Starting phenix.real_space_refine
on Mon Sep 23 13:23:20 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk8_33890/09_2024/7yk8_33890.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk8_33890/09_2024/7yk8_33890.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk8_33890/09_2024/7yk8_33890.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk8_33890/09_2024/7yk8_33890.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk8_33890/09_2024/7yk8_33890.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk8_33890/09_2024/7yk8_33890.cif"
  }
  resolution = 2.8
  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=   0.004
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    1938      2.51       5
     N     546      2.21       5
     O     624      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 3108
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 438
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
    Chain: "A"
      Number of atoms: 80
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 80
          Classifications: {'peptide': 12}
          Link IDs: {'TRANS': 11}
  Restraints were copied for chains:
    C, D, G, I, H, E, F, K, J, L
  Time building chain proxies: 1.90, per 1000 atoms: 0.61
  Number of scatterers: 3108
  At special positions: 0
  Unit cell: (94.34, 117.66, 32.86, 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     624      8.00
     N     546      7.00
     C    1938      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=0, symmetry=0
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 418.7 milliseconds
  

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  768

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 49.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'J' and resid 46 through 57
      removed outlier: 6.878A  pdb=" N   VAL J  48 " --> pdb=" O   GLY L  47 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   VAL L  49 " --> pdb=" O   VAL J  48 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   HIS J  50 " --> pdb=" O   VAL L  49 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLY L  51 " --> pdb=" O   HIS J  50 " (cutoff:3.500A)
      removed outlier: 8.837A  pdb=" N   GLU L  46 " --> pdb=" O   GLY K  47 " (cutoff:3.500A)
      removed outlier: 8.895A  pdb=" N   VAL K  49 " --> pdb=" O   GLU L  46 " (cutoff:3.500A)
      removed outlier: 9.073A  pdb=" N   VAL L  48 " --> pdb=" O   VAL K  49 " (cutoff:3.500A)
      removed outlier: 10.477A  pdb=" N   GLY K  51 " --> pdb=" O   VAL L  48 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   HIS L  50 " --> pdb=" O   GLY K  51 " (cutoff:3.500A)
      removed outlier: 9.043A  pdb=" N   ALA K  53 " --> pdb=" O   HIS L  50 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   VAL L  52 " --> pdb=" O   ALA K  53 " (cutoff:3.500A)
      removed outlier: 8.316A  pdb=" N   VAL K  55 " --> pdb=" O   VAL L  52 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   THR L  54 " --> pdb=" O   VAL K  55 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   GLU K  57 " --> pdb=" O   THR L  54 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   ALA L  56 " --> pdb=" O   GLU K  57 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 61 through 66
      removed outlier: 6.312A  pdb=" N   GLN L  62 " --> pdb=" O   VAL J  63 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   ASN J  65 " --> pdb=" O   GLN L  62 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   THR L  64 " --> pdb=" O   ASN J  65 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'J' and resid 69 through 82
      removed outlier: 6.597A  pdb=" N   ALA L  69 " --> pdb=" O   VAL J  70 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   THR J  72 " --> pdb=" O   ALA L  69 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   VAL L  71 " --> pdb=" O   THR J  72 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   VAL J  74 " --> pdb=" O   VAL L  71 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   GLY L  73 " --> pdb=" O   VAL J  74 " (cutoff:3.500A)
      removed outlier: 9.763A  pdb=" N   ALA J  76 " --> pdb=" O   GLY L  73 " (cutoff:3.500A)
      removed outlier: 5.619A  pdb=" N   THR L  75 " --> pdb=" O   ALA J  76 " (cutoff:3.500A)
      removed outlier: 8.702A  pdb=" N   ALA J  78 " --> pdb=" O   THR L  75 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   VAL L  77 " --> pdb=" O   ALA J  78 " (cutoff:3.500A)
      removed outlier: 8.502A  pdb=" N   LYS J  80 " --> pdb=" O   VAL L  77 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   GLN L  79 " --> pdb=" O   LYS J  80 " (cutoff:3.500A)
      removed outlier: 8.545A  pdb=" N   VAL J  82 " --> pdb=" O   GLN L  79 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   THR L  81 " --> pdb=" O   VAL J  82 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   VAL L  74 " --> pdb=" O   GLY K  73 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   THR K  75 " --> pdb=" O   VAL L  74 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   ALA L  76 " --> pdb=" O   THR K  75 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'J' and resid 86 through 92
      removed outlier: 6.976A  pdb=" N   SER L  87 " --> pdb=" O   GLY J  86 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   ILE J  88 " --> pdb=" O   SER L  87 " (cutoff:3.500A)
      removed outlier: 9.028A  pdb=" N   GLY L  86 " --> pdb=" O   SER K  87 " (cutoff:3.500A)
      removed outlier: 9.503A  pdb=" N   ALA K  89 " --> pdb=" O   GLY L  86 " (cutoff:3.500A)
      removed outlier: 5.750A  pdb=" N   ILE L  88 " --> pdb=" O   ALA K  89 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   ALA K  91 " --> pdb=" O   ILE L  88 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   ALA L  90 " --> pdb=" O   ALA K  91 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'G' and resid 16 through 18
      removed outlier: 6.225A  pdb=" N   VAL I  16 " --> pdb=" O   ALA H  17 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 46 through 57
      removed outlier: 6.883A  pdb=" N   VAL E  48 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   VAL B  49 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   HIS E  50 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   GLY B  51 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
      removed outlier: 8.822A  pdb=" N   GLU B  46 " --> pdb=" O   GLY F  47 " (cutoff:3.500A)
      removed outlier: 8.890A  pdb=" N   VAL F  49 " --> pdb=" O   GLU B  46 " (cutoff:3.500A)
      removed outlier: 9.067A  pdb=" N   VAL B  48 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 10.475A  pdb=" N   GLY F  51 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 5.782A  pdb=" N   HIS B  50 " --> pdb=" O   GLY F  51 " (cutoff:3.500A)
      removed outlier: 9.039A  pdb=" N   ALA F  53 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   VAL B  52 " --> pdb=" O   ALA F  53 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   VAL F  55 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   THR B  54 " --> pdb=" O   VAL F  55 " (cutoff:3.500A)
      removed outlier: 8.092A  pdb=" N   GLU F  57 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   ALA B  56 " --> pdb=" O   GLU F  57 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 61 through 66
      removed outlier: 6.310A  pdb=" N   GLN B  62 " --> pdb=" O   VAL E  63 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   ASN E  65 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   THR B  64 " --> pdb=" O   ASN E  65 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 82
      removed outlier: 6.598A  pdb=" N   ALA B  69 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)
      removed outlier: 8.214A  pdb=" N   THR E  72 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   VAL B  71 " --> pdb=" O   THR E  72 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   VAL E  74 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   GLY B  73 " --> pdb=" O   VAL E  74 " (cutoff:3.500A)
      removed outlier: 9.767A  pdb=" N   ALA E  76 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
      removed outlier: 5.623A  pdb=" N   THR B  75 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
      removed outlier: 8.706A  pdb=" N   ALA E  78 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   VAL B  77 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 8.506A  pdb=" N   LYS E  80 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   GLN B  79 " --> pdb=" O   LYS E  80 " (cutoff:3.500A)
      removed outlier: 8.548A  pdb=" N   VAL E  82 " --> pdb=" O   GLN B  79 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   THR B  81 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   VAL B  74 " --> pdb=" O   GLY F  73 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   THR F  75 " --> pdb=" O   VAL B  74 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ALA B  76 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 86 through 92
      removed outlier: 6.980A  pdb=" N   SER B  87 " --> pdb=" O   GLY E  86 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ILE E  88 " --> pdb=" O   SER B  87 " (cutoff:3.500A)
      removed outlier: 9.015A  pdb=" N   GLY B  86 " --> pdb=" O   SER F  87 " (cutoff:3.500A)
      removed outlier: 9.494A  pdb=" N   ALA F  89 " --> pdb=" O   GLY B  86 " (cutoff:3.500A)
      removed outlier: 5.741A  pdb=" N   ILE B  88 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   ALA F  91 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ALA B  90 " --> pdb=" O   ALA F  91 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 16 through 18
      removed outlier: 6.220A  pdb=" N   VAL A  16 " --> pdb=" O   ALA D  17 " (cutoff:3.500A)

    56 hydrogen bonds defined for protein.
    168 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: 0.66

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 552
        1.29 -     1.35: 482
        1.35 -     1.42: 106
        1.42 -     1.48: 498
        1.48 -     1.55: 1476
  Bond restraints: 3114
  Sorted by residual:
  bond pdb=" N   LEU E  38 "
       pdb=" CA  LEU E  38 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.25e-02 6.40e+03 6.53e+00
  bond pdb=" N   LEU F  38 "
       pdb=" CA  LEU F  38 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.25e-02 6.40e+03 6.50e+00
  bond pdb=" N   LEU L  38 "
       pdb=" CA  LEU L  38 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.25e-02 6.40e+03 6.49e+00
  bond pdb=" N   LEU J  38 "
       pdb=" CA  LEU J  38 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.25e-02 6.40e+03 6.49e+00
  bond pdb=" N   LEU K  38 "
       pdb=" CA  LEU K  38 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.25e-02 6.40e+03 6.26e+00
  ... (remaining 3109 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.80: 3578
        0.80 -     1.61: 463
        1.61 -     2.41: 96
        2.41 -     3.21: 45
        3.21 -     4.02: 12
  Bond angle restraints: 4194
  Sorted by residual:
  angle pdb=" N   LEU L  38 "
        pdb=" CA  LEU L  38 "
        pdb=" C   LEU L  38 "
      ideal   model   delta    sigma   weight residual
     112.93  108.91    4.02 1.33e+00 5.65e-01 9.12e+00
  angle pdb=" N   LEU E  38 "
        pdb=" CA  LEU E  38 "
        pdb=" C   LEU E  38 "
      ideal   model   delta    sigma   weight residual
     112.93  108.92    4.01 1.33e+00 5.65e-01 9.08e+00
  angle pdb=" N   LEU F  38 "
        pdb=" CA  LEU F  38 "
        pdb=" C   LEU F  38 "
      ideal   model   delta    sigma   weight residual
     112.93  108.93    4.00 1.33e+00 5.65e-01 9.04e+00
  angle pdb=" N   LEU K  38 "
        pdb=" CA  LEU K  38 "
        pdb=" C   LEU K  38 "
      ideal   model   delta    sigma   weight residual
     112.93  108.94    3.99 1.33e+00 5.65e-01 9.01e+00
  angle pdb=" N   LEU B  38 "
        pdb=" CA  LEU B  38 "
        pdb=" C   LEU B  38 "
      ideal   model   delta    sigma   weight residual
     112.93  108.96    3.97 1.33e+00 5.65e-01 8.92e+00
  ... (remaining 4189 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.91: 1572
       10.91 -    21.82: 192
       21.82 -    32.73: 48
       32.73 -    43.63: 12
       43.63 -    54.54: 12
  Dihedral angle restraints: 1836
    sinusoidal: 624
      harmonic: 1212
  Sorted by residual:
  dihedral pdb=" N   LYS F  45 "
           pdb=" CA  LYS F  45 "
           pdb=" CB  LYS F  45 "
           pdb=" CG  LYS F  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.46  -54.54     3      1.50e+01 4.44e-03 9.29e+00
  dihedral pdb=" N   LYS J  45 "
           pdb=" CA  LYS J  45 "
           pdb=" CB  LYS J  45 "
           pdb=" CG  LYS J  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.46  -54.54     3      1.50e+01 4.44e-03 9.29e+00
  dihedral pdb=" N   LYS L  45 "
           pdb=" CA  LYS L  45 "
           pdb=" CB  LYS L  45 "
           pdb=" CG  LYS L  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.47  -54.53     3      1.50e+01 4.44e-03 9.29e+00
  ... (remaining 1833 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 261
       0.033 -    0.067: 150
       0.067 -    0.100: 50
       0.100 -    0.134: 61
       0.134 -    0.167: 24
  Chirality restraints: 546
  Sorted by residual:
  chirality pdb=" CA  VAL E  37 "
            pdb=" N   VAL E  37 "
            pdb=" C   VAL E  37 "
            pdb=" CB  VAL E  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 6.99e-01
  chirality pdb=" CA  VAL F  37 "
            pdb=" N   VAL F  37 "
            pdb=" C   VAL F  37 "
            pdb=" CB  VAL F  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 6.93e-01
  chirality pdb=" CA  VAL L  37 "
            pdb=" N   VAL L  37 "
            pdb=" C   VAL L  37 "
            pdb=" CB  VAL L  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 6.81e-01
  ... (remaining 543 not shown)

  Planarity restraints: 522
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL L  95 "   -0.004 2.00e-02 2.50e+03   7.83e-03 6.13e-01
        pdb=" C   VAL L  95 "    0.014 2.00e-02 2.50e+03
        pdb=" O   VAL L  95 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   LYS L  96 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL J  95 "   -0.004 2.00e-02 2.50e+03   7.80e-03 6.09e-01
        pdb=" C   VAL J  95 "    0.013 2.00e-02 2.50e+03
        pdb=" O   VAL J  95 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   LYS J  96 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F  95 "   -0.004 2.00e-02 2.50e+03   7.73e-03 5.97e-01
        pdb=" C   VAL F  95 "    0.013 2.00e-02 2.50e+03
        pdb=" O   VAL F  95 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   LYS F  96 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 519 not shown)

  Histogram of nonbonded interaction distances:
        2.46 -     2.95: 1354
        2.95 -     3.44: 2895
        3.44 -     3.93: 4431
        3.93 -     4.41: 4982
        4.41 -     4.90: 10182
  Nonbonded interactions: 23844
  Sorted by model distance:
  nonbonded pdb=" N   VAL B  37 "
            pdb=" O   VAL F  37 "
     model   vdw
     2.465 3.120
  nonbonded pdb=" N   VAL L  37 "
            pdb=" O   VAL K  37 "
     model   vdw
     2.480 3.120
  nonbonded pdb=" O   VAL L  37 "
            pdb=" N   VAL J  37 "
     model   vdw
     2.488 3.120
  nonbonded pdb=" O   VAL B  37 "
            pdb=" N   VAL E  37 "
     model   vdw
     2.495 3.120
  nonbonded pdb=" O   ILE B  88 "
            pdb=" N   ALA F  89 "
     model   vdw
     2.650 3.120
  ... (remaining 23839 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.090
  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:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     11.690
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3114  Z= 0.320
  Angle     :  0.661   4.016   4194  Z= 0.415
  Chirality :  0.063   0.167    546
  Planarity :  0.002   0.008    522
  Dihedral  : 11.560  54.540   1068
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 18.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.55 (0.34), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.26), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS J  50 
 PHE   0.011   0.003   PHE K  94 
 TYR   0.004   0.001   TYR L  39 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.7565 (tt0) cc_final: 0.7271 (tt0)
REVERT: J   60 LYS cc_start: 0.8416 (tttt) cc_final: 0.8130 (tmtm)
REVERT: G   20 GLU cc_start: 0.7482 (tt0) cc_final: 0.7044 (tt0)
REVERT: E   43 LYS cc_start: 0.7492 (tppp) cc_final: 0.7288 (mmmm)
REVERT: C   20 GLU cc_start: 0.7548 (tt0) cc_final: 0.7217 (tt0)
REVERT: K   43 LYS cc_start: 0.7492 (tppp) cc_final: 0.7087 (mmmm)
REVERT: F   43 LYS cc_start: 0.7536 (tppp) cc_final: 0.7163 (mmmt)
REVERT: F   45 LYS cc_start: 0.8026 (tttt) cc_final: 0.7791 (ttmt)
REVERT: D   20 GLU cc_start: 0.7446 (tt0) cc_final: 0.7127 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 1.0075
  time to fit residues: 91.3474
Evaluate side-chains
  77 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.0030
   chunk 31 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 21 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   chunk 12 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   overall best weight:    3.5998

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

Flipped N/Q/H residues before XYZ refinement:
B  50 HIS
B  65 ASN
J  50 HIS
E  50 HIS
K  65 ASN
F  65 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.1683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032   3114  Z= 0.385
  Angle     :  0.665   4.123   4194  Z= 0.389
  Chirality :  0.057   0.156    546
  Planarity :  0.003   0.014    522
  Dihedral  :  4.860  11.824    444
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.50 %
    Favored  : 88.50 %
  Rotamer:
    Outliers : 11.86 %
    Allowed  :  9.94 %
    Favored  : 78.21 %
  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: -3.43 (0.36), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.61 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS J  50 
 PHE   0.010   0.003   PHE F  94 
 TYR   0.016   0.004   TYR E  39 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 81
  time to evaluate  : 0.328 
Fit side-chains
REVERT: L   58 LYS cc_start: 0.7890 (mttt) cc_final: 0.7636 (mttt)
REVERT: B   45 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7651 (tttp)
REVERT: A   20 GLU cc_start: 0.7576 (tt0) cc_final: 0.7254 (tt0)
REVERT: J   60 LYS cc_start: 0.8419 (tttt) cc_final: 0.8139 (tmtm)
REVERT: G   20 GLU cc_start: 0.7516 (tt0) cc_final: 0.7050 (tt0)
REVERT: E   43 LYS cc_start: 0.7563 (tppp) cc_final: 0.7356 (mmmm)
REVERT: C   20 GLU cc_start: 0.7542 (tt0) cc_final: 0.7222 (tt0)
REVERT: F   43 LYS cc_start: 0.7506 (tppp) cc_final: 0.7127 (mmmt)
  outliers start: 37
  outliers final: 22
  residues processed: 90
  average time/residue: 1.1074
  time to fit residues: 102.3827
Evaluate side-chains
  100 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 77
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   65 ASN
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain J residue   42 SER
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain G residue   15 VAL
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   65 ASN
Chi-restraints excluded: chain D residue   15 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   chunk 41 optimal weight:    8.9990
   chunk 34 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 30 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 19 optimal weight:    8.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
B  65 ASN
K  65 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3114  Z= 0.216
  Angle     :  0.523   3.409   4194  Z= 0.304
  Chirality :  0.052   0.139    546
  Planarity :  0.002   0.010    522
  Dihedral  :  4.495  12.918    444
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers : 10.58 %
    Allowed  : 16.35 %
    Favored  : 73.08 %
  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: -3.16 (0.37), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.40 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B  50 
 PHE   0.010   0.003   PHE F  94 
 TYR   0.007   0.002   TYR L  39 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 83
  time to evaluate  : 0.355 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.7560 (tt0) cc_final: 0.7299 (tt0)
REVERT: J   60 LYS cc_start: 0.8410 (tttt) cc_final: 0.8158 (tmtm)
REVERT: G   20 GLU cc_start: 0.7558 (tt0) cc_final: 0.7160 (tt0)
REVERT: E   60 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7810 (tmtp)
REVERT: C   20 GLU cc_start: 0.7564 (tt0) cc_final: 0.7251 (tt0)
REVERT: F   43 LYS cc_start: 0.7468 (tppp) cc_final: 0.7044 (mmmt)
REVERT: F   83 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7529 (mt-10)
  outliers start: 33
  outliers final: 21
  residues processed: 87
  average time/residue: 0.9967
  time to fit residues: 89.5422
Evaluate side-chains
  102 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   40 VAL
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   65 ASN
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   75 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   60 LYS
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   65 ASN
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain D residue   15 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 18 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 40 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
B  65 ASN
K  65 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   3114  Z= 0.208
  Angle     :  0.522   3.834   4194  Z= 0.304
  Chirality :  0.052   0.138    546
  Planarity :  0.002   0.012    522
  Dihedral  :  4.357  13.349    444
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  9.62 %
    Allowed  : 16.67 %
    Favored  : 73.72 %
  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: -3.04 (0.37), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.31 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS B  50 
 PHE   0.011   0.003   PHE F  94 
 TYR   0.008   0.002   TYR L  39 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 80
  time to evaluate  : 0.350 
Fit side-chains
REVERT: B   45 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7882 (ttmt)
REVERT: A   20 GLU cc_start: 0.7541 (tt0) cc_final: 0.7258 (tt0)
REVERT: J   43 LYS cc_start: 0.7303 (mmtt) cc_final: 0.6839 (mmmm)
REVERT: J   60 LYS cc_start: 0.8406 (tttt) cc_final: 0.8162 (tmtm)
REVERT: G   20 GLU cc_start: 0.7569 (tt0) cc_final: 0.7109 (tt0)
REVERT: E   60 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7823 (tmtp)
REVERT: C   20 GLU cc_start: 0.7577 (tt0) cc_final: 0.7274 (tt0)
REVERT: F   43 LYS cc_start: 0.7473 (tppp) cc_final: 0.7051 (mmmt)
REVERT: F   83 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7388 (mt-10)
  outliers start: 30
  outliers final: 22
  residues processed: 86
  average time/residue: 0.9486
  time to fit residues: 84.1656
Evaluate side-chains
  100 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 75
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   40 VAL
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   65 ASN
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain J residue   42 SER
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   75 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   60 LYS
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   65 ASN
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   83 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9990
   chunk 28 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 20 optimal weight:    7.9990
   chunk 36 optimal weight:    0.2980
   chunk 10 optimal weight:   10.0000
   chunk 13 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    2.4586

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

Flipped N/Q/H residues before XYZ refinement:
B  65 ASN
K  65 ASN
F  65 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3114  Z= 0.274
  Angle     :  0.572   4.301   4194  Z= 0.337
  Chirality :  0.053   0.144    546
  Planarity :  0.002   0.013    522
  Dihedral  :  4.522  15.540    444
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.39 %
    Favored  : 90.61 %
  Rotamer:
    Outliers : 11.86 %
    Allowed  : 14.74 %
    Favored  : 73.40 %
  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: -3.06 (0.37), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS B  50 
 PHE   0.010   0.003   PHE L  94 
 TYR   0.011   0.002   TYR L  39 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 83
  time to evaluate  : 0.358 
Fit side-chains
REVERT: B   45 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7959 (ttmt)
REVERT: B   60 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8059 (tmtp)
REVERT: A   20 GLU cc_start: 0.7551 (tt0) cc_final: 0.7283 (tt0)
REVERT: J   43 LYS cc_start: 0.7294 (mmtt) cc_final: 0.6819 (mmmm)
REVERT: J   60 LYS cc_start: 0.8414 (tttt) cc_final: 0.8172 (tmtm)
REVERT: G   20 GLU cc_start: 0.7563 (tt0) cc_final: 0.7091 (tt0)
REVERT: E   60 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7829 (tmtp)
REVERT: C   20 GLU cc_start: 0.7560 (tt0) cc_final: 0.7247 (tt0)
REVERT: K   60 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7686 (tmtp)
REVERT: F   38 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6615 (tm)
REVERT: F   43 LYS cc_start: 0.7612 (tppp) cc_final: 0.7120 (mmmt)
REVERT: F   83 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7397 (mt-10)
  outliers start: 37
  outliers final: 25
  residues processed: 91
  average time/residue: 1.0249
  time to fit residues: 96.0000
Evaluate side-chains
  112 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 81
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   40 VAL
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   60 LYS
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain J residue   42 SER
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   75 THR
Chi-restraints excluded: chain G residue   22 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   60 LYS
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   60 LYS
Chi-restraints excluded: chain K residue   65 ASN
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   65 ASN
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain D residue   15 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0030
   chunk 33 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 13 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0370
   chunk 29 optimal weight:    0.4980
   overall best weight:    1.1072

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

Flipped N/Q/H residues before XYZ refinement:
B  65 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   3114  Z= 0.166
  Angle     :  0.497   4.722   4194  Z= 0.289
  Chirality :  0.051   0.132    546
  Planarity :  0.002   0.011    522
  Dihedral  :  4.264  15.831    444
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers : 10.26 %
    Allowed  : 16.67 %
    Favored  : 73.08 %
  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: -2.90 (0.38), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS J  50 
 PHE   0.010   0.003   PHE F  94 
 TYR   0.007   0.001   TYR L  39 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 81
  time to evaluate  : 0.348 
Fit side-chains
REVERT: B   45 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7794 (ttmt)
REVERT: B   60 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8087 (tmtp)
REVERT: B   61 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.7033 (tp30)
REVERT: A   20 GLU cc_start: 0.7539 (tt0) cc_final: 0.7256 (tt0)
REVERT: J   60 LYS cc_start: 0.8416 (tttt) cc_final: 0.8193 (tmtm)
REVERT: G   20 GLU cc_start: 0.7528 (tt0) cc_final: 0.7068 (tt0)
REVERT: C   20 GLU cc_start: 0.7571 (tt0) cc_final: 0.7267 (tt0)
REVERT: K   60 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.7666 (tmtp)
REVERT: F   38 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6493 (tm)
REVERT: F   43 LYS cc_start: 0.7575 (tppp) cc_final: 0.7094 (mmmt)
REVERT: F   83 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7364 (mt-10)
REVERT: D   20 GLU cc_start: 0.7386 (tt0) cc_final: 0.7017 (tt0)
  outliers start: 32
  outliers final: 19
  residues processed: 91
  average time/residue: 1.0053
  time to fit residues: 94.2525
Evaluate side-chains
  103 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 78
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   40 VAL
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   65 ASN
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   60 LYS
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain J residue   42 SER
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   75 THR
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   60 LYS
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain D residue   15 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 34 optimal weight:    9.9990
   chunk 40 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   chunk 24 optimal weight:    9.9990
   chunk 18 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    4.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.035   3114  Z= 0.493
  Angle     :  0.782   9.076   4194  Z= 0.451
  Chirality :  0.059   0.160    546
  Planarity :  0.003   0.019    522
  Dihedral  :  5.077  14.974    444
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.21 %
    Favored  : 87.79 %
  Rotamer:
    Outliers : 12.82 %
    Allowed  : 14.42 %
    Favored  : 72.76 %
  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: -3.21 (0.36), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.44 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS L  50 
 PHE   0.012   0.003   PHE L  94 
 TYR   0.016   0.004   TYR B  39 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 78
  time to evaluate  : 0.358 
Fit side-chains
REVERT: L   61 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7069 (tp30)
REVERT: A   20 GLU cc_start: 0.7412 (tt0) cc_final: 0.7093 (tt0)
REVERT: J   43 LYS cc_start: 0.7365 (mmtt) cc_final: 0.6881 (mmmm)
REVERT: J   60 LYS cc_start: 0.8427 (tttt) cc_final: 0.8161 (tmtm)
REVERT: J   80 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8137 (tttt)
REVERT: G   20 GLU cc_start: 0.7531 (tt0) cc_final: 0.7062 (tt0)
REVERT: C   20 GLU cc_start: 0.7569 (tt0) cc_final: 0.7256 (tt0)
REVERT: K   60 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7668 (tmtp)
REVERT: F   43 LYS cc_start: 0.7624 (tppp) cc_final: 0.7160 (mmmt)
REVERT: F   83 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7390 (mt-10)
  outliers start: 40
  outliers final: 27
  residues processed: 90
  average time/residue: 1.0282
  time to fit residues: 95.1843
Evaluate side-chains
  108 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 77
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   61 GLU
Chi-restraints excluded: chain L residue   65 ASN
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   65 ASN
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain J residue   42 SER
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   75 THR
Chi-restraints excluded: chain J residue   80 LYS
Chi-restraints excluded: chain G residue   22 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   65 ASN
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue   80 LYS
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   60 LYS
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain D residue   15 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
F  65 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   3114  Z= 0.178
  Angle     :  0.575  10.009   4194  Z= 0.316
  Chirality :  0.052   0.137    546
  Planarity :  0.002   0.010    522
  Dihedral  :  4.522  17.502    444
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  8.97 %
    Allowed  : 18.27 %
    Favored  : 72.76 %
  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: -2.97 (0.37), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS J  50 
 PHE   0.011   0.003   PHE L  94 
 TYR   0.006   0.001   TYR B  39 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 81
  time to evaluate  : 0.354 
Fit side-chains
REVERT: B   45 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7646 (ttmt)
REVERT: A   20 GLU cc_start: 0.7513 (tt0) cc_final: 0.7209 (tt0)
REVERT: J   60 LYS cc_start: 0.8420 (tttt) cc_final: 0.8195 (tmtm)
REVERT: J   80 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8029 (tttt)
REVERT: G   20 GLU cc_start: 0.7531 (tt0) cc_final: 0.7080 (tt0)
REVERT: C   20 GLU cc_start: 0.7549 (tt0) cc_final: 0.7236 (tt0)
REVERT: K   60 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7670 (tmtp)
REVERT: F   43 LYS cc_start: 0.7661 (tppp) cc_final: 0.7165 (mmmt)
REVERT: F   83 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7335 (mt-10)
REVERT: D   20 GLU cc_start: 0.7359 (tt0) cc_final: 0.6998 (tt0)
  outliers start: 28
  outliers final: 20
  residues processed: 90
  average time/residue: 0.9465
  time to fit residues: 87.8537
Evaluate side-chains
  101 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 77
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   65 ASN
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   65 ASN
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   75 THR
Chi-restraints excluded: chain J residue   80 LYS
Chi-restraints excluded: chain G residue   22 THR
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   60 LYS
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain D residue   15 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 37 optimal weight:    8.9990
   chunk 24 optimal weight:    9.9990
   chunk 39 optimal weight:    4.9990
   chunk 18 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   chunk 41 optimal weight:    0.0370
   chunk 38 optimal weight:    3.9990
   chunk 33 optimal weight:    0.4980
   chunk 3 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    2.9064

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

Flipped N/Q/H residues before XYZ refinement:
K  65 ASN
F  65 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.025   3114  Z= 0.315
  Angle     :  0.682   8.992   4194  Z= 0.382
  Chirality :  0.055   0.148    546
  Planarity :  0.002   0.015    522
  Dihedral  :  4.807  16.586    444
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.50 %
    Favored  : 88.50 %
  Rotamer:
    Outliers :  9.29 %
    Allowed  : 17.63 %
    Favored  : 73.08 %
  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: -3.05 (0.37), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS B  50 
 PHE   0.011   0.003   PHE E  94 
 TYR   0.015   0.003   TYR E  39 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 79
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: L   61 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6993 (tp30)
REVERT: B   45 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7876 (ttmt)
REVERT: A   20 GLU cc_start: 0.7561 (tt0) cc_final: 0.7236 (tt0)
REVERT: J   43 LYS cc_start: 0.7294 (mmtt) cc_final: 0.6803 (mmmm)
REVERT: J   60 LYS cc_start: 0.8438 (tttt) cc_final: 0.8192 (tmtm)
REVERT: G   20 GLU cc_start: 0.7543 (tt0) cc_final: 0.7125 (tt0)
REVERT: C   20 GLU cc_start: 0.7562 (tt0) cc_final: 0.7247 (tt0)
REVERT: K   60 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7665 (tmtp)
REVERT: F   43 LYS cc_start: 0.7642 (tppp) cc_final: 0.7156 (mmmt)
REVERT: F   83 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7358 (mt-10)
  outliers start: 29
  outliers final: 23
  residues processed: 87
  average time/residue: 1.1464
  time to fit residues: 102.4579
Evaluate side-chains
  104 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 77
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   61 GLU
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain J residue   42 SER
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   75 THR
Chi-restraints excluded: chain J residue   80 LYS
Chi-restraints excluded: chain G residue   22 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue   80 LYS
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   60 LYS
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain D residue   15 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 26 optimal weight:    6.9990
   chunk 35 optimal weight:    0.0040
   chunk 10 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 13 optimal weight:    8.9990
   chunk 34 optimal weight:    7.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    2.1398

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   3114  Z= 0.246
  Angle     :  0.654   9.299   4194  Z= 0.361
  Chirality :  0.053   0.145    546
  Planarity :  0.002   0.011    522
  Dihedral  :  4.744  19.615    444
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 19.87 %
    Favored  : 71.79 %
  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: -2.97 (0.37), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS J  50 
 PHE   0.011   0.003   PHE E  94 
 TYR   0.009   0.002   TYR L  39 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 75
  time to evaluate  : 0.345 
Fit side-chains
REVERT: B   45 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7697 (ttmt)
REVERT: A   20 GLU cc_start: 0.7554 (tt0) cc_final: 0.7218 (tt0)
REVERT: J   60 LYS cc_start: 0.8432 (tttt) cc_final: 0.8195 (tmtm)
REVERT: J   80 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8124 (tttt)
REVERT: G   20 GLU cc_start: 0.7497 (tt0) cc_final: 0.7073 (tt0)
REVERT: E   60 LYS cc_start: 0.8505 (tmtp) cc_final: 0.8084 (tmtm)
REVERT: C   20 GLU cc_start: 0.7551 (tt0) cc_final: 0.7232 (tt0)
REVERT: K   60 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7658 (tmtp)
REVERT: F   43 LYS cc_start: 0.7681 (tppp) cc_final: 0.7211 (mmmt)
REVERT: F   83 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7341 (mt-10)
REVERT: D   20 GLU cc_start: 0.7361 (tt0) cc_final: 0.6992 (tt0)
  outliers start: 26
  outliers final: 21
  residues processed: 84
  average time/residue: 0.9220
  time to fit residues: 79.9359
Evaluate side-chains
  99 residues out of total 312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain J residue   42 SER
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   75 THR
Chi-restraints excluded: chain J residue   80 LYS
Chi-restraints excluded: chain G residue   22 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue   80 LYS
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   60 LYS
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain D residue   15 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 24 optimal weight:    9.9990
   chunk 38 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 16 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0170
   overall best weight:    0.6620

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

Flipped N/Q/H residues before XYZ refinement:
F  65 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.200234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.157004 restraints weight = 2963.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.4137 rms_B_bonded: 2.34
r_work: 0.4038 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3914 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   3114  Z= 0.124
  Angle     :  0.556   9.094   4194  Z= 0.297
  Chirality :  0.051   0.136    546
  Planarity :  0.002   0.009    522
  Dihedral  :  4.238  17.936    444
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 22.44 %
    Favored  : 72.12 %
  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: -2.79 (0.38), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS J  50 
 PHE   0.010   0.003   PHE L  94 
 TYR   0.006   0.001   TYR L  39 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1991.49 seconds
wall clock time: 35 minutes 25.40 seconds (2125.40 seconds total)