restraints excluded: chain C2 residue   76 TYR
Chi-restraints excluded: chain C2 residue  215 LEU
Chi-restraints excluded: chain C2 residue  259 ILE
Chi-restraints excluded: chain C2 residue  303 GLN
Chi-restraints excluded: chain C2 residue  356 ILE
Chi-restraints excluded: chain C2 residue  370 VAL
Chi-restraints excluded: chain C2 residue  393 ASP
Chi-restraints excluded: chain C2 residue  422 ILE
Chi-restraints excluded: chain P2 residue   22 VAL
Chi-restraints excluded: chain P2 residue   77 ASP
Chi-restraints excluded: chain P2 residue  123 VAL
Chi-restraints excluded: chain P2 residue  147 ILE
Chi-restraints excluded: chain P2 residue  149 ASP
Chi-restraints excluded: chain P2 residue  157 VAL
Chi-restraints excluded: chain P2 residue  166 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 129 optimal weight:    3.9990
   chunk 165 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 152 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 89 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 86 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** C1 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C3 149 GLN
** P3 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C2  63 GLN
C2 149 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.127895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.107474 restraints weight = 19522.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.111032 restraints weight = 10702.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.113469 restraints weight = 7050.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.115117 restraints weight = 5254.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.116263 restraints weight = 4262.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.1008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  13734  Z= 0.213
  Angle     :  0.601   8.216  18678  Z= 0.321
  Chirality :  0.040   0.154   2154
  Planarity :  0.004   0.059   2502
  Dihedral  :  4.432  55.603   1925
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.90 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 26.83 %
    Favored  : 67.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.21), residues: 1740
  helix:  3.25 (0.15), residues: 999
  sheet:  0.91 (0.32), residues: 219
  loop : -3.30 (0.23), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARGC1  40 
 TYR   0.020   0.002   TYRC1 135 
 PHE   0.020   0.002   PHEP3  48 
 TRP   0.012   0.002   TRPP3 132 
 HIS   0.009   0.001   HISP1 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 (13731)
  covalent geometry    : angle       0.60058 (18672)
  SS BOND              : bond        0.00351 (    3)
  SS BOND              : angle       0.76993 (    6)
  hydrogen bonds       : bond        0.06353 ( 1052)
  hydrogen bonds       : angle       4.39713 ( 3096)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 124
  time to evaluate  : 0.484 
Fit side-chains
REVERT: C1  263 GLN cc_start: 0.5174 (OUTLIER) cc_final: 0.4756 (pm20)
REVERT: C1  304 ASN cc_start: 0.6980 (OUTLIER) cc_final: 0.6731 (p0)
REVERT: C1  350 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.6436 (mpt-90)
REVERT: P1   91 ASP cc_start: 0.8724 (t0) cc_final: 0.8174 (t0)
REVERT: P1  113 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.8053 (p0)
REVERT: C3  149 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7634 (tt0)
REVERT: C3  250 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7118 (mm)
REVERT: C3  263 GLN cc_start: 0.4929 (OUTLIER) cc_final: 0.4714 (pm20)
REVERT: C3  350 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7466 (mmt-90)
REVERT: C3  428 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8318 (m)
REVERT: P3   23 THR cc_start: 0.8631 (m) cc_final: 0.8155 (p)
REVERT: C2   76 TYR cc_start: 0.4560 (OUTLIER) cc_final: 0.2804 (t80)
REVERT: C2  123 ASP cc_start: 0.8465 (t70) cc_final: 0.8248 (t0)
REVERT: C2  159 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7171 (tt)
REVERT: C2  250 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6845 (mm)
REVERT: C2  337 GLN cc_start: 0.7350 (tm-30) cc_final: 0.7081 (tm-30)
REVERT: P2   96 ARG cc_start: 0.7379 (mtp180) cc_final: 0.6822 (mtp180)
REVERT: P2  149 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.6667 (t0)
REVERT: P2  158 HIS cc_start: 0.6677 (t-90) cc_final: 0.5952 (t70)
  outliers start: 79
  outliers final: 48
  residues processed: 184
  average time/residue: 0.1024
  time to fit residues: 28.7993
Evaluate side-chains
  176 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 115
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C1 residue   50 PHE
Chi-restraints excluded: chain C1 residue  192 THR
Chi-restraints excluded: chain C1 residue  215 LEU
Chi-restraints excluded: chain C1 residue  231 VAL
Chi-restraints excluded: chain C1 residue  243 LEU
Chi-restraints excluded: chain C1 residue  259 ILE
Chi-restraints excluded: chain C1 residue  263 GLN
Chi-restraints excluded: chain C1 residue  269 THR
Chi-restraints excluded: chain C1 residue  304 ASN
Chi-restraints excluded: chain C1 residue  345 VAL
Chi-restraints excluded: chain C1 residue  350 ARG
Chi-restraints excluded: chain C1 residue  371 VAL
Chi-restraints excluded: chain C1 residue  422 ILE
Chi-restraints excluded: chain C1 residue  434 LEU
Chi-restraints excluded: chain P1 residue   22 VAL
Chi-restraints excluded: chain P1 residue   77 ASP
Chi-restraints excluded: chain P1 residue   88 LEU
Chi-restraints excluded: chain P1 residue  113 ASN
Chi-restraints excluded: chain P1 residue  123 VAL
Chi-restraints excluded: chain P1 residue  139 ILE
Chi-restraints excluded: chain P1 residue  147 ILE
Chi-restraints excluded: chain C3 residue   50 PHE
Chi-restraints excluded: chain C3 residue  149 GLN
Chi-restraints excluded: chain C3 residue  231 VAL
Chi-restraints excluded: chain C3 residue  250 LEU
Chi-restraints excluded: chain C3 residue  259 ILE
Chi-restraints excluded: chain C3 residue  263 GLN
Chi-restraints excluded: chain C3 residue  267 LEU
Chi-restraints excluded: chain C3 residue  281 THR
Chi-restraints excluded: chain C3 residue  314 ILE
Chi-restraints excluded: chain C3 residue  350 ARG
Chi-restraints excluded: chain C3 residue  360 ILE
Chi-restraints excluded: chain C3 residue  424 SER
Chi-restraints excluded: chain C3 residue  428 THR
Chi-restraints excluded: chain P3 residue   22 VAL
Chi-restraints excluded: chain P3 residue   31 THR
Chi-restraints excluded: chain P3 residue   67 LEU
Chi-restraints excluded: chain P3 residue   77 ASP
Chi-restraints excluded: chain P3 residue  123 VAL
Chi-restraints excluded: chain P3 residue  136 VAL
Chi-restraints excluded: chain P3 residue  147 ILE
Chi-restraints excluded: chain P3 residue  163 THR
Chi-restraints excluded: chain C2 residue   76 TYR
Chi-restraints excluded: chain C2 residue   87 THR
Chi-restraints excluded: chain C2 residue  159 LEU
Chi-restraints excluded: chain C2 residue  195 ASN
Chi-restraints excluded: chain C2 residue  215 LEU
Chi-restraints excluded: chain C2 residue  239 GLU
Chi-restraints excluded: chain C2 residue  250 LEU
Chi-restraints excluded: chain C2 residue  259 ILE
Chi-restraints excluded: chain C2 residue  303 GLN
Chi-restraints excluded: chain C2 residue  356 ILE
Chi-restraints excluded: chain C2 residue  370 VAL
Chi-restraints excluded: chain C2 residue  393 ASP
Chi-restraints excluded: chain C2 residue  422 ILE
Chi-restraints excluded: chain P2 residue   22 VAL
Chi-restraints excluded: chain P2 residue   77 ASP
Chi-restraints excluded: chain P2 residue  123 VAL
Chi-restraints excluded: chain P2 residue  147 ILE
Chi-restraints excluded: chain P2 residue  149 ASP
Chi-restraints excluded: chain P2 residue  157 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 167 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9980
   chunk 108 optimal weight:    0.5980
   chunk 149 optimal weight:    0.5980
   chunk 54 optimal weight:    0.4980
   chunk 135 optimal weight:    2.9990
   chunk 99 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9990
   chunk 173 optimal weight:    0.9990
   chunk 97 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
C1  36 ASN
** C1 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P3 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P2  29 ASN
P2 140 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.132444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.112230 restraints weight = 19161.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.115871 restraints weight = 10453.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.118322 restraints weight = 6849.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.119943 restraints weight = 5090.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.121102 restraints weight = 4135.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.1007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13734  Z= 0.136
  Angle     :  0.524   5.883  18678  Z= 0.282
  Chirality :  0.037   0.174   2154
  Planarity :  0.004   0.056   2502
  Dihedral  :  4.292  51.437   1925
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.72 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 27.78 %
    Favored  : 68.50 %
  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:  1.94 (0.21), residues: 1740
  helix:  3.45 (0.15), residues: 999
  sheet:  0.86 (0.33), residues: 213
  loop : -3.23 (0.22), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARGC1  40 
 TYR   0.014   0.001   TYRC1 135 
 PHE   0.011   0.001   PHEC3 310 
 TRP   0.009   0.001   TRPP3 132 
 HIS   0.007   0.001   HISP1 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (13731)
  covalent geometry    : angle       0.52423 (18672)
  SS BOND              : bond        0.00302 (    3)
  SS BOND              : angle       0.60692 (    6)
  hydrogen bonds       : bond        0.05638 ( 1052)
  hydrogen bonds       : angle       4.15349 ( 3096)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 120
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
REVERT: C1  263 GLN cc_start: 0.4975 (OUTLIER) cc_final: 0.4627 (pm20)
REVERT: C1  304 ASN cc_start: 0.6916 (OUTLIER) cc_final: 0.6709 (p0)
REVERT: C1  350 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.6402 (mpt-90)
REVERT: C1  380 MET cc_start: 0.8394 (mtt) cc_final: 0.8094 (mtt)
REVERT: P1   52 ARG cc_start: 0.6570 (OUTLIER) cc_final: 0.5951 (ttp80)
REVERT: P1   91 ASP cc_start: 0.8665 (t0) cc_final: 0.8250 (t70)
REVERT: C3   76 TYR cc_start: 0.4843 (OUTLIER) cc_final: 0.3674 (t80)
REVERT: C3  250 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7203 (mm)
REVERT: C3  428 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8081 (m)
REVERT: P3   23 THR cc_start: 0.8604 (m) cc_final: 0.8155 (p)
REVERT: C2   76 TYR cc_start: 0.4891 (OUTLIER) cc_final: 0.2483 (t80)
REVERT: C2  135 TYR cc_start: 0.8619 (t80) cc_final: 0.8343 (t80)
REVERT: C2  250 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7038 (mm)
  outliers start: 55
  outliers final: 30
  residues processed: 161
  average time/residue: 0.0943
  time to fit residues: 23.5512
Evaluate side-chains
  155 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 116
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C1 residue   50 PHE
Chi-restraints excluded: chain C1 residue  235 LEU
Chi-restraints excluded: chain C1 residue  259 ILE
Chi-restraints excluded: chain C1 residue  263 GLN
Chi-restraints excluded: chain C1 residue  304 ASN
Chi-restraints excluded: chain C1 residue  350 ARG
Chi-restraints excluded: chain C1 residue  422 ILE
Chi-restraints excluded: chain C1 residue  434 LEU
Chi-restraints excluded: chain P1 residue   22 VAL
Chi-restraints excluded: chain P1 residue   52 ARG
Chi-restraints excluded: chain P1 residue   77 ASP
Chi-restraints excluded: chain P1 residue  123 VAL
Chi-restraints excluded: chain P1 residue  147 ILE
Chi-restraints excluded: chain C3 residue   50 PHE
Chi-restraints excluded: chain C3 residue   76 TYR
Chi-restraints excluded: chain C3 residue  142 ILE
Chi-restraints excluded: chain C3 residue  220 VAL
Chi-restraints excluded: chain C3 residue  250 LEU
Chi-restraints excluded: chain C3 residue  259 ILE
Chi-restraints excluded: chain C3 residue  350 ARG
Chi-restraints excluded: chain C3 residue  360 ILE
Chi-restraints excluded: chain C3 residue  428 THR
Chi-restraints excluded: chain P3 residue   22 VAL
Chi-restraints excluded: chain P3 residue   77 ASP
Chi-restraints excluded: chain P3 residue  123 VAL
Chi-restraints excluded: chain C2 residue   76 TYR
Chi-restraints excluded: chain C2 residue  215 LEU
Chi-restraints excluded: chain C2 residue  250 LEU
Chi-restraints excluded: chain C2 residue  259 ILE
Chi-restraints excluded: chain C2 residue  303 GLN
Chi-restraints excluded: chain C2 residue  356 ILE
Chi-restraints excluded: chain C2 residue  393 ASP
Chi-restraints excluded: chain C2 residue  401 LEU
Chi-restraints excluded: chain C2 residue  433 ASP
Chi-restraints excluded: chain P2 residue   22 VAL
Chi-restraints excluded: chain P2 residue   77 ASP
Chi-restraints excluded: chain P2 residue  123 VAL
Chi-restraints excluded: chain P2 residue  147 ILE
Chi-restraints excluded: chain P2 residue  157 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 99 optimal weight:    0.7980
   chunk 61 optimal weight:    0.1980
   chunk 132 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 170 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 130 optimal weight:    5.9990
   chunk 173 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C1  36 ASN
** C1 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C3 149 GLN
C3 178 ASN
P3 158 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.151627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.135492 restraints weight = 17808.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.138050 restraints weight = 10904.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.140148 restraints weight = 7811.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.141433 restraints weight = 6099.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.142196 restraints weight = 5103.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.1091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13734  Z= 0.142
  Angle     :  0.520   6.700  18678  Z= 0.280
  Chirality :  0.037   0.173   2154
  Planarity :  0.004   0.047   2502
  Dihedral  :  4.079  49.832   1923
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.72 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 27.51 %
    Favored  : 67.95 %
  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:  1.95 (0.21), residues: 1740
  helix:  3.49 (0.15), residues: 996
  sheet:  0.86 (0.33), residues: 213
  loop : -3.25 (0.22), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARGC1  40 
 TYR   0.014   0.001   TYRC1 135 
 PHE   0.012   0.002   PHEP3  48 
 TRP   0.010   0.001   TRPP3 132 
 HIS   0.008   0.001   HISP1 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (13731)
  covalent geometry    : angle       0.51948 (18672)
  SS BOND              : bond        0.00303 (    3)
  SS BOND              : angle       0.59805 (    6)
  hydrogen bonds       : bond        0.05574 ( 1052)
  hydrogen bonds       : angle       4.10068 ( 3096)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 122
  time to evaluate  : 0.558 
Fit side-chains
REVERT: C1  263 GLN cc_start: 0.5209 (OUTLIER) cc_final: 0.4848 (pm20)
REVERT: C1  350 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7082 (mpt-90)
REVERT: P1   52 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.6111 (ttp80)
REVERT: P1   91 ASP cc_start: 0.8311 (t0) cc_final: 0.7869 (t70)
REVERT: C3   76 TYR cc_start: 0.5227 (OUTLIER) cc_final: 0.3896 (t80)
REVERT: C3  149 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7760 (tt0)
REVERT: C3  250 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7936 (mm)
REVERT: C3  263 GLN cc_start: 0.5106 (OUTLIER) cc_final: 0.4826 (pm20)
REVERT: C3  428 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.8118 (m)
REVERT: P3   23 THR cc_start: 0.8532 (m) cc_final: 0.8146 (p)
REVERT: C2   76 TYR cc_start: 0.5289 (OUTLIER) cc_final: 0.2716 (t80)
REVERT: C2  123 ASP cc_start: 0.8023 (t70) cc_final: 0.7665 (t0)
REVERT: C2  135 TYR cc_start: 0.8657 (t80) cc_final: 0.8350 (t80)
REVERT: C2  250 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7768 (mm)
  outliers start: 67
  outliers final: 41
  residues processed: 174
  average time/residue: 0.0984
  time to fit residues: 26.5081
Evaluate side-chains
  169 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 118
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C1 residue   50 PHE
Chi-restraints excluded: chain C1 residue   58 SER
Chi-restraints excluded: chain C1 residue  192 THR
Chi-restraints excluded: chain C1 residue  235 LEU
Chi-restraints excluded: chain C1 residue  259 ILE
Chi-restraints excluded: chain C1 residue  263 GLN
Chi-restraints excluded: chain C1 residue  269 THR
Chi-restraints excluded: chain C1 residue  350 ARG
Chi-restraints excluded: chain C1 residue  422 ILE
Chi-restraints excluded: chain C1 residue  434 LEU
Chi-restraints excluded: chain P1 residue   22 VAL
Chi-restraints excluded: chain P1 residue   52 ARG
Chi-restraints excluded: chain P1 residue   77 ASP
Chi-restraints excluded: chain P1 residue  123 VAL
Chi-restraints excluded: chain P1 residue  147 ILE
Chi-restraints excluded: chain C3 residue   50 PHE
Chi-restraints excluded: chain C3 residue   76 TYR
Chi-restraints excluded: chain C3 residue  149 GLN
Chi-restraints excluded: chain C3 residue  215 LEU
Chi-restraints excluded: chain C3 residue  220 VAL
Chi-restraints excluded: chain C3 residue  250 LEU
Chi-restraints excluded: chain C3 residue  259 ILE
Chi-restraints excluded: chain C3 residue  263 GLN
Chi-restraints excluded: chain C3 residue  424 SER
Chi-restraints excluded: chain C3 residue  428 THR
Chi-restraints excluded: chain P3 residue   22 VAL
Chi-restraints excluded: chain P3 residue   31 THR
Chi-restraints excluded: chain P3 residue   67 LEU
Chi-restraints excluded: chain P3 residue   77 ASP
Chi-restraints excluded: chain P3 residue  123 VAL
Chi-restraints excluded: chain P3 residue  136 VAL
Chi-restraints excluded: chain P3 residue  158 HIS
Chi-restraints excluded: chain P3 residue  163 THR
Chi-restraints excluded: chain P3 residue  167 SER
Chi-restraints excluded: chain C2 residue   34 LEU
Chi-restraints excluded: chain C2 residue   76 TYR
Chi-restraints excluded: chain C2 residue  159 LEU
Chi-restraints excluded: chain C2 residue  195 ASN
Chi-restraints excluded: chain C2 residue  215 LEU
Chi-restraints excluded: chain C2 residue  250 LEU
Chi-restraints excluded: chain C2 residue  259 ILE
Chi-restraints excluded: chain C2 residue  303 GLN
Chi-restraints excluded: chain C2 residue  356 ILE
Chi-restraints excluded: chain C2 residue  393 ASP
Chi-restraints excluded: chain C2 residue  433 ASP
Chi-restraints excluded: chain P2 residue   22 VAL
Chi-restraints excluded: chain P2 residue   77 ASP
Chi-restraints excluded: chain P2 residue  123 VAL
Chi-restraints excluded: chain P2 residue  147 ILE
Chi-restraints excluded: chain P2 residue  157 VAL
Chi-restraints excluded: chain P2 residue  163 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 121 optimal weight:    0.9990
   chunk 161 optimal weight:    3.9990
   chunk 138 optimal weight:    2.9990
   chunk 105 optimal weight:    0.5980
   chunk 86 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 4 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 144 optimal weight:    3.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
C1  36 ASN
** C1 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P1 113 ASN
** P1 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P3 158 HIS
P2 158 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.130888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.110497 restraints weight = 19281.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.114173 restraints weight = 10497.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.116538 restraints weight = 6867.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.118272 restraints weight = 5138.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.119395 restraints weight = 4164.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.1193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13734  Z= 0.165
  Angle     :  0.545   6.656  18678  Z= 0.293
  Chirality :  0.038   0.164   2154
  Planarity :  0.004   0.050   2502
  Dihedral  :  4.116  50.470   1923
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.95 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 26.96 %
    Favored  : 67.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.86 (0.21), residues: 1740
  helix:  3.40 (0.15), residues: 999
  sheet:  0.78 (0.33), residues: 213
  loop : -3.26 (0.22), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARGC1  40 
 TYR   0.016   0.001   TYRC1 135 
 PHE   0.015   0.002   PHEP3  48 
 TRP   0.011   0.001   TRPP3 132 
 HIS   0.008   0.001   HISP3 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (13731)
  covalent geometry    : angle       0.54459 (18672)
  SS BOND              : bond        0.00334 (    3)
  SS BOND              : angle       0.67596 (    6)
  hydrogen bonds       : bond        0.05762 ( 1052)
  hydrogen bonds       : angle       4.13596 ( 3096)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 119
  time to evaluate  : 0.350 
Fit side-chains
REVERT: C1  263 GLN cc_start: 0.4987 (OUTLIER) cc_final: 0.4626 (pm20)
REVERT: C1  350 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.6399 (mpt-90)
REVERT: P1   52 ARG cc_start: 0.6507 (OUTLIER) cc_final: 0.5744 (ttp80)
REVERT: P1   91 ASP cc_start: 0.8736 (t0) cc_final: 0.8318 (t70)
REVERT: P1  113 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.7961 (p0)
REVERT: C3   76 TYR cc_start: 0.4891 (OUTLIER) cc_final: 0.3699 (t80)
REVERT: C3  149 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7238 (tt0)
REVERT: C3  250 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7160 (mm)
REVERT: C3  263 GLN cc_start: 0.4822 (OUTLIER) cc_final: 0.4599 (pm20)
REVERT: C3  428 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8140 (m)
REVERT: C2   76 TYR cc_start: 0.4993 (OUTLIER) cc_final: 0.2553 (t80)
REVERT: C2  123 ASP cc_start: 0.8285 (t70) cc_final: 0.7985 (t0)
REVERT: C2  243 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7783 (mm)
REVERT: C2  250 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6858 (mm)
REVERT: P2  158 HIS cc_start: 0.6624 (t-90) cc_final: 0.6021 (t70)
  outliers start: 78
  outliers final: 56
  residues processed: 179
  average time/residue: 0.0931
  time to fit residues: 25.7048
Evaluate side-chains
  184 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 116
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C1 residue   50 PHE
Chi-restraints excluded: chain C1 residue   58 SER
Chi-restraints excluded: chain C1 residue  192 THR
Chi-restraints excluded: chain C1 residue  215 LEU
Chi-restraints excluded: chain C1 residue  235 LEU
Chi-restraints excluded: chain C1 residue  243 LEU
Chi-restraints excluded: chain C1 residue  259 ILE
Chi-restraints excluded: chain C1 residue  263 GLN
Chi-restraints excluded: chain C1 residue  269 THR
Chi-restraints excluded: chain C1 residue  338 LEU
Chi-restraints excluded: chain C1 residue  345 VAL
Chi-restraints excluded: chain C1 residue  350 ARG
Chi-restraints excluded: chain C1 residue  422 ILE
Chi-restraints excluded: chain C1 residue  434 LEU
Chi-restraints excluded: chain P1 residue   22 VAL
Chi-restraints excluded: chain P1 residue   52 ARG
Chi-restraints excluded: chain P1 residue   77 ASP
Chi-restraints excluded: chain P1 residue  113 ASN
Chi-restraints excluded: chain P1 residue  123 VAL
Chi-restraints excluded: chain P1 residue  147 ILE
Chi-restraints excluded: chain C3 residue   50 PHE
Chi-restraints excluded: chain C3 residue   58 SER
Chi-restraints excluded: chain C3 residue   76 TYR
Chi-restraints excluded: chain C3 residue   87 THR
Chi-restraints excluded: chain C3 residue  142 ILE
Chi-restraints excluded: chain C3 residue  149 GLN
Chi-restraints excluded: chain C3 residue  215 LEU
Chi-restraints excluded: chain C3 residue  220 VAL
Chi-restraints excluded: chain C3 residue  250 LEU
Chi-restraints excluded: chain C3 residue  259 ILE
Chi-restraints excluded: chain C3 residue  263 GLN
Chi-restraints excluded: chain C3 residue  314 ILE
Chi-restraints excluded: chain C3 residue  345 VAL
Chi-restraints excluded: chain C3 residue  424 SER
Chi-restraints excluded: chain C3 residue  428 THR
Chi-restraints excluded: chain P3 residue   22 VAL
Chi-restraints excluded: chain P3 residue   31 THR
Chi-restraints excluded: chain P3 residue   67 LEU
Chi-restraints excluded: chain P3 residue   77 ASP
Chi-restraints excluded: chain P3 residue  123 VAL
Chi-restraints excluded: chain P3 residue  136 VAL
Chi-restraints excluded: chain P3 residue  147 ILE
Chi-restraints excluded: chain P3 residue  163 THR
Chi-restraints excluded: chain P3 residue  167 SER
Chi-restraints excluded: chain C2 residue   34 LEU
Chi-restraints excluded: chain C2 residue   76 TYR
Chi-restraints excluded: chain C2 residue   87 THR
Chi-restraints excluded: chain C2 residue  159 LEU
Chi-restraints excluded: chain C2 residue  195 ASN
Chi-restraints excluded: chain C2 residue  215 LEU
Chi-restraints excluded: chain C2 residue  243 LEU
Chi-restraints excluded: chain C2 residue  250 LEU
Chi-restraints excluded: chain C2 residue  259 ILE
Chi-restraints excluded: chain C2 residue  301 MET
Chi-restraints excluded: chain C2 residue  303 GLN
Chi-restraints excluded: chain C2 residue  345 VAL
Chi-restraints excluded: chain C2 residue  356 ILE
Chi-restraints excluded: chain C2 residue  370 VAL
Chi-restraints excluded: chain C2 residue  393 ASP
Chi-restraints excluded: chain C2 residue  401 LEU
Chi-restraints excluded: chain C2 residue  422 ILE
Chi-restraints excluded: chain C2 residue  433 ASP
Chi-restraints excluded: chain P2 residue   22 VAL
Chi-restraints excluded: chain P2 residue   77 ASP
Chi-restraints excluded: chain P2 residue  123 VAL
Chi-restraints excluded: chain P2 residue  147 ILE
Chi-restraints excluded: chain P2 residue  157 VAL
Chi-restraints excluded: chain P2 residue  163 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 112 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 142 optimal weight:    5.9990
   chunk 99 optimal weight:    0.4980
   chunk 128 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 147 optimal weight:    0.6980
   chunk 108 optimal weight:    0.0020
   chunk 98 optimal weight:    0.9990
   chunk 124 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
** C1 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C3 149 GLN
P3 158 HIS
** C2  36 ASN ** 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 = 0.3573 r_free = 0.3573 target = 0.133274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.112902 restraints weight = 19104.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.116609 restraints weight = 10348.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.119122 restraints weight = 6766.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.120802 restraints weight = 5029.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.121977 restraints weight = 4069.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.1229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13734  Z= 0.136
  Angle     :  0.521   6.277  18678  Z= 0.281
  Chirality :  0.037   0.173   2154
  Planarity :  0.004   0.052   2502
  Dihedral  :  4.065  51.112   1923
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.55 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 27.64 %
    Favored  : 67.68 %
  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:  1.97 (0.21), residues: 1740
  helix:  3.53 (0.15), residues: 996
  sheet:  0.80 (0.34), residues: 204
  loop : -3.18 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARGP1  96 
 TYR   0.018   0.001   TYRC3 135 
 PHE   0.011   0.001   PHEC3 310 
 TRP   0.009   0.001   TRPP3 132 
 HIS   0.006   0.001   HISP3 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (13731)
  covalent geometry    : angle       0.52066 (18672)
  SS BOND              : bond        0.00297 (    3)
  SS BOND              : angle       0.58943 (    6)
  hydrogen bonds       : bond        0.05482 ( 1052)
  hydrogen bonds       : angle       4.04207 ( 3096)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 123
  time to evaluate  : 0.521 
Fit side-chains
REVERT: C1  263 GLN cc_start: 0.4911 (OUTLIER) cc_final: 0.4585 (pm20)
REVERT: C1  350 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6374 (mpt-90)
REVERT: P1   52 ARG cc_start: 0.6491 (OUTLIER) cc_final: 0.5842 (ttp80)
REVERT: P1   91 ASP cc_start: 0.8716 (t0) cc_final: 0.8319 (t70)
REVERT: C3   76 TYR cc_start: 0.4851 (OUTLIER) cc_final: 0.3591 (t80)
REVERT: C3  149 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7533 (tt0)
REVERT: C3  250 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7275 (mm)
REVERT: C3  428 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.8117 (m)
REVERT: C2   76 TYR cc_start: 0.4931 (OUTLIER) cc_final: 0.2526 (t80)
REVERT: C2  123 ASP cc_start: 0.8218 (t70) cc_final: 0.7963 (t0)
REVERT: C2  243 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7723 (mm)
REVERT: C2  250 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7058 (mm)
  outliers start: 69
  outliers final: 49
  residues processed: 175
  average time/residue: 0.1051
  time to fit residues: 27.8238
Evaluate side-chains
  179 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 120
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C1 residue   50 PHE
Chi-restraints excluded: chain C1 residue   58 SER
Chi-restraints excluded: chain C1 residue  192 THR
Chi-restraints excluded: chain C1 residue  235 LEU
Chi-restraints excluded: chain C1 residue  243 LEU
Chi-restraints excluded: chain C1 residue  259 ILE
Chi-restraints excluded: chain C1 residue  263 GLN
Chi-restraints excluded: chain C1 residue  350 ARG
Chi-restraints excluded: chain C1 residue  414 ASN
Chi-restraints excluded: chain C1 residue  422 ILE
Chi-restraints excluded: chain C1 residue  434 LEU
Chi-restraints excluded: chain P1 residue   22 VAL
Chi-restraints excluded: chain P1 residue   52 ARG
Chi-restraints excluded: chain P1 residue   77 ASP
Chi-restraints excluded: chain P1 residue  123 VAL
Chi-restraints excluded: chain P1 residue  147 ILE
Chi-restraints excluded: chain C3 residue   50 PHE
Chi-restraints excluded: chain C3 residue   58 SER
Chi-restraints excluded: chain C3 residue   76 TYR
Chi-restraints excluded: chain C3 residue  142 ILE
Chi-restraints excluded: chain C3 residue  149 GLN
Chi-restraints excluded: chain C3 residue  215 LEU
Chi-restraints excluded: chain C3 residue  220 VAL
Chi-restraints excluded: chain C3 residue  250 LEU
Chi-restraints excluded: chain C3 residue  259 ILE
Chi-restraints excluded: chain C3 residue  269 THR
Chi-restraints excluded: chain C3 residue  314 ILE
Chi-restraints excluded: chain C3 residue  345 VAL
Chi-restraints excluded: chain C3 residue  424 SER
Chi-restraints excluded: chain C3 residue  428 THR
Chi-restraints excluded: chain P3 residue   22 VAL
Chi-restraints excluded: chain P3 residue   31 THR
Chi-restraints excluded: chain P3 residue   67 LEU
Chi-restraints excluded: chain P3 residue   77 ASP
Chi-restraints excluded: chain P3 residue  123 VAL
Chi-restraints excluded: chain P3 residue  136 VAL
Chi-restraints excluded: chain P3 residue  158 HIS
Chi-restraints excluded: chain P3 residue  163 THR
Chi-restraints excluded: chain P3 residue  167 SER
Chi-restraints excluded: chain C2 residue   34 LEU
Chi-restraints excluded: chain C2 residue   76 TYR
Chi-restraints excluded: chain C2 residue   87 THR
Chi-restraints excluded: chain C2 residue  159 LEU
Chi-restraints excluded: chain C2 residue  195 ASN
Chi-restraints excluded: chain C2 residue  215 LEU
Chi-restraints excluded: chain C2 residue  243 LEU
Chi-restraints excluded: chain C2 residue  250 LEU
Chi-restraints excluded: chain C2 residue  259 ILE
Chi-restraints excluded: chain C2 residue  301 MET
Chi-restraints excluded: chain C2 residue  303 GLN
Chi-restraints excluded: chain C2 residue  356 ILE
Chi-restraints excluded: chain C2 residue  393 ASP
Chi-restraints excluded: chain C2 residue  433 ASP
Chi-restraints excluded: chain P2 residue   22 VAL
Chi-restraints excluded: chain P2 residue   77 ASP
Chi-restraints excluded: chain P2 residue  123 VAL
Chi-restraints excluded: chain P2 residue  147 ILE
Chi-restraints excluded: chain P2 residue  157 VAL
Chi-restraints excluded: chain P2 residue  163 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 106 optimal weight:    0.9980
   chunk 119 optimal weight:    0.0770
   chunk 172 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 81 optimal weight:    0.8980
   chunk 124 optimal weight:    0.8980
   chunk 160 optimal weight:    0.0070
   chunk 165 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.4356

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

Flipped N/Q/H residues before XYZ refinement:
C1  36 ASN
** C1 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P1 113 ASN
** P1 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C3 149 GLN
P3 158 HIS
** C2  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C2  95 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.134977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.114777 restraints weight = 18862.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.118463 restraints weight = 10259.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.120934 restraints weight = 6731.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.122588 restraints weight = 5016.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.123788 restraints weight = 4070.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.1284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13734  Z= 0.127
  Angle     :  0.512   5.513  18678  Z= 0.276
  Chirality :  0.037   0.162   2154
  Planarity :  0.003   0.049   2502
  Dihedral  :  4.025  51.477   1923
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.78 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 28.05 %
    Favored  : 67.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.05 (0.21), residues: 1740
  helix:  3.58 (0.15), residues: 996
  sheet:  0.85 (0.33), residues: 204
  loop : -3.13 (0.23), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARGP1  96 
 TYR   0.015   0.001   TYRC3 135 
 PHE   0.011   0.001   PHEC3 310 
 TRP   0.008   0.001   TRPP3 132 
 HIS   0.018   0.001   HISP3 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (13731)
  covalent geometry    : angle       0.51234 (18672)
  SS BOND              : bond        0.00278 (    3)
  SS BOND              : angle       0.55222 (    6)
  hydrogen bonds       : bond        0.05268 ( 1052)
  hydrogen bonds       : angle       3.97140 ( 3096)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 125
  time to evaluate  : 0.584 
Fit side-chains
REVERT: C1  263 GLN cc_start: 0.4935 (OUTLIER) cc_final: 0.4614 (pm20)
REVERT: C1  350 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6227 (mpt-90)
REVERT: P1   52 ARG cc_start: 0.6447 (OUTLIER) cc_final: 0.5817 (ttp80)
REVERT: P1   91 ASP cc_start: 0.8697 (t0) cc_final: 0.8295 (t0)
REVERT: P1   96 ARG cc_start: 0.7582 (mpp80) cc_final: 0.6783 (mpp80)
REVERT: P1  113 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7945 (p0)
REVERT: C3   76 TYR cc_start: 0.4733 (OUTLIER) cc_final: 0.3502 (t80)
REVERT: C3  250 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7295 (mm)
REVERT: C3  428 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.8078 (m)
REVERT: C2   76 TYR cc_start: 0.5020 (OUTLIER) cc_final: 0.2563 (t80)
REVERT: C2  123 ASP cc_start: 0.8194 (t70) cc_final: 0.7953 (t0)
REVERT: C2  243 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7712 (mm)
REVERT: C2  250 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7134 (mm)
  outliers start: 66
  outliers final: 42
  residues processed: 176
  average time/residue: 0.1001
  time to fit residues: 27.2273
Evaluate side-chains
  172 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 120
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C1 residue   50 PHE
Chi-restraints excluded: chain C1 residue   58 SER
Chi-restraints excluded: chain C1 residue  192 THR
Chi-restraints excluded: chain C1 residue  215 LEU
Chi-restraints excluded: chain C1 residue  235 LEU
Chi-restraints excluded: chain C1 residue  259 ILE
Chi-restraints excluded: chain C1 residue  263 GLN
Chi-restraints excluded: chain C1 residue  269 THR
Chi-restraints excluded: chain C1 residue  350 ARG
Chi-restraints excluded: chain C1 residue  414 ASN
Chi-restraints excluded: chain C1 residue  434 LEU
Chi-restraints excluded: chain P1 residue   22 VAL
Chi-restraints excluded: chain P1 residue   52 ARG
Chi-restraints excluded: chain P1 residue   77 ASP
Chi-restraints excluded: chain P1 residue  113 ASN
Chi-restraints excluded: chain P1 residue  123 VAL
Chi-restraints excluded: chain P1 residue  147 ILE
Chi-restraints excluded: chain C3 residue   58 SER
Chi-restraints excluded: chain C3 residue   76 TYR
Chi-restraints excluded: chain C3 residue  215 LEU
Chi-restraints excluded: chain C3 residue  220 VAL
Chi-restraints excluded: chain C3 residue  250 LEU
Chi-restraints excluded: chain C3 residue  259 ILE
Chi-restraints excluded: chain C3 residue  269 THR
Chi-restraints excluded: chain C3 residue  314 ILE
Chi-restraints excluded: chain C3 residue  424 SER
Chi-restraints excluded: chain C3 residue  428 THR
Chi-restraints excluded: chain P3 residue   22 VAL
Chi-restraints excluded: chain P3 residue   67 LEU
Chi-restraints excluded: chain P3 residue   77 ASP
Chi-restraints excluded: chain P3 residue   88 LEU
Chi-restraints excluded: chain P3 residue  123 VAL
Chi-restraints excluded: chain P3 residue  136 VAL
Chi-restraints excluded: chain C2 residue   34 LEU
Chi-restraints excluded: chain C2 residue   76 TYR
Chi-restraints excluded: chain C2 residue   87 THR
Chi-restraints excluded: chain C2 residue  159 LEU
Chi-restraints excluded: chain C2 residue  215 LEU
Chi-restraints excluded: chain C2 residue  243 LEU
Chi-restraints excluded: chain C2 residue  250 LEU
Chi-restraints excluded: chain C2 residue  259 ILE
Chi-restraints excluded: chain C2 residue  301 MET
Chi-restraints excluded: chain C2 residue  303 GLN
Chi-restraints excluded: chain C2 residue  356 ILE
Chi-restraints excluded: chain C2 residue  370 VAL
Chi-restraints excluded: chain C2 residue  433 ASP
Chi-restraints excluded: chain P2 residue   22 VAL
Chi-restraints excluded: chain P2 residue   77 ASP
Chi-restraints excluded: chain P2 residue  123 VAL
Chi-restraints excluded: chain P2 residue  147 ILE
Chi-restraints excluded: chain P2 residue  157 VAL
Chi-restraints excluded: chain P2 residue  163 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 104 optimal weight:    0.9980
   chunk 96 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 114 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 167 optimal weight:    0.0770
   chunk 66 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** C1  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C2  36 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 = 0.3589 r_free = 0.3589 target = 0.134541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.114259 restraints weight = 19054.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.117944 restraints weight = 10366.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.120428 restraints weight = 6803.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.122146 restraints weight = 5042.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.123257 restraints weight = 4086.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.1293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13734  Z= 0.134
  Angle     :  0.519   6.050  18678  Z= 0.280
  Chirality :  0.037   0.162   2154
  Planarity :  0.004   0.067   2502
  Dihedral  :  3.983  51.455   1921
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.55 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 28.18 %
    Favored  : 67.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.21), residues: 1740
  helix:  3.55 (0.15), residues: 996
  sheet:  0.89 (0.33), residues: 204
  loop : -3.13 (0.23), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARGP1  96 
 TYR   0.014   0.001   TYRC3 135 
 PHE   0.011   0.001   PHEC3 310 
 TRP   0.009   0.001   TRPP1 132 
 HIS   0.013   0.001   HISP3 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (13731)
  covalent geometry    : angle       0.51878 (18672)
  SS BOND              : bond        0.00293 (    3)
  SS BOND              : angle       0.57363 (    6)
  hydrogen bonds       : bond        0.05287 ( 1052)
  hydrogen bonds       : angle       3.97702 ( 3096)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 124
  time to evaluate  : 0.322 
Fit side-chains
REVERT: C1  263 GLN cc_start: 0.4943 (OUTLIER) cc_final: 0.4605 (pm20)
REVERT: C1  350 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6231 (mpt-90)
REVERT: P1   52 ARG cc_start: 0.6461 (OUTLIER) cc_final: 0.5822 (ttp80)
REVERT: P1   91 ASP cc_start: 0.8706 (t0) cc_final: 0.8319 (t0)
REVERT: P1   96 ARG cc_start: 0.7658 (mpp80) cc_final: 0.6853 (mpp80)
REVERT: C3   76 TYR cc_start: 0.4746 (OUTLIER) cc_final: 0.3433 (t80)
REVERT: C3  250 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7260 (mm)
REVERT: C3  428 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8080 (m)
REVERT: C2   76 TYR cc_start: 0.4959 (OUTLIER) cc_final: 0.2423 (t80)
REVERT: C2  123 ASP cc_start: 0.8194 (t70) cc_final: 0.7960 (t0)
REVERT: C2  243 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7726 (mm)
REVERT: C2  250 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7082 (mm)
REVERT: C2  359 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.7810 (t)
  outliers start: 64
  outliers final: 49
  residues processed: 175
  average time/residue: 0.0963
  time to fit residues: 25.9614
Evaluate side-chains
  179 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 120
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C1 residue   50 PHE
Chi-restraints excluded: chain C1 residue   58 SER
Chi-restraints excluded: chain C1 residue  192 THR
Chi-restraints excluded: chain C1 residue  215 LEU
Chi-restraints excluded: chain C1 residue  235 LEU
Chi-restraints excluded: chain C1 residue  259 ILE
Chi-restraints excluded: chain C1 residue  263 GLN
Chi-restraints excluded: chain C1 residue  269 THR
Chi-restraints excluded: chain C1 residue  345 VAL
Chi-restraints excluded: chain C1 residue  350 ARG
Chi-restraints excluded: chain C1 residue  414 ASN
Chi-restraints excluded: chain C1 residue  434 LEU
Chi-restraints excluded: chain P1 residue   22 VAL
Chi-restraints excluded: chain P1 residue   52 ARG
Chi-restraints excluded: chain P1 residue   77 ASP
Chi-restraints excluded: chain P1 residue  123 VAL
Chi-restraints excluded: chain P1 residue  147 ILE
Chi-restraints excluded: chain C3 residue   58 SER
Chi-restraints excluded: chain C3 residue   76 TYR
Chi-restraints excluded: chain C3 residue  142 ILE
Chi-restraints excluded: chain C3 residue  215 LEU
Chi-restraints excluded: chain C3 residue  220 VAL
Chi-restraints excluded: chain C3 residue  250 LEU
Chi-restraints excluded: chain C3 residue  259 ILE
Chi-restraints excluded: chain C3 residue  269 THR
Chi-restraints excluded: chain C3 residue  314 ILE
Chi-restraints excluded: chain C3 residue  345 VAL
Chi-restraints excluded: chain C3 residue  424 SER
Chi-restraints excluded: chain C3 residue  428 THR
Chi-restraints excluded: chain P3 residue   22 VAL
Chi-restraints excluded: chain P3 residue   67 LEU
Chi-restraints excluded: chain P3 residue   77 ASP
Chi-restraints excluded: chain P3 residue   88 LEU
Chi-restraints excluded: chain P3 residue  123 VAL
Chi-restraints excluded: chain P3 residue  136 VAL
Chi-restraints excluded: chain P3 residue  163 THR
Chi-restraints excluded: chain C2 residue   34 LEU
Chi-restraints excluded: chain C2 residue   76 TYR
Chi-restraints excluded: chain C2 residue   87 THR
Chi-restraints excluded: chain C2 residue  159 LEU
Chi-restraints excluded: chain C2 residue  195 ASN
Chi-restraints excluded: chain C2 residue  215 LEU
Chi-restraints excluded: chain C2 residue  243 LEU
Chi-restraints excluded: chain C2 residue  250 LEU
Chi-restraints excluded: chain C2 residue  259 ILE
Chi-restraints excluded: chain C2 residue  301 MET
Chi-restraints excluded: chain C2 residue  303 GLN
Chi-restraints excluded: chain C2 residue  345 VAL
Chi-restraints excluded: chain C2 residue  356 ILE
Chi-restraints excluded: chain C2 residue  359 SER
Chi-restraints excluded: chain C2 residue  370 VAL
Chi-restraints excluded: chain C2 residue  422 ILE
Chi-restraints excluded: chain C2 residue  433 ASP
Chi-restraints excluded: chain P2 residue   22 VAL
Chi-restraints excluded: chain P2 residue   77 ASP
Chi-restraints excluded: chain P2 residue  123 VAL
Chi-restraints excluded: chain P2 residue  147 ILE
Chi-restraints excluded: chain P2 residue  157 VAL
Chi-restraints excluded: chain P2 residue  163 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 113 optimal weight:    0.0570
   chunk 101 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 114 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 26 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
** C1  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P1 113 ASN
** P1 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C3 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C2  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.134230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.113989 restraints weight = 19048.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.117675 restraints weight = 10384.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.120121 restraints weight = 6800.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.121867 restraints weight = 5059.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.122978 restraints weight = 4095.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.1326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13734  Z= 0.137
  Angle     :  0.524   5.727  18678  Z= 0.283
  Chirality :  0.037   0.161   2154
  Planarity :  0.004   0.070   2502
  Dihedral  :  3.977  51.525   1921
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.72 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 27.98 %
    Favored  : 67.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.98 (0.21), residues: 1740
  helix:  3.54 (0.15), residues: 996
  sheet:  0.73 (0.33), residues: 204
  loop : -3.14 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARGP1  96 
 TYR   0.013   0.001   TYRC1 135 
 PHE   0.011   0.002   PHEP3  48 
 TRP   0.010   0.001   TRPP1 132 
 HIS   0.013   0.001   HISP3 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (13731)
  covalent geometry    : angle       0.52421 (18672)
  SS BOND              : bond        0.00287 (    3)
  SS BOND              : angle       0.58005 (    6)
  hydrogen bonds       : bond        0.05310 ( 1052)
  hydrogen bonds       : angle       3.98069 ( 3096)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 124
  time to evaluate  : 0.498 
Fit side-chains
REVERT: C1  263 GLN cc_start: 0.4953 (OUTLIER) cc_final: 0.4617 (pm20)
REVERT: C1  350 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.6238 (mpt-90)
REVERT: P1   52 ARG cc_start: 0.6463 (OUTLIER) cc_final: 0.5854 (ttp80)
REVERT: P1   96 ARG cc_start: 0.7635 (mpp80) cc_final: 0.6826 (mpp80)
REVERT: C3   76 TYR cc_start: 0.4758 (OUTLIER) cc_final: 0.3375 (t80)
REVERT: C3  250 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7235 (mm)
REVERT: C3  428 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.8083 (m)
REVERT: C2   76 TYR cc_start: 0.4835 (OUTLIER) cc_final: 0.2386 (t80)
REVERT: C2  123 ASP cc_start: 0.8196 (t70) cc_final: 0.7965 (t0)
REVERT: C2  243 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7733 (mm)
REVERT: C2  250 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7088 (mm)
REVERT: C2  359 SER cc_start: 0.8379 (OUTLIER) cc_final: 0.7817 (t)
  outliers start: 67
  outliers final: 51
  residues processed: 176
  average time/residue: 0.0912
  time to fit residues: 24.9184
Evaluate side-chains
  181 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 120
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C1 residue   50 PHE
Chi-restraints excluded: chain C1 residue   58 SER
Chi-restraints excluded: chain C1 residue  192 THR
Chi-restraints excluded: chain C1 residue  215 LEU
Chi-restraints excluded: chain C1 residue  231 VAL
Chi-restraints excluded: chain C1 residue  235 LEU
Chi-restraints excluded: chain C1 residue  259 ILE
Chi-restraints excluded: chain C1 residue  263 GLN
Chi-restraints excluded: chain C1 residue  269 THR
Chi-restraints excluded: chain C1 residue  345 VAL
Chi-restraints excluded: chain C1 residue  350 ARG
Chi-restraints excluded: chain C1 residue  414 ASN
Chi-restraints excluded: chain C1 residue  434 LEU
Chi-restraints excluded: chain P1 residue   22 VAL
Chi-restraints excluded: chain P1 residue   52 ARG
Chi-restraints excluded: chain P1 residue   77 ASP
Chi-restraints excluded: chain P1 residue  123 VAL
Chi-restraints excluded: chain P1 residue  147 ILE
Chi-restraints excluded: chain P1 residue  166 GLN
Chi-restraints excluded: chain C3 residue   50 PHE
Chi-restraints excluded: chain C3 residue   58 SER
Chi-restraints excluded: chain C3 residue   76 TYR
Chi-restraints excluded: chain C3 residue  142 ILE
Chi-restraints excluded: chain C3 residue  215 LEU
Chi-restraints excluded: chain C3 residue  250 LEU
Chi-restraints excluded: chain C3 residue  259 ILE
Chi-restraints excluded: chain C3 residue  269 THR
Chi-restraints excluded: chain C3 residue  314 ILE
Chi-restraints excluded: chain C3 residue  345 VAL
Chi-restraints excluded: chain C3 residue  424 SER
Chi-restraints excluded: chain C3 residue  428 THR
Chi-restraints excluded: chain P3 residue   22 VAL
Chi-restraints excluded: chain P3 residue   67 LEU
Chi-restraints excluded: chain P3 residue   77 ASP
Chi-restraints excluded: chain P3 residue   88 LEU
Chi-restraints excluded: chain P3 residue  123 VAL
Chi-restraints excluded: chain P3 residue  136 VAL
Chi-restraints excluded: chain P3 residue  147 ILE
Chi-restraints excluded: chain P3 residue  163 THR
Chi-restraints excluded: chain C2 residue   34 LEU
Chi-restraints excluded: chain C2 residue   76 TYR
Chi-restraints excluded: chain C2 residue   87 THR
Chi-restraints excluded: chain C2 residue  159 LEU
Chi-restraints excluded: chain C2 residue  195 ASN
Chi-restraints excluded: chain C2 residue  215 LEU
Chi-restraints excluded: chain C2 residue  243 LEU
Chi-restraints excluded: chain C2 residue  250 LEU
Chi-restraints excluded: chain C2 residue  259 ILE
Chi-restraints excluded: chain C2 residue  303 GLN
Chi-restraints excluded: chain C2 residue  345 VAL
Chi-restraints excluded: chain C2 residue  356 ILE
Chi-restraints excluded: chain C2 residue  359 SER
Chi-restraints excluded: chain C2 residue  370 VAL
Chi-restraints excluded: chain C2 residue  422 ILE
Chi-restraints excluded: chain C2 residue  433 ASP
Chi-restraints excluded: chain P2 residue   22 VAL
Chi-restraints excluded: chain P2 residue   77 ASP
Chi-restraints excluded: chain P2 residue  123 VAL
Chi-restraints excluded: chain P2 residue  147 ILE
Chi-restraints excluded: chain P2 residue  157 VAL
Chi-restraints excluded: chain P2 residue  163 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 111 optimal weight:    0.8980
   chunk 59 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 141 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 99 optimal weight:    1.9990
   chunk 168 optimal weight:    0.2980
   chunk 134 optimal weight:    0.6980
   chunk 109 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** C1  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C3 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C2  36 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 = 0.3588 r_free = 0.3588 target = 0.134442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.114152 restraints weight = 19138.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.117842 restraints weight = 10420.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.120342 restraints weight = 6832.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.121995 restraints weight = 5085.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.123170 restraints weight = 4122.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.1350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13734  Z= 0.137
  Angle     :  0.527   6.015  18678  Z= 0.283
  Chirality :  0.037   0.165   2154
  Planarity :  0.004   0.069   2502
  Dihedral  :  3.976  51.612   1921
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.67 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 27.91 %
    Favored  : 67.62 %
  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:  2.00 (0.21), residues: 1740
  helix:  3.55 (0.15), residues: 996
  sheet:  0.74 (0.33), residues: 204
  loop : -3.13 (0.23), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARGP1  96 
 TYR   0.013   0.001   TYRC1 135 
 PHE   0.011   0.001   PHEP3  48 
 TRP   0.010   0.001   TRPP3 132 
 HIS   0.013   0.001   HISP3 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (13731)
  covalent geometry    : angle       0.52683 (18672)
  SS BOND              : bond        0.00306 (    3)
  SS BOND              : angle       0.58271 (    6)
  hydrogen bonds       : bond        0.05302 ( 1052)
  hydrogen bonds       : angle       3.97586 ( 3096)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1803.53 seconds
wall clock time: 32 minutes 4.07 seconds (1924.07 seconds total)