Starting phenix.real_space_refine
on Fri May  9 16:58:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gzy_51737/05_2025/9gzy_51737.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gzy_51737/05_2025/9gzy_51737.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gzy_51737/05_2025/9gzy_51737.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gzy_51737/05_2025/9gzy_51737.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gzy_51737/05_2025/9gzy_51737.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gzy_51737/05_2025/9gzy_51737.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    2040      2.51       5
     N     576      2.21       5
     O     660      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3276
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 171
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 171
          Classifications: {'peptide': 23}
          Link IDs: {'TRANS': 22}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 101
          Classifications: {'peptide': 14}
          Link IDs: {'TRANS': 13}
  Restraints were copied for chains:
    B, E, F, I, J, M, N, Q, R, U, V, D, G, H, K, L, O, P, S, T, W, X
  Time building chain proxies: 1.55, per 1000 atoms: 0.47
  Number of scatterers: 3276
  At special positions: 0
  Unit cell: (111.005, 72.265, 46.935, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     660      8.00
     N     576      7.00
     C    2040      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=12, symmetry=0
  Number of additional bonds: simple=12, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 387.6 milliseconds
  

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  816

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 56.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 22
      removed outlier: 6.321A  pdb=" N   VAL I  17 " --> pdb=" O   HIS M  18 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   SER M  20 " --> pdb=" O   VAL I  17 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   SER I  19 " --> pdb=" O   SER M  20 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   ASN M  22 " --> pdb=" O   SER I  19 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ASN I  21 " --> pdb=" O   ASN M  22 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 33
      removed outlier: 6.446A  pdb=" N   LEU I  27 " --> pdb=" O   SER M  28 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   THR M  30 " --> pdb=" O   LEU I  27 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   SER I  29 " --> pdb=" O   THR M  30 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   VAL M  32 " --> pdb=" O   SER I  29 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ASN I  31 " --> pdb=" O   VAL M  32 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   LEU Q  27 " --> pdb=" O   SER U  28 " (cutoff:3.500A)
      removed outlier: 7.922A  pdb=" N   THR U  30 " --> pdb=" O   LEU Q  27 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   SER Q  29 " --> pdb=" O   THR U  30 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   VAL U  32 " --> pdb=" O   SER Q  29 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   ASN Q  31 " --> pdb=" O   VAL U  32 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 16 through 22
    Processing sheet with id=AA4, first strand: chain 'B' and resid 26 through 33
      removed outlier: 6.420A  pdb=" N   LEU B  27 " --> pdb=" O   SER F  28 " (cutoff:3.500A)
      removed outlier: 7.895A  pdb=" N   THR F  30 " --> pdb=" O   LEU B  27 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   SER B  29 " --> pdb=" O   THR F  30 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   VAL F  32 " --> pdb=" O   SER B  29 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   ASN B  31 " --> pdb=" O   VAL F  32 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   LEU F  27 " --> pdb=" O   SER J  28 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   THR J  30 " --> pdb=" O   LEU F  27 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   SER F  29 " --> pdb=" O   THR J  30 " (cutoff:3.500A)
      removed outlier: 7.963A  pdb=" N   VAL J  32 " --> pdb=" O   SER F  29 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   ASN F  31 " --> pdb=" O   VAL J  32 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   LEU J  27 " --> pdb=" O   SER N  28 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   THR N  30 " --> pdb=" O   LEU J  27 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   SER J  29 " --> pdb=" O   THR N  30 " (cutoff:3.500A)
      removed outlier: 7.958A  pdb=" N   VAL N  32 " --> pdb=" O   SER J  29 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   ASN J  31 " --> pdb=" O   VAL N  32 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   LEU N  27 " --> pdb=" O   SER R  28 " (cutoff:3.500A)
      removed outlier: 7.895A  pdb=" N   THR R  30 " --> pdb=" O   LEU N  27 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   SER N  29 " --> pdb=" O   THR R  30 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   VAL R  32 " --> pdb=" O   SER N  29 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   ASN N  31 " --> pdb=" O   VAL R  32 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   LEU R  27 " --> pdb=" O   SER V  28 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   THR V  30 " --> pdb=" O   LEU R  27 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   SER R  29 " --> pdb=" O   THR V  30 " (cutoff:3.500A)
      removed outlier: 7.963A  pdb=" N   VAL V  32 " --> pdb=" O   SER R  29 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   ASN R  31 " --> pdb=" O   VAL V  32 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 17 through 22
      removed outlier: 6.562A  pdb=" N   VAL C  17 " --> pdb=" O   HIS G  18 " (cutoff:3.500A)
      removed outlier: 8.057A  pdb=" N   SER G  20 " --> pdb=" O   VAL C  17 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   SER C  19 " --> pdb=" O   SER G  20 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ASN G  22 " --> pdb=" O   SER C  19 " (cutoff:3.500A)
      removed outlier: 8.337A  pdb=" N   ASN C  21 " --> pdb=" O   ASN G  22 " (cutoff:3.500A)
      removed outlier: 6.067A  pdb=" N   VAL G  17 " --> pdb=" O   HIS K  18 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   SER K  20 " --> pdb=" O   VAL G  17 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   SER G  19 " --> pdb=" O   SER K  20 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   ASN K  22 " --> pdb=" O   SER G  19 " (cutoff:3.500A)
      removed outlier: 7.754A  pdb=" N   ASN G  21 " --> pdb=" O   ASN K  22 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   VAL K  17 " --> pdb=" O   HIS O  18 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   SER O  20 " --> pdb=" O   VAL K  17 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   SER K  19 " --> pdb=" O   SER O  20 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ASN O  22 " --> pdb=" O   SER K  19 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   ASN K  21 " --> pdb=" O   ASN O  22 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   VAL O  17 " --> pdb=" O   HIS S  18 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   SER S  20 " --> pdb=" O   VAL O  17 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   SER O  19 " --> pdb=" O   SER S  20 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   ASN S  22 " --> pdb=" O   SER O  19 " (cutoff:3.500A)
      removed outlier: 7.814A  pdb=" N   ASN O  21 " --> pdb=" O   ASN S  22 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   VAL S  17 " --> pdb=" O   HIS W  18 " (cutoff:3.500A)
      removed outlier: 7.757A  pdb=" N   SER W  20 " --> pdb=" O   VAL S  17 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   SER S  19 " --> pdb=" O   SER W  20 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   ASN W  22 " --> pdb=" O   SER S  19 " (cutoff:3.500A)
      removed outlier: 8.386A  pdb=" N   ASN S  21 " --> pdb=" O   ASN W  22 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 25 through 28
      removed outlier: 6.701A  pdb=" N   ILE C  26 " --> pdb=" O   LEU G  27 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   ILE G  26 " --> pdb=" O   LEU K  27 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   ILE K  26 " --> pdb=" O   LEU O  27 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   ILE S  26 " --> pdb=" O   LEU W  27 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 17 through 22
      removed outlier: 6.432A  pdb=" N   VAL D  17 " --> pdb=" O   HIS H  18 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   SER H  20 " --> pdb=" O   VAL D  17 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   SER D  19 " --> pdb=" O   SER H  20 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   ASN H  22 " --> pdb=" O   SER D  19 " (cutoff:3.500A)
      removed outlier: 8.253A  pdb=" N   ASN D  21 " --> pdb=" O   ASN H  22 " (cutoff:3.500A)
      removed outlier: 5.981A  pdb=" N   VAL H  17 " --> pdb=" O   HIS L  18 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   SER L  20 " --> pdb=" O   VAL H  17 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   SER H  19 " --> pdb=" O   SER L  20 " (cutoff:3.500A)
      removed outlier: 5.882A  pdb=" N   ASN L  22 " --> pdb=" O   SER H  19 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   ASN H  21 " --> pdb=" O   ASN L  22 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   VAL L  17 " --> pdb=" O   HIS P  18 " (cutoff:3.500A)
      removed outlier: 7.958A  pdb=" N   SER P  20 " --> pdb=" O   VAL L  17 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   SER L  19 " --> pdb=" O   SER P  20 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   ASN P  22 " --> pdb=" O   SER L  19 " (cutoff:3.500A)
      removed outlier: 8.085A  pdb=" N   ASN L  21 " --> pdb=" O   ASN P  22 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   VAL P  17 " --> pdb=" O   HIS T  18 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   SER T  20 " --> pdb=" O   VAL P  17 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   SER P  19 " --> pdb=" O   SER T  20 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   ASN T  22 " --> pdb=" O   SER P  19 " (cutoff:3.500A)
      removed outlier: 7.861A  pdb=" N   ASN P  21 " --> pdb=" O   ASN T  22 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   VAL T  17 " --> pdb=" O   HIS X  18 " (cutoff:3.500A)
      removed outlier: 8.032A  pdb=" N   SER X  20 " --> pdb=" O   VAL T  17 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   SER T  19 " --> pdb=" O   SER X  20 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ASN X  22 " --> pdb=" O   SER T  19 " (cutoff:3.500A)
      removed outlier: 8.205A  pdb=" N   ASN T  21 " --> pdb=" O   ASN X  22 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'D' and resid 25 through 28
      removed outlier: 6.526A  pdb=" N   ILE H  26 " --> pdb=" O   LEU L  27 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ILE L  26 " --> pdb=" O   LEU P  27 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   ILE T  26 " --> pdb=" O   LEU X  27 " (cutoff:3.500A)

    84 hydrogen bonds defined for protein.
    252 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: 0.78

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 516
        1.29 -     1.35: 540
        1.35 -     1.41: 395
        1.41 -     1.48: 565
        1.48 -     1.54: 1296
  Bond restraints: 3312
  Sorted by residual:
  bond pdb=" CG1 ILE J  26 "
       pdb=" CD1 ILE J  26 "
    ideal  model  delta    sigma   weight residual
    1.513  1.473  0.040 3.90e-02 6.57e+02 1.04e+00
  bond pdb=" CG1 ILE F  26 "
       pdb=" CD1 ILE F  26 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 1.02e+00
  bond pdb=" CG1 ILE A  26 "
       pdb=" CD1 ILE A  26 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 1.02e+00
  bond pdb=" CG1 ILE I  26 "
       pdb=" CD1 ILE I  26 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 1.01e+00
  bond pdb=" CG1 ILE Q  26 "
       pdb=" CD1 ILE Q  26 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 1.01e+00
  ... (remaining 3307 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.99: 3906
        0.99 -     1.97: 393
        1.97 -     2.96: 129
        2.96 -     3.95: 24
        3.95 -     4.93: 24
  Bond angle restraints: 4476
  Sorted by residual:
  angle pdb=" N   VAL M  17 "
        pdb=" CA  VAL M  17 "
        pdb=" C   VAL M  17 "
      ideal   model   delta    sigma   weight residual
     107.24  111.92   -4.68 1.68e+00 3.54e-01 7.76e+00
  angle pdb=" N   VAL J  17 "
        pdb=" CA  VAL J  17 "
        pdb=" C   VAL J  17 "
      ideal   model   delta    sigma   weight residual
     107.24  111.92   -4.68 1.68e+00 3.54e-01 7.76e+00
  angle pdb=" N   VAL V  17 "
        pdb=" CA  VAL V  17 "
        pdb=" C   VAL V  17 "
      ideal   model   delta    sigma   weight residual
     107.24  111.91   -4.67 1.68e+00 3.54e-01 7.73e+00
  angle pdb=" N   VAL U  17 "
        pdb=" CA  VAL U  17 "
        pdb=" C   VAL U  17 "
      ideal   model   delta    sigma   weight residual
     107.24  111.91   -4.67 1.68e+00 3.54e-01 7.72e+00
  angle pdb=" N   VAL E  17 "
        pdb=" CA  VAL E  17 "
        pdb=" C   VAL E  17 "
      ideal   model   delta    sigma   weight residual
     107.24  111.90   -4.66 1.68e+00 3.54e-01 7.70e+00
  ... (remaining 4471 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.65: 1596
        8.65 -    17.29: 156
       17.29 -    25.94: 0
       25.94 -    34.59: 72
       34.59 -    43.23: 24
  Dihedral angle restraints: 1848
    sinusoidal: 600
      harmonic: 1248
  Sorted by residual:
  dihedral pdb=" CA  LEU V  16 "
           pdb=" CB  LEU V  16 "
           pdb=" CG  LEU V  16 "
           pdb=" CD1 LEU V  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.77   43.23     3      1.50e+01 4.44e-03 7.77e+00
  dihedral pdb=" CA  LEU J  16 "
           pdb=" CB  LEU J  16 "
           pdb=" CG  LEU J  16 "
           pdb=" CD1 LEU J  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.80   43.20     3      1.50e+01 4.44e-03 7.76e+00
  dihedral pdb=" CA  LEU I  16 "
           pdb=" CB  LEU I  16 "
           pdb=" CG  LEU I  16 "
           pdb=" CD1 LEU I  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.80   43.20     3      1.50e+01 4.44e-03 7.76e+00
  ... (remaining 1845 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 232
       0.024 -    0.048: 166
       0.048 -    0.072: 58
       0.072 -    0.096: 35
       0.096 -    0.121: 49
  Chirality restraints: 540
  Sorted by residual:
  chirality pdb=" CA  ILE X  26 "
            pdb=" N   ILE X  26 "
            pdb=" C   ILE X  26 "
            pdb=" CB  ILE X  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.63e-01
  chirality pdb=" CA  ILE C  26 "
            pdb=" N   ILE C  26 "
            pdb=" C   ILE C  26 "
            pdb=" CB  ILE C  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.55e-01
  chirality pdb=" CA  ILE T  26 "
            pdb=" N   ILE T  26 "
            pdb=" C   ILE T  26 "
            pdb=" CB  ILE T  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.55e-01
  ... (remaining 537 not shown)

  Planarity restraints: 564
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE L  23 "    0.001 2.00e-02 2.50e+03   1.02e-02 1.82e+00
        pdb=" CG  PHE L  23 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD1 PHE L  23 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE L  23 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE L  23 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE L  23 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE L  23 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE S  23 "   -0.001 2.00e-02 2.50e+03   1.02e-02 1.81e+00
        pdb=" CG  PHE S  23 "    0.017 2.00e-02 2.50e+03
        pdb=" CD1 PHE S  23 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE S  23 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE S  23 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 PHE S  23 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE S  23 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE O  23 "   -0.001 2.00e-02 2.50e+03   1.02e-02 1.81e+00
        pdb=" CG  PHE O  23 "    0.017 2.00e-02 2.50e+03
        pdb=" CD1 PHE O  23 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE O  23 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE O  23 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 PHE O  23 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE O  23 "    0.000 2.00e-02 2.50e+03
  ... (remaining 561 not shown)

  Histogram of nonbonded interaction distances:
        2.45 -     2.94: 1418
        2.94 -     3.43: 2536
        3.43 -     3.92: 5586
        3.92 -     4.41: 5602
        4.41 -     4.90: 11361
  Nonbonded interactions: 26503
  Sorted by model distance:
  nonbonded pdb=" N   NH2 Q  38 "
            pdb=" O   TYR U  37 "
     model   vdw
     2.446 3.120
  nonbonded pdb=" O   ASN P  22 "
            pdb=" N   PHE T  23 "
     model   vdw
     2.625 3.120
  nonbonded pdb=" N   NH2 I  38 "
            pdb=" O   TYR M  37 "
     model   vdw
     2.644 3.120
  nonbonded pdb=" N   NH2 M  38 "
            pdb=" O   TYR Q  37 "
     model   vdw
     2.660 3.120
  nonbonded pdb=" ND2 ASN P  22 "
            pdb=" OD1 ASN T  22 "
     model   vdw
     2.679 3.120
  ... (remaining 26498 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'Q'
  selection = chain 'R'
  selection = chain 'U'
  selection = chain 'V'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'S'
  selection = chain 'T'
  selection = chain 'W'
  selection = chain 'X'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.600
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     11.470
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
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      :  0.008   0.104   3324  Z= 0.654
  Angle     :  0.801   4.935   4476  Z= 0.461
  Chirality :  0.048   0.121    540
  Planarity :  0.003   0.010    564
  Dihedral  : 11.922  43.232   1032
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.34), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.26), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS R  18 
 PHE   0.018   0.004   PHE K  23 
 TYR   0.009   0.002   TYR J  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09233 (   84)
  hydrogen bonds       : angle       7.53311 (  252)
  covalent geometry    : bond        0.00492 ( 3312)
  covalent geometry    : angle       0.80132 ( 4476)
  Misc. bond           : bond        0.10298 (   12)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.332 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.2310
  time to fit residues: 14.4567
Evaluate side-chains
  36 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 15 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 28 optimal weight:   20.0000
   chunk 10 optimal weight:   30.0000
   chunk 17 optimal weight:   30.0000
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
B  21 ASN
E  21 ASN
F  21 ASN
I  31 ASN
I  35 ASN
J  21 ASN
J  31 ASN
M  21 ASN
M  31 ASN
N  21 ASN
Q  21 ASN
Q  31 ASN
Q  35 ASN
R  21 ASN
U  21 ASN
V  21 ASN
X  18 HIS

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.127984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.099116 restraints weight = 4592.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 2.33
r_work: 0.3819 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3698 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3324  Z= 0.116
  Angle     :  0.602   7.079   4476  Z= 0.285
  Chirality :  0.045   0.118    540
  Planarity :  0.002   0.007    564
  Dihedral  :  3.737  16.696    432
  Min Nonbonded Distance : 2.693

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  9.11 %
    Favored  : 90.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.54 (0.33), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.25), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS X  18 
 PHE   0.005   0.001   PHE Q  23 
 TYR   0.002   0.000   TYR A  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02040 (   84)
  hydrogen bonds       : angle       5.14474 (  252)
  covalent geometry    : bond        0.00243 ( 3312)
  covalent geometry    : angle       0.60213 ( 4476)
  Misc. bond           : bond        0.00068 (   12)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 34
  time to evaluate  : 0.396 
Fit side-chains
REVERT: S   22 ASN cc_start: 0.7924 (t0) cc_final: 0.7715 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 35
  average time/residue: 0.2197
  time to fit residues: 9.1930
Evaluate side-chains
  28 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 28 optimal weight:   30.0000
   chunk 11 optimal weight:   20.0000
   chunk 16 optimal weight:   30.0000
   chunk 25 optimal weight:    9.9990
   chunk 19 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 14 optimal weight:    7.9990
   chunk 2 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   overall best weight:    8.9990

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

Flipped N/Q/H residues before XYZ refinement:
X  18 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.121352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.094240 restraints weight = 4685.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 2.27
r_work: 0.3632 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3506 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.073   3324  Z= 0.475
  Angle     :  0.778   6.937   4476  Z= 0.420
  Chirality :  0.051   0.130    540
  Planarity :  0.004   0.012    564
  Dihedral  :  5.169  19.263    432
  Min Nonbonded Distance : 2.663

Molprobity Statistics.
  All-atom Clashscore : 1.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 11.72 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.33 (0.29), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.53 (0.22), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.004   HIS R  18 
 PHE   0.014   0.003   PHE B  23 
 TYR   0.011   0.002   TYR E  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03828 (   84)
  hydrogen bonds       : angle       4.82691 (  252)
  covalent geometry    : bond        0.01015 ( 3312)
  covalent geometry    : angle       0.77770 ( 4476)
  Misc. bond           : bond        0.00206 (   12)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.363 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 34
  average time/residue: 0.2254
  time to fit residues: 9.2316
Evaluate side-chains
  27 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 ILE
Chi-restraints excluded: chain N residue   26 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 17 optimal weight:   20.0000
   chunk 11 optimal weight:    9.9990
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:   20.0000
   chunk 6 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
S  22 ASN
X  18 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.123601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.096939 restraints weight = 4753.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 2.31
r_work: 0.3680 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3552 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.3346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3324  Z= 0.146
  Angle     :  0.540   6.186   4476  Z= 0.273
  Chirality :  0.045   0.121    540
  Planarity :  0.002   0.006    564
  Dihedral  :  4.183  18.489    432
  Min Nonbonded Distance : 2.682

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 11.20 %
    Favored  : 88.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.22 (0.30), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.45 (0.23), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS M  18 
 PHE   0.012   0.001   PHE G  23 
 TYR   0.003   0.001   TYR F  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02551 (   84)
  hydrogen bonds       : angle       4.13806 (  252)
  covalent geometry    : bond        0.00314 ( 3312)
  covalent geometry    : angle       0.53977 ( 4476)
  Misc. bond           : bond        0.00055 (   12)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 29
  time to evaluate  : 0.392 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 31
  average time/residue: 0.2112
  time to fit residues: 8.0084
Evaluate side-chains
  24 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 30 optimal weight:    8.9990
   chunk 28 optimal weight:   20.0000
   chunk 22 optimal weight:   20.0000
   chunk 19 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 29 optimal weight:   30.0000
   chunk 26 optimal weight:    9.9990
   overall best weight:    4.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.126807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.098953 restraints weight = 5333.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.3792 rms_B_bonded: 2.48
r_work: 0.3681 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3558 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.3592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   3324  Z= 0.267
  Angle     :  0.587   6.642   4476  Z= 0.311
  Chirality :  0.046   0.124    540
  Planarity :  0.002   0.007    564
  Dihedral  :  4.532  18.895    432
  Min Nonbonded Distance : 2.685

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 14.84 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.39 (0.29), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.22), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS J  18 
 PHE   0.011   0.002   PHE O  23 
 TYR   0.006   0.002   TYR E  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03146 (   84)
  hydrogen bonds       : angle       4.28904 (  252)
  covalent geometry    : bond        0.00576 ( 3312)
  covalent geometry    : angle       0.58725 ( 4476)
  Misc. bond           : bond        0.00111 (   12)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.351 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 26
  average time/residue: 0.2001
  time to fit residues: 6.3867
Evaluate side-chains
  22 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 22 optimal weight:   30.0000
   chunk 25 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:   20.0000
   chunk 28 optimal weight:   10.0000
   chunk 6 optimal weight:    2.9990
   chunk 4 optimal weight:    8.9990
   chunk 21 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:   30.0000
   overall best weight:    3.1788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.127855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.100172 restraints weight = 5136.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 2.43
r_work: 0.3701 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3572 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.3653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3324  Z= 0.173
  Angle     :  0.521   7.084   4476  Z= 0.272
  Chirality :  0.045   0.121    540
  Planarity :  0.002   0.006    564
  Dihedral  :  4.154  18.165    432
  Min Nonbonded Distance : 2.681

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 16.93 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.30 (0.29), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.51 (0.22), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS J  18 
 PHE   0.013   0.001   PHE O  23 
 TYR   0.004   0.001   TYR R  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02637 (   84)
  hydrogen bonds       : angle       4.00137 (  252)
  covalent geometry    : bond        0.00374 ( 3312)
  covalent geometry    : angle       0.52145 ( 4476)
  Misc. bond           : bond        0.00068 (   12)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.352 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1908
  time to fit residues: 5.9267
Evaluate side-chains
  23 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 22 optimal weight:   30.0000
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 23 optimal weight:   30.0000
   chunk 17 optimal weight:    9.9990
   chunk 12 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 24 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 11 optimal weight:   20.0000
   overall best weight:    5.7986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.126305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.098403 restraints weight = 5078.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 2.39
r_work: 0.3653 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3521 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.3840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053   3324  Z= 0.310
  Angle     :  0.603   7.033   4476  Z= 0.324
  Chirality :  0.046   0.125    540
  Planarity :  0.002   0.008    564
  Dihedral  :  4.608  18.578    432
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 20.05 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.55 (0.27), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.21), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS J  18 
 PHE   0.014   0.002   PHE O  23 
 TYR   0.008   0.002   TYR E  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03398 (   84)
  hydrogen bonds       : angle       4.31544 (  252)
  covalent geometry    : bond        0.00662 ( 3312)
  covalent geometry    : angle       0.60325 ( 4476)
  Misc. bond           : bond        0.00129 (   12)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 29
  time to evaluate  : 0.417 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 30
  average time/residue: 0.1935
  time to fit residues: 7.1893
Evaluate side-chains
  23 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   26 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 9 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 21 optimal weight:    7.9990
   chunk 6 optimal weight:    9.9990
   chunk 11 optimal weight:   20.0000
   chunk 12 optimal weight:    2.9990
   overall best weight:    3.7588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.127107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.099186 restraints weight = 5218.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3780 rms_B_bonded: 2.44
r_work: 0.3672 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3549 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.3871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3324  Z= 0.204
  Angle     :  0.538   7.346   4476  Z= 0.282
  Chirality :  0.045   0.122    540
  Planarity :  0.002   0.006    564
  Dihedral  :  4.285  18.409    432
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 1.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 20.83 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.54 (0.28), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.21), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS J  18 
 PHE   0.015   0.002   PHE O  23 
 TYR   0.005   0.002   TYR J  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02862 (   84)
  hydrogen bonds       : angle       4.06516 (  252)
  covalent geometry    : bond        0.00442 ( 3312)
  covalent geometry    : angle       0.53849 ( 4476)
  Misc. bond           : bond        0.00084 (   12)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.342 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 28
  average time/residue: 0.1813
  time to fit residues: 6.4011
Evaluate side-chains
  26 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 16 optimal weight:   30.0000
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    8.9990
   chunk 28 optimal weight:   30.0000
   chunk 23 optimal weight:   30.0000
   chunk 4 optimal weight:   20.0000
   chunk 2 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0040
   chunk 14 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    5.2000

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.126334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.097948 restraints weight = 5795.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 2.56
r_work: 0.3669 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3541 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.4015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   3324  Z= 0.279
  Angle     :  0.588   7.743   4476  Z= 0.312
  Chirality :  0.046   0.125    540
  Planarity :  0.002   0.008    564
  Dihedral  :  4.490  18.406    432
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 21.88 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.66 (0.27), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.78 (0.21), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS J  18 
 PHE   0.018   0.002   PHE H  23 
 TYR   0.008   0.002   TYR J  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03304 (   84)
  hydrogen bonds       : angle       4.24550 (  252)
  covalent geometry    : bond        0.00600 ( 3312)
  covalent geometry    : angle       0.58841 ( 4476)
  Misc. bond           : bond        0.00115 (   12)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 29
  time to evaluate  : 0.386 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 30
  average time/residue: 0.1716
  time to fit residues: 6.5130
Evaluate side-chains
  29 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 4 optimal weight:   20.0000
   chunk 10 optimal weight:   10.0000
   chunk 17 optimal weight:   30.0000
   chunk 22 optimal weight:   20.0000
   chunk 24 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 34 optimal weight:   30.0000
   chunk 12 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 27 optimal weight:   20.0000
   chunk 20 optimal weight:    9.9990
   overall best weight:    7.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.125276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.096650 restraints weight = 5592.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3767 rms_B_bonded: 2.50
r_work: 0.3662 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3542 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.4184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.067   3324  Z= 0.424
  Angle     :  0.689   7.715   4476  Z= 0.373
  Chirality :  0.049   0.127    540
  Planarity :  0.003   0.010    564
  Dihedral  :  4.865  18.694    432
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 22.14 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.78 (0.26), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.88 (0.20), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS Q  18 
 PHE   0.024   0.002   PHE H  23 
 TYR   0.012   0.003   TYR B  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04078 (   84)
  hydrogen bonds       : angle       4.47965 (  252)
  covalent geometry    : bond        0.00899 ( 3312)
  covalent geometry    : angle       0.68870 ( 4476)
  Misc. bond           : bond        0.00168 (   12)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.362 
Fit side-chains
REVERT: C   29 SER cc_start: 0.6880 (t) cc_final: 0.6621 (m)
  outliers start: 1
  outliers final: 1
  residues processed: 42
  average time/residue: 0.1775
  time to fit residues: 9.1172
Evaluate side-chains
  37 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   26 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 23 optimal weight:   20.0000
   chunk 11 optimal weight:   20.0000
   chunk 12 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 22 optimal weight:   20.0000
   chunk 10 optimal weight:   20.0000
   chunk 21 optimal weight:   20.0000
   chunk 34 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    4.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.126459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.098114 restraints weight = 5685.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3797 rms_B_bonded: 2.54
r_work: 0.3690 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3568 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.4243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   3324  Z= 0.240
  Angle     :  0.632   7.928   4476  Z= 0.313
  Chirality :  0.046   0.122    540
  Planarity :  0.002   0.016    564
  Dihedral  :  4.454  18.383    432
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.18 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.71 (0.27), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.82 (0.21), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS E  18 
 PHE   0.038   0.003   PHE I  15 
 TYR   0.006   0.002   TYR J  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03122 (   84)
  hydrogen bonds       : angle       4.23684 (  252)
  covalent geometry    : bond        0.00515 ( 3312)
  covalent geometry    : angle       0.63194 ( 4476)
  Misc. bond           : bond        0.00095 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2630.37 seconds
wall clock time: 45 minutes 56.70 seconds (2756.70 seconds total)