Starting phenix.real_space_refine
on Wed Sep 17 03:33:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gzy_51737/09_2025/9gzy_51737.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gzy_51737/09_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_51737/09_2025/9gzy_51737.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gzy_51737/09_2025/9gzy_51737.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gzy_51737/09_2025/9gzy_51737.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gzy_51737/09_2025/9gzy_51737.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 0.61, per 1000 atoms: 0.19
  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: 0.30
  Conformation dependent library (CDL) restraints added in 87.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.15
  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: 0.45

  Time building geometry restraints manager: 0.37 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: 0.01
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:             2.320
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.660
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  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:6.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.420
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 TYR   0.009   0.002   TYR J  37 
 PHE   0.018   0.004   PHE K  23 
 HIS   0.009   0.003   HIS R  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 3312)
  covalent geometry    : angle       0.80132 ( 4476)
  hydrogen bonds       : bond        0.09233 (   84)
  hydrogen bonds       : angle       7.53311 (  252)
  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  : 0.126 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1009
  time to fit residues: 6.2877
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  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:   30.0000
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.5990

-------------------------------------------------------------------------------
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 = 0.4232 r_free = 0.4232 target = 0.128996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.099919 restraints weight = 4701.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3954 rms_B_bonded: 2.27
r_work: 0.3820 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3692 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3324  Z= 0.098
  Angle     :  0.593   7.003   4476  Z= 0.278
  Chirality :  0.044   0.120    540
  Planarity :  0.002   0.007    564
  Dihedral  :  3.579  16.261    432
  Min Nonbonded Distance : 2.690

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  8.33 %
    Favored  : 91.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.48 (0.33), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.25), residues: 396

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 3312)
  covalent geometry    : angle       0.59309 ( 4476)
  hydrogen bonds       : bond        0.01991 (   84)
  hydrogen bonds       : angle       5.05942 (  252)
  Misc. bond           : bond        0.00035 (   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
  36 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 35
  time to evaluate  : 0.089 
Fit side-chains
REVERT: S   22 ASN cc_start: 0.7912 (t0) cc_final: 0.7686 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0939
  time to fit residues: 3.9576
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  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 23 optimal weight:   30.0000
   chunk 24 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 16 optimal weight:   30.0000
   chunk 34 optimal weight:   20.0000
   chunk 29 optimal weight:   20.0000
   chunk 21 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 20 optimal weight:   10.0000
   overall best weight:    3.3788

-------------------------------------------------------------------------------
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 = 0.4233 r_free = 0.4233 target = 0.126976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.098320 restraints weight = 4639.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3821 rms_B_bonded: 2.35
r_work: 0.3722 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3596 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3324  Z= 0.176
  Angle     :  0.595   7.352   4476  Z= 0.294
  Chirality :  0.046   0.123    540
  Planarity :  0.002   0.007    564
  Dihedral  :  4.182  17.892    432
  Min Nonbonded Distance : 2.693

Molprobity Statistics.
  All-atom Clashscore : 1.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  7.81 %
    Favored  : 91.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.88 (0.31), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.18 (0.24), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR B  37 
 PHE   0.010   0.002   PHE G  23 
 HIS   0.005   0.002   HIS R  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 3312)
  covalent geometry    : angle       0.59498 ( 4476)
  hydrogen bonds       : bond        0.02603 (   84)
  hydrogen bonds       : angle       4.78685 (  252)
  Misc. bond           : bond        0.00064 (   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
  32 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 30
  time to evaluate  : 0.124 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0890
  time to fit residues: 3.3924
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  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 34 optimal weight:   20.0000
   chunk 7 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 10 optimal weight:   30.0000
   chunk 21 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   chunk 16 optimal weight:   10.0000
   chunk 22 optimal weight:   20.0000
   chunk 32 optimal weight:    1.9990
   overall best weight:    3.3588

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.128715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.100541 restraints weight = 4500.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3836 rms_B_bonded: 2.33
r_work: 0.3733 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3601 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3324  Z= 0.177
  Angle     :  0.553   6.832   4476  Z= 0.279
  Chirality :  0.045   0.123    540
  Planarity :  0.002   0.009    564
  Dihedral  :  4.013  17.758    432
  Min Nonbonded Distance : 2.683

Molprobity Statistics.
  All-atom Clashscore : 1.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  9.11 %
    Favored  : 90.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.89 (0.31), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.24), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR U  37 
 PHE   0.009   0.001   PHE U  23 
 HIS   0.005   0.002   HIS J  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 3312)
  covalent geometry    : angle       0.55292 ( 4476)
  hydrogen bonds       : bond        0.02581 (   84)
  hydrogen bonds       : angle       4.27523 (  252)
  Misc. bond           : bond        0.00078 (   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: 3
    poor density    : 28
  time to evaluate  : 0.142 
Fit side-chains
  outliers start: 3
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0867
  time to fit residues: 3.2447
Evaluate side-chains
  21 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 20 optimal weight:    9.9990
   chunk 9 optimal weight:    5.9990
   chunk 10 optimal weight:   30.0000
   chunk 16 optimal weight:    9.9990
   chunk 29 optimal weight:   30.0000
   chunk 6 optimal weight:    9.9990
   chunk 22 optimal weight:   20.0000
   chunk 14 optimal weight:    0.8980
   overall best weight:    4.5788

-------------------------------------------------------------------------------
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 = 0.4222 r_free = 0.4222 target = 0.126282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.098356 restraints weight = 4962.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3805 rms_B_bonded: 2.45
r_work: 0.3703 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3573 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.3549

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= 0.245
  Angle     :  0.571   7.006   4476  Z= 0.301
  Chirality :  0.046   0.126    540
  Planarity :  0.002   0.007    564
  Dihedral  :  4.322  18.328    432
  Min Nonbonded Distance : 2.680

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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.04 (0.31), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.31 (0.23), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR U  37 
 PHE   0.009   0.002   PHE B  23 
 HIS   0.006   0.003   HIS J  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00529 ( 3312)
  covalent geometry    : angle       0.57084 ( 4476)
  hydrogen bonds       : bond        0.03009 (   84)
  hydrogen bonds       : angle       4.30943 (  252)
  Misc. bond           : bond        0.00110 (   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
  27 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.078 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 27
  average time/residue: 0.0961
  time to fit residues: 3.0866
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  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 22 optimal weight:   30.0000
   chunk 7 optimal weight:    8.9990
   chunk 1 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:   20.0000
   chunk 17 optimal weight:   30.0000
   chunk 27 optimal weight:   10.0000
   chunk 30 optimal weight:    8.9990
   chunk 20 optimal weight:    9.9990
   chunk 23 optimal weight:   20.0000
   overall best weight:    6.7990

-------------------------------------------------------------------------------
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 = 0.4214 r_free = 0.4214 target = 0.126008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.098274 restraints weight = 5020.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 2.39
r_work: 0.3649 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3516 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.059   3324  Z= 0.362
  Angle     :  0.644   7.094   4476  Z= 0.348
  Chirality :  0.047   0.128    540
  Planarity :  0.003   0.009    564
  Dihedral  :  4.635  18.856    432
  Min Nonbonded Distance : 2.657

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 13.80 %
    Favored  : 85.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.38 (0.28), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.21), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.002   TYR M  37 
 PHE   0.011   0.002   PHE F  23 
 HIS   0.007   0.003   HIS R  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00772 ( 3312)
  covalent geometry    : angle       0.64366 ( 4476)
  hydrogen bonds       : bond        0.03592 (   84)
  hydrogen bonds       : angle       4.33513 (  252)
  Misc. bond           : bond        0.00153 (   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
  32 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 30
  time to evaluate  : 0.134 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 32
  average time/residue: 0.0762
  time to fit residues: 2.9955
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  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   18 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 4 optimal weight:   20.0000
   chunk 16 optimal weight:   20.0000
   chunk 12 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 22 optimal weight:    9.9990
   chunk 11 optimal weight:   30.0000
   chunk 10 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.4229 r_free = 0.4229 target = 0.126753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.098842 restraints weight = 5144.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 2.43
r_work: 0.3662 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3528 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.3864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   3324  Z= 0.237
  Angle     :  0.562   7.320   4476  Z= 0.296
  Chirality :  0.046   0.124    540
  Planarity :  0.002   0.006    564
  Dihedral  :  4.349  18.567    432
  Min Nonbonded Distance : 2.659

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 15.89 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.44 (0.27), 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
 TYR   0.006   0.002   TYR B  37 
 PHE   0.009   0.002   PHE H  23 
 HIS   0.007   0.002   HIS X  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 3312)
  covalent geometry    : angle       0.56196 ( 4476)
  hydrogen bonds       : bond        0.03090 (   84)
  hydrogen bonds       : angle       4.14829 (  252)
  Misc. bond           : bond        0.00101 (   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: 3
    poor density    : 27
  time to evaluate  : 0.134 
Fit side-chains
  outliers start: 3
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0871
  time to fit residues: 3.0570
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  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 11 optimal weight:   30.0000
   chunk 7 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 19 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    2.9588

-------------------------------------------------------------------------------
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 = 0.4243 r_free = 0.4243 target = 0.127580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.099682 restraints weight = 5111.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3791 rms_B_bonded: 2.41
r_work: 0.3684 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3550 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.3889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3324  Z= 0.163
  Angle     :  0.540   8.343   4476  Z= 0.271
  Chirality :  0.045   0.122    540
  Planarity :  0.002   0.005    564
  Dihedral  :  4.046  18.027    432
  Min Nonbonded Distance : 2.662

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 17.45 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.39 (0.28), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.58 (0.21), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR B  37 
 PHE   0.008   0.001   PHE H  23 
 HIS   0.005   0.002   HIS J  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 3312)
  covalent geometry    : angle       0.54028 ( 4476)
  hydrogen bonds       : bond        0.02602 (   84)
  hydrogen bonds       : angle       3.93391 (  252)
  Misc. bond           : bond        0.00064 (   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
  29 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.132 
Fit side-chains
REVERT: X   23 PHE cc_start: 0.7541 (m-80) cc_final: 0.7250 (m-80)
  outliers start: 2
  outliers final: 1
  residues processed: 29
  average time/residue: 0.0980
  time to fit residues: 3.4088
Evaluate side-chains
  27 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   18 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 24 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 5 optimal weight:   20.0000
   chunk 34 optimal weight:   20.0000
   chunk 19 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 9 optimal weight:    8.9990
   chunk 6 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   overall best weight:    4.5988

-------------------------------------------------------------------------------
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 = 0.4216 r_free = 0.4216 target = 0.125730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.097340 restraints weight = 5439.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3791 rms_B_bonded: 2.52
r_work: 0.3688 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3559 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.4004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   3324  Z= 0.247
  Angle     :  0.585   7.721   4476  Z= 0.302
  Chirality :  0.046   0.127    540
  Planarity :  0.002   0.007    564
  Dihedral  :  4.259  18.028    432
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 1.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 18.75 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.53 (0.27), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.68 (0.21), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR B  37 
 PHE   0.009   0.002   PHE H  23 
 HIS   0.007   0.003   HIS X  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 ( 3312)
  covalent geometry    : angle       0.58462 ( 4476)
  hydrogen bonds       : bond        0.03061 (   84)
  hydrogen bonds       : angle       4.12541 (  252)
  Misc. bond           : bond        0.00104 (   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: 2
    poor density    : 28
  time to evaluate  : 0.129 
Fit side-chains
REVERT: X   23 PHE cc_start: 0.7541 (m-80) cc_final: 0.7262 (m-80)
  outliers start: 2
  outliers final: 1
  residues processed: 30
  average time/residue: 0.0759
  time to fit residues: 2.7370
Evaluate side-chains
  27 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   18 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 29 optimal weight:   30.0000
   chunk 24 optimal weight:    4.9990
   chunk 4 optimal weight:   20.0000
   chunk 32 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 28 optimal weight:   20.0000
   chunk 11 optimal weight:   20.0000
   chunk 12 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 17 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   overall best weight:    5.9990

-------------------------------------------------------------------------------
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 = 0.4224 r_free = 0.4224 target = 0.126185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.097674 restraints weight = 5641.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3784 rms_B_bonded: 2.54
r_work: 0.3678 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3545 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.4097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   3324  Z= 0.319
  Angle     :  0.628   7.798   4476  Z= 0.331
  Chirality :  0.047   0.127    540
  Planarity :  0.003   0.016    564
  Dihedral  :  4.475  18.140    432
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.62 (0.27), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.75 (0.20), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR R  37 
 PHE   0.036   0.002   PHE A  15 
 HIS   0.011   0.003   HIS X  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00683 ( 3312)
  covalent geometry    : angle       0.62761 ( 4476)
  hydrogen bonds       : bond        0.03450 (   84)
  hydrogen bonds       : angle       4.27117 (  252)
  Misc. bond           : bond        0.00132 (   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
  33 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 32
  time to evaluate  : 0.126 
Fit side-chains
REVERT: C   29 SER cc_start: 0.6831 (t) cc_final: 0.6557 (m)
REVERT: S   28 SER cc_start: 0.8546 (m) cc_final: 0.8213 (t)
REVERT: X   23 PHE cc_start: 0.7611 (m-80) cc_final: 0.7330 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 33
  average time/residue: 0.0849
  time to fit residues: 3.4024
Evaluate side-chains
  31 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 30
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   18 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   chunk 8 optimal weight:    9.9990
   chunk 31 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 20 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 22 optimal weight:   20.0000
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:   20.0000
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A  21 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 = 0.4255 r_free = 0.4255 target = 0.128626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.100812 restraints weight = 5481.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3837 rms_B_bonded: 2.49
r_work: 0.3731 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3607 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.4064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3324  Z= 0.091
  Angle     :  0.503   7.891   4476  Z= 0.248
  Chirality :  0.045   0.136    540
  Planarity :  0.001   0.012    564
  Dihedral  :  3.830  17.597    432
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 2.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 20.05 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.35 (0.29), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.54 (0.22), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR R  37 
 PHE   0.028   0.001   PHE A  15 
 HIS   0.010   0.001   HIS X  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 ( 3312)
  covalent geometry    : angle       0.50252 ( 4476)
  hydrogen bonds       : bond        0.02045 (   84)
  hydrogen bonds       : angle       3.83936 (  252)
  Misc. bond           : bond        0.00030 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1232.74 seconds
wall clock time: 21 minutes 43.39 seconds (1303.39 seconds total)