Starting phenix.real_space_refine
on Sat Apr 26 19:24:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gzy_51737/04_2025/9gzy_51737.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gzy_51737/04_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_51737/04_2025/9gzy_51737.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gzy_51737/04_2025/9gzy_51737.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gzy_51737/04_2025/9gzy_51737.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gzy_51737/04_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 1.73, per 1000 atoms: 0.53
  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: 0.80
  Conformation dependent library (CDL) restraints added in 377.5 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: 0.50
  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: 0.74

  Time building geometry restraints manager: 0.95 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:             2.250
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.650
  Find NCS groups from input model:        0.080
  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:11.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.840
-------------------------------------------------------------------------------
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  : 0.330 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.2290
  time to fit residues: 14.2885
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  : 0.378 
-------------------------------------------------------------------------------
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  : 0.374 
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: 0.2124
  time to fit residues: 8.8597
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  : 0.329 
-------------------------------------------------------------------------------
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:    8.9990
   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:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    8.3990

-------------------------------------------------------------------------------
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 = 0.4181 r_free = 0.4181 target = 0.122212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.095155 restraints weight = 4678.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 2.26
r_work: 0.3641 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3513 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.3444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.070   3324  Z= 0.445
  Angle     :  0.757   7.009   4476  Z= 0.406
  Chirality :  0.050   0.131    540
  Planarity :  0.003   0.011    564
  Dihedral  :  5.231  19.595    432
  Min Nonbonded Distance : 2.675

Molprobity Statistics.
  All-atom Clashscore : 1.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 11.98 %
    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: -3.32 (0.29), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.52 (0.22), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.004   HIS R  18 
 PHE   0.013   0.002   PHE B  23 
 TYR   0.011   0.002   TYR E  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03697 (   84)
  hydrogen bonds       : angle       4.89711 (  252)
  covalent geometry    : bond        0.00960 ( 3312)
  covalent geometry    : angle       0.75733 ( 4476)
  Misc. bond           : bond        0.00174 (   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
  33 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.385 
Fit side-chains
  outliers start: 4
  outliers final: 0
  residues processed: 33
  average time/residue: 0.2165
  time to fit residues: 8.6582
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  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 17 optimal weight:   20.0000
   chunk 11 optimal weight:   10.0000
   chunk 7 optimal weight:    2.9990
   chunk 28 optimal weight:   20.0000
   chunk 6 optimal weight:    1.9990
   chunk 22 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4247 r_free = 0.4247 target = 0.128899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.101236 restraints weight = 4606.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3825 rms_B_bonded: 2.31
r_work: 0.3721 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3594 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
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      :  0.002   0.022   3324  Z= 0.116
  Angle     :  0.527   6.555   4476  Z= 0.263
  Chirality :  0.045   0.120    540
  Planarity :  0.001   0.006    564
  Dihedral  :  4.048  18.105    432
  Min Nonbonded Distance : 2.683

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 10.94 %
    Favored  : 88.54 %
  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: -3.17 (0.30), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.41 (0.23), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS M  18 
 PHE   0.011   0.001   PHE G  23 
 TYR   0.003   0.001   TYR A  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02308 (   84)
  hydrogen bonds       : angle       4.10456 (  252)
  covalent geometry    : bond        0.00250 ( 3312)
  covalent geometry    : angle       0.52718 ( 4476)
  Misc. bond           : bond        0.00042 (   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
  34 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.383 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 34
  average time/residue: 0.2020
  time to fit residues: 8.3554
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  : 0.377 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 30 optimal weight:    9.9990
   chunk 28 optimal weight:   30.0000
   chunk 22 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   chunk 12 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   chunk 31 optimal weight:   10.0000
   chunk 29 optimal weight:   30.0000
   chunk 26 optimal weight:    9.9990
   overall best weight:    5.7788

-------------------------------------------------------------------------------
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 = 0.4212 r_free = 0.4212 target = 0.126283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.098410 restraints weight = 5488.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3759 rms_B_bonded: 2.51
r_work: 0.3651 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3526 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.3641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.054   3324  Z= 0.306
  Angle     :  0.615   6.875   4476  Z= 0.328
  Chirality :  0.047   0.125    540
  Planarity :  0.002   0.008    564
  Dihedral  :  4.654  18.950    432
  Min Nonbonded Distance : 2.672

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 14.32 %
    Favored  : 85.42 %
  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: -3.41 (0.28), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.59 (0.22), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS J  18 
 PHE   0.012   0.002   PHE O  23 
 TYR   0.008   0.002   TYR U  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03340 (   84)
  hydrogen bonds       : angle       4.33213 (  252)
  covalent geometry    : bond        0.00658 ( 3312)
  covalent geometry    : angle       0.61452 ( 4476)
  Misc. bond           : bond        0.00125 (   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
  28 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.361 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 28
  average time/residue: 0.2079
  time to fit residues: 7.2064
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  : 0.356 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:   20.0000
   chunk 28 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 21 optimal weight:    6.9990
   chunk 18 optimal weight:    8.9990
   chunk 19 optimal weight:    4.9990
   chunk 17 optimal weight:   30.0000
   overall best weight:    4.7990

-------------------------------------------------------------------------------
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 = 0.4220 r_free = 0.4220 target = 0.126812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.098958 restraints weight = 5367.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3769 rms_B_bonded: 2.47
r_work: 0.3661 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3536 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.3773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   3324  Z= 0.258
  Angle     :  0.575   7.069   4476  Z= 0.305
  Chirality :  0.046   0.123    540
  Planarity :  0.002   0.007    564
  Dihedral  :  4.470  18.504    432
  Min Nonbonded Distance : 2.664

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 17.71 %
    Favored  : 82.03 %
  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: -3.45 (0.28), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.62 (0.21), residues: 396

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03173 (   84)
  hydrogen bonds       : angle       4.14998 (  252)
  covalent geometry    : bond        0.00554 ( 3312)
  covalent geometry    : angle       0.57464 ( 4476)
  Misc. bond           : bond        0.00105 (   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
  30 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 29
  time to evaluate  : 0.324 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 30
  average time/residue: 0.1725
  time to fit residues: 6.4485
Evaluate side-chains
  25 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 23 optimal weight:   20.0000
   chunk 17 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 24 optimal weight:   10.0000
   chunk 28 optimal weight:    7.9990
   chunk 11 optimal weight:   20.0000
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 = 0.4215 r_free = 0.4215 target = 0.126105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.098088 restraints weight = 5185.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3756 rms_B_bonded: 2.41
r_work: 0.3654 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3520 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.3933

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= 0.312
  Angle     :  0.611   7.262   4476  Z= 0.326
  Chirality :  0.046   0.124    540
  Planarity :  0.002   0.008    564
  Dihedral  :  4.660  18.760    432
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 20.31 %
    Favored  : 79.43 %
  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: -3.68 (0.27), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.80 (0.20), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS E  18 
 PHE   0.015   0.002   PHE O  23 
 TYR   0.008   0.002   TYR Q  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03475 (   84)
  hydrogen bonds       : angle       4.25931 (  252)
  covalent geometry    : bond        0.00665 ( 3312)
  covalent geometry    : angle       0.61091 ( 4476)
  Misc. bond           : bond        0.00127 (   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
  28 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.353 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 28
  average time/residue: 0.1830
  time to fit residues: 6.5469
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  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 20 optimal weight:    8.9990
   chunk 3 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 11 optimal weight:   20.0000
   chunk 12 optimal weight:    0.9990
   overall best weight:    3.3788

-------------------------------------------------------------------------------
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 = 0.4227 r_free = 0.4227 target = 0.127262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.099390 restraints weight = 5203.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 2.43
r_work: 0.3700 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3575 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.3939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3324  Z= 0.185
  Angle     :  0.534   7.521   4476  Z= 0.276
  Chirality :  0.045   0.121    540
  Planarity :  0.002   0.007    564
  Dihedral  :  4.257  18.345    432
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 1.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 21.09 %
    Favored  : 78.65 %
  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: -3.60 (0.28), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.74 (0.21), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS J  18 
 PHE   0.015   0.001   PHE O  23 
 TYR   0.004   0.001   TYR R  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02754 (   84)
  hydrogen bonds       : angle       4.02751 (  252)
  covalent geometry    : bond        0.00401 ( 3312)
  covalent geometry    : angle       0.53390 ( 4476)
  Misc. bond           : bond        0.00074 (   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
  30 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 29
  time to evaluate  : 0.392 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 30
  average time/residue: 0.1835
  time to fit residues: 6.8558
Evaluate side-chains
  27 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   chunk 28 optimal weight:   30.0000
   chunk 23 optimal weight:   30.0000
   chunk 4 optimal weight:   20.0000
   chunk 2 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 14 optimal weight:   10.0000
   chunk 18 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    3.9588

-------------------------------------------------------------------------------
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 = 0.4225 r_free = 0.4225 target = 0.126967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.098664 restraints weight = 5767.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3790 rms_B_bonded: 2.56
r_work: 0.3680 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3554 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.4017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   3324  Z= 0.215
  Angle     :  0.557   7.795   4476  Z= 0.288
  Chirality :  0.045   0.121    540
  Planarity :  0.002   0.007    564
  Dihedral  :  4.338  18.227    432
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  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: -3.62 (0.28), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.75 (0.21), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS J  18 
 PHE   0.017   0.002   PHE H  23 
 TYR   0.005   0.002   TYR R  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02923 (   84)
  hydrogen bonds       : angle       4.12353 (  252)
  covalent geometry    : bond        0.00464 ( 3312)
  covalent geometry    : angle       0.55688 ( 4476)
  Misc. bond           : bond        0.00089 (   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  : 0.367 
Fit side-chains
REVERT: C   29 SER cc_start: 0.6894 (t) cc_final: 0.6634 (m)
REVERT: S   28 SER cc_start: 0.8535 (m) cc_final: 0.8171 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 30
  average time/residue: 0.1973
  time to fit residues: 7.3535
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  : 0.381 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 17 optimal weight:   30.0000
   chunk 22 optimal weight:   30.0000
   chunk 24 optimal weight:   10.0000
   chunk 13 optimal weight:    0.2980
   chunk 34 optimal weight:   20.0000
   chunk 12 optimal weight:    8.9990
   chunk 16 optimal weight:    5.9990
   chunk 27 optimal weight:   20.0000
   chunk 20 optimal weight:    9.9990
   overall best weight:    6.8588

-------------------------------------------------------------------------------
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 = 0.4209 r_free = 0.4209 target = 0.125862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.097330 restraints weight = 5570.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3775 rms_B_bonded: 2.51
r_work: 0.3672 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3552 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.4158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.060   3324  Z= 0.366
  Angle     :  0.651   7.533   4476  Z= 0.348
  Chirality :  0.047   0.124    540
  Planarity :  0.003   0.010    564
  Dihedral  :  4.712  18.449    432
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 22.40 %
    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: -3.73 (0.27), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.84 (0.21), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS E  18 
 PHE   0.023   0.002   PHE H  23 
 TYR   0.010   0.003   TYR R  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03745 (   84)
  hydrogen bonds       : angle       4.39850 (  252)
  covalent geometry    : bond        0.00779 ( 3312)
  covalent geometry    : angle       0.65051 ( 4476)
  Misc. bond           : bond        0.00149 (   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
  34 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.370 
Fit side-chains
REVERT: C   29 SER cc_start: 0.6843 (t) cc_final: 0.6590 (m)
REVERT: S   28 SER cc_start: 0.8531 (m) cc_final: 0.8226 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.1671
  time to fit residues: 7.1276
Evaluate side-chains
  33 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 23 optimal weight:   30.0000
   chunk 11 optimal weight:   20.0000
   chunk 12 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 22 optimal weight:   20.0000
   chunk 10 optimal weight:   20.0000
   chunk 21 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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 = 0.127200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.098845 restraints weight = 5627.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 2.52
r_work: 0.3690 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3566 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.4189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3324  Z= 0.208
  Angle     :  0.596   7.801   4476  Z= 0.295
  Chirality :  0.045   0.121    540
  Planarity :  0.002   0.015    564
  Dihedral  :  4.323  18.244    432
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 22.66 %
    Favored  : 77.08 %
  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: -3.64 (0.28), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.21), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS J  18 
 PHE   0.034   0.002   PHE A  15 
 TYR   0.006   0.002   TYR R  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02884 (   84)
  hydrogen bonds       : angle       4.16583 (  252)
  covalent geometry    : bond        0.00450 ( 3312)
  covalent geometry    : angle       0.59631 ( 4476)
  Misc. bond           : bond        0.00084 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2595.19 seconds
wall clock time: 45 minutes 9.04 seconds (2709.04 seconds total)