Starting phenix.real_space_refine
on Fri May  9 14:44:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yk2_33884/05_2025/7yk2_33884.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yk2_33884/05_2025/7yk2_33884.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/cci-nas-00/data/ceres_data/7yk2_33884/05_2025/7yk2_33884.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yk2_33884/05_2025/7yk2_33884.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yk2_33884/05_2025/7yk2_33884.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yk2_33884/05_2025/7yk2_33884.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=   0.003
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    1644      2.51       5
     N     456      2.21       5
     O     528      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 2628
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 438
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 1.77, per 1000 atoms: 0.67
  Number of scatterers: 2628
  At special positions: 0
  Unit cell: (98.58, 117.66, 31.8, 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     528      8.00
     N     456      7.00
     C    1644      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: 0.69
  Conformation dependent library (CDL) restraints added in 380.8 milliseconds
  

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  648

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 42.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 58
      removed outlier: 8.665A  pdb=" N   GLU C  46 " --> pdb=" O   GLY F  47 " (cutoff:3.500A)
      removed outlier: 8.307A  pdb=" N   VAL F  49 " --> pdb=" O   GLU C  46 " (cutoff:3.500A)
      removed outlier: 9.163A  pdb=" N   VAL C  48 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 10.541A  pdb=" N   GLY F  51 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   HIS C  50 " --> pdb=" O   GLY F  51 " (cutoff:3.500A)
      removed outlier: 8.834A  pdb=" N   ALA F  53 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   VAL C  52 " --> pdb=" O   ALA F  53 " (cutoff:3.500A)
      removed outlier: 8.215A  pdb=" N   VAL F  55 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   THR C  54 " --> pdb=" O   VAL F  55 " (cutoff:3.500A)
      removed outlier: 8.210A  pdb=" N   GLU F  57 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   ALA C  56 " --> pdb=" O   GLU F  57 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   VAL F  48 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   VAL E  49 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   HIS F  50 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   GLY E  51 " --> pdb=" O   HIS F  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 62 through 65
      removed outlier: 6.908A  pdb=" N   GLN E  62 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 8.121A  pdb=" N   ASN F  65 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   THR E  64 " --> pdb=" O   ASN F  65 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 71 through 82
      removed outlier: 8.999A  pdb=" N   VAL C  71 " --> pdb=" O   THR F  72 " (cutoff:3.500A)
      removed outlier: 9.394A  pdb=" N   VAL F  74 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   GLY C  73 " --> pdb=" O   VAL F  74 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   ALA F  76 " --> pdb=" O   GLY C  73 " (cutoff:3.500A)
      removed outlier: 8.630A  pdb=" N   THR C  75 " --> pdb=" O   ALA F  76 " (cutoff:3.500A)
      removed outlier: 7.975A  pdb=" N   ALA F  78 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 9.108A  pdb=" N   VAL C  77 " --> pdb=" O   ALA F  78 " (cutoff:3.500A)
      removed outlier: 10.641A  pdb=" N   LYS F  80 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 9.094A  pdb=" N   GLN C  79 " --> pdb=" O   LYS F  80 " (cutoff:3.500A)
      removed outlier: 10.364A  pdb=" N   VAL F  82 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 8.922A  pdb=" N   THR C  81 " --> pdb=" O   VAL F  82 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   THR E  72 " --> pdb=" O   VAL F  71 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   GLY F  73 " --> pdb=" O   THR E  72 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   VAL F  77 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   ALA E  78 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   GLN F  79 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   LYS E  80 " --> pdb=" O   GLN F  79 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   THR F  81 " --> pdb=" O   LYS E  80 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   VAL E  82 " --> pdb=" O   THR F  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 86 through 87
      removed outlier: 6.238A  pdb=" N   GLY E  86 " --> pdb=" O   SER F  87 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 46 through 58
      removed outlier: 8.658A  pdb=" N   GLU D  46 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 8.306A  pdb=" N   VAL B  49 " --> pdb=" O   GLU D  46 " (cutoff:3.500A)
      removed outlier: 9.164A  pdb=" N   VAL D  48 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 10.542A  pdb=" N   GLY B  51 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   HIS D  50 " --> pdb=" O   GLY B  51 " (cutoff:3.500A)
      removed outlier: 8.823A  pdb=" N   ALA B  53 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   VAL D  52 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 8.203A  pdb=" N   VAL B  55 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   THR D  54 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 8.196A  pdb=" N   GLU B  57 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ALA D  56 " --> pdb=" O   GLU B  57 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   VAL B  48 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   VAL A  49 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   HIS B  50 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   GLY A  51 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 62 through 65
      removed outlier: 6.271A  pdb=" N   VAL D  63 " --> pdb=" O   THR B  64 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   GLN A  62 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      removed outlier: 8.115A  pdb=" N   ASN B  65 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   THR A  64 " --> pdb=" O   ASN B  65 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'D' and resid 71 through 82
      removed outlier: 6.919A  pdb=" N   THR B  72 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   GLY D  73 " --> pdb=" O   THR B  72 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL D  77 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   ALA B  78 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   GLN D  79 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   LYS B  80 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   THR D  81 " --> pdb=" O   LYS B  80 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   VAL B  82 " --> pdb=" O   THR D  81 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   THR A  72 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   GLY B  73 " --> pdb=" O   THR A  72 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   VAL B  77 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   ALA A  78 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   GLN B  79 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   LYS A  80 " --> pdb=" O   GLN B  79 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   THR B  81 " --> pdb=" O   LYS A  80 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   VAL A  82 " --> pdb=" O   THR B  81 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 86 through 87
      removed outlier: 6.234A  pdb=" N   GLY A  86 " --> pdb=" O   SER B  87 " (cutoff:3.500A)

    30 hydrogen bonds defined for protein.
    90 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: 0.55

  Time building geometry restraints manager: 0.80 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: 462
        1.29 -     1.35: 414
        1.35 -     1.42: 102
        1.42 -     1.48: 426
        1.48 -     1.55: 1236
  Bond restraints: 2640
  Sorted by residual:
  bond pdb=" CG  LEU D  38 "
       pdb=" CD1 LEU D  38 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.21e+00
  bond pdb=" CG  LEU A  38 "
       pdb=" CD1 LEU A  38 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.20e+00
  bond pdb=" CG  LEU F  38 "
       pdb=" CD1 LEU F  38 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.20e+00
  bond pdb=" CG  LEU B  38 "
       pdb=" CD1 LEU B  38 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.19e+00
  bond pdb=" CG  LEU C  38 "
       pdb=" CD1 LEU C  38 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.18e+00
  ... (remaining 2635 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.89: 2905
        0.89 -     1.77: 475
        1.77 -     2.66: 129
        2.66 -     3.55: 49
        3.55 -     4.43: 12
  Bond angle restraints: 3570
  Sorted by residual:
  angle pdb=" CA  ILE B  88 "
        pdb=" C   ILE B  88 "
        pdb=" N   ALA B  89 "
      ideal   model   delta    sigma   weight residual
     117.15  119.77   -2.62 7.80e-01 1.64e+00 1.13e+01
  angle pdb=" CA  ILE A  88 "
        pdb=" C   ILE A  88 "
        pdb=" N   ALA A  89 "
      ideal   model   delta    sigma   weight residual
     117.15  119.75   -2.60 7.80e-01 1.64e+00 1.11e+01
  angle pdb=" CA  ILE C  88 "
        pdb=" C   ILE C  88 "
        pdb=" N   ALA C  89 "
      ideal   model   delta    sigma   weight residual
     117.15  119.75   -2.60 7.80e-01 1.64e+00 1.11e+01
  angle pdb=" CA  ILE F  88 "
        pdb=" C   ILE F  88 "
        pdb=" N   ALA F  89 "
      ideal   model   delta    sigma   weight residual
     117.15  119.74   -2.59 7.80e-01 1.64e+00 1.11e+01
  angle pdb=" CA  ILE D  88 "
        pdb=" C   ILE D  88 "
        pdb=" N   ALA D  89 "
      ideal   model   delta    sigma   weight residual
     117.15  119.74   -2.59 7.80e-01 1.64e+00 1.10e+01
  ... (remaining 3565 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.30: 1308
       10.30 -    20.60: 162
       20.60 -    30.90: 54
       30.90 -    41.20: 18
       41.20 -    51.50: 6
  Dihedral angle restraints: 1548
    sinusoidal: 522
      harmonic: 1026
  Sorted by residual:
  dihedral pdb=" CA  TYR E  39 "
           pdb=" CB  TYR E  39 "
           pdb=" CG  TYR E  39 "
           pdb=" CD1 TYR E  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -20.00   31.50  -51.50     2      2.00e+01 2.50e-03 7.35e+00
  dihedral pdb=" CA  TYR F  39 "
           pdb=" CB  TYR F  39 "
           pdb=" CG  TYR F  39 "
           pdb=" CD1 TYR F  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -20.00   31.42  -51.42     2      2.00e+01 2.50e-03 7.33e+00
  dihedral pdb=" CA  TYR B  39 "
           pdb=" CB  TYR B  39 "
           pdb=" CG  TYR B  39 "
           pdb=" CD1 TYR B  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -20.00   31.40  -51.40     2      2.00e+01 2.50e-03 7.33e+00
  ... (remaining 1545 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.027: 232
       0.027 -    0.053: 120
       0.053 -    0.080: 48
       0.080 -    0.106: 39
       0.106 -    0.132: 29
  Chirality restraints: 468
  Sorted by residual:
  chirality pdb=" CA  VAL A  70 "
            pdb=" N   VAL A  70 "
            pdb=" C   VAL A  70 "
            pdb=" CB  VAL A  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.38e-01
  chirality pdb=" CA  VAL E  70 "
            pdb=" N   VAL E  70 "
            pdb=" C   VAL E  70 "
            pdb=" CB  VAL E  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.31e-01
  chirality pdb=" CA  VAL F  70 "
            pdb=" N   VAL F  70 "
            pdb=" C   VAL F  70 "
            pdb=" CB  VAL F  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 465 not shown)

  Planarity restraints: 444
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  83 "   -0.006 2.00e-02 2.50e+03   1.15e-02 1.32e+00
        pdb=" C   GLU B  83 "    0.020 2.00e-02 2.50e+03
        pdb=" O   GLU B  83 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   GLY B  84 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A  83 "   -0.006 2.00e-02 2.50e+03   1.14e-02 1.31e+00
        pdb=" C   GLU A  83 "    0.020 2.00e-02 2.50e+03
        pdb=" O   GLU A  83 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   GLY A  84 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU D  83 "   -0.006 2.00e-02 2.50e+03   1.14e-02 1.31e+00
        pdb=" C   GLU D  83 "    0.020 2.00e-02 2.50e+03
        pdb=" O   GLU D  83 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   GLY D  84 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 441 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.92: 1092
        2.92 -     3.41: 2311
        3.41 -     3.91: 3902
        3.91 -     4.40: 4330
        4.40 -     4.90: 8827
  Nonbonded interactions: 20462
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN F  62 "
            pdb=" OG1 THR F  64 "
     model   vdw
     2.424 3.120
  nonbonded pdb=" NE2 GLN E  62 "
            pdb=" OG1 THR E  64 "
     model   vdw
     2.424 3.120
  nonbonded pdb=" NE2 GLN B  62 "
            pdb=" OG1 THR B  64 "
     model   vdw
     2.424 3.120
  nonbonded pdb=" NE2 GLN A  62 "
            pdb=" OG1 THR A  64 "
     model   vdw
     2.425 3.120
  nonbonded pdb=" NE2 GLN C  62 "
            pdb=" OG1 THR C  64 "
     model   vdw
     2.425 3.120
  ... (remaining 20457 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

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:             0.980
  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:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.340
  Find NCS groups from input model:        0.050
  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:12.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
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   2640  Z= 0.260
  Angle     :  0.816   4.432   3570  Z= 0.547
  Chirality :  0.051   0.132    468
  Planarity :  0.002   0.011    444
  Dihedral  : 11.384  51.497    900
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.48 %
    Favored  : 88.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.89 (0.35), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.96 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.004   HIS D  50 
 PHE   0.013   0.004   PHE B  94 
 TYR   0.007   0.002   TYR C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16252 (   30)
  hydrogen bonds       : angle       7.28354 (   90)
  covalent geometry    : bond        0.00528 ( 2640)
  covalent geometry    : angle       0.81622 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.295 
Fit side-chains
REVERT: C   80 LYS cc_start: 0.8084 (tttm) cc_final: 0.7741 (tttp)
REVERT: F   83 GLU cc_start: 0.6983 (tm-30) cc_final: 0.6714 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 1.3880
  time to fit residues: 72.2941
Evaluate side-chains
  43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0060
   chunk 18 optimal weight:    6.9990
   chunk 14 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   overall best weight:    1.8002

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

Flipped N/Q/H residues before XYZ refinement:
C  65 ASN
D  65 ASN
E  65 ASN
E  79 GLN
A  65 ASN
F  65 ASN
B  65 ASN
B  79 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4880 r_free = 0.4880 target = 0.219573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.169180 restraints weight = 2475.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.4406 rms_B_bonded: 2.58
r_work: 0.4293 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.4172 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.4172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.1310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2640  Z= 0.146
  Angle     :  0.542   3.436   3570  Z= 0.306
  Chirality :  0.050   0.134    468
  Planarity :  0.002   0.006    444
  Dihedral  :  4.750  12.364    378
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 16.67 %
    Favored  : 82.22 %
  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: -3.14 (0.38), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.38 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS C  50 
 PHE   0.014   0.004   PHE D  94 
 TYR   0.005   0.001   TYR F  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02478 (   30)
  hydrogen bonds       : angle       5.06224 (   90)
  covalent geometry    : bond        0.00323 ( 2640)
  covalent geometry    : angle       0.54166 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.293 
Fit side-chains
REVERT: D   62 GLN cc_start: 0.7026 (tt0) cc_final: 0.6720 (tm130)
REVERT: E   62 GLN cc_start: 0.6784 (tt0) cc_final: 0.6398 (tp40)
REVERT: A   62 GLN cc_start: 0.7066 (tt0) cc_final: 0.6749 (tp40)
REVERT: F   62 GLN cc_start: 0.6680 (tt0) cc_final: 0.6156 (tp40)
REVERT: F   83 GLU cc_start: 0.7345 (tm-30) cc_final: 0.7079 (tm-30)
  outliers start: 3
  outliers final: 2
  residues processed: 49
  average time/residue: 1.4005
  time to fit residues: 70.1318
Evaluate side-chains
  51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain B residue   66 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   chunk 11 optimal weight:    8.9990
   chunk 22 optimal weight:    8.9990
   chunk 13 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
C  62 GLN
D  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4835 r_free = 0.4835 target = 0.221017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.175867 restraints weight = 2621.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.4356 rms_B_bonded: 2.35
r_work: 0.4233 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.4114 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   2640  Z= 0.281
  Angle     :  0.683   3.722   3570  Z= 0.393
  Chirality :  0.054   0.133    468
  Planarity :  0.003   0.010    444
  Dihedral  :  5.493  15.184    378
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.21 %
    Favored  : 85.79 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 15.19 %
    Favored  : 79.26 %
  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 (0.39), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.005   HIS D  50 
 PHE   0.021   0.006   PHE B  94 
 TYR   0.006   0.002   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03132 (   30)
  hydrogen bonds       : angle       5.07560 (   90)
  covalent geometry    : bond        0.00619 ( 2640)
  covalent geometry    : angle       0.68261 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.273 
Fit side-chains
REVERT: E   43 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7426 (mptp)
REVERT: A   62 GLN cc_start: 0.7073 (tt0) cc_final: 0.6683 (tp40)
REVERT: F   62 GLN cc_start: 0.6688 (tt0) cc_final: 0.6292 (tp40)
REVERT: F   83 GLU cc_start: 0.7384 (tm-30) cc_final: 0.7142 (tm-30)
REVERT: B   57 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8264 (mt-10)
REVERT: B   62 GLN cc_start: 0.7270 (tm-30) cc_final: 0.6943 (tm-30)
  outliers start: 15
  outliers final: 9
  residues processed: 57
  average time/residue: 1.2525
  time to fit residues: 73.0124
Evaluate side-chains
  57 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   66 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
D  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4866 r_free = 0.4866 target = 0.219275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.168605 restraints weight = 2579.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.4397 rms_B_bonded: 2.67
r_work: 0.4277 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.4277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2640  Z= 0.142
  Angle     :  0.517   3.231   3570  Z= 0.295
  Chirality :  0.050   0.130    468
  Planarity :  0.002   0.008    444
  Dihedral  :  4.847  12.743    378
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.92 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 17.78 %
    Favored  : 78.15 %
  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 (0.39), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS F  50 
 PHE   0.012   0.003   PHE F  94 
 TYR   0.004   0.001   TYR E  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02306 (   30)
  hydrogen bonds       : angle       4.79440 (   90)
  covalent geometry    : bond        0.00316 ( 2640)
  covalent geometry    : angle       0.51717 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.259 
Fit side-chains
REVERT: D   46 GLU cc_start: 0.8005 (pt0) cc_final: 0.7671 (pt0)
REVERT: D   60 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7286 (tttt)
REVERT: E   43 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7335 (mptp)
REVERT: A   62 GLN cc_start: 0.7035 (tt0) cc_final: 0.6806 (tp40)
REVERT: F   83 GLU cc_start: 0.7247 (tm-30) cc_final: 0.7021 (tm-30)
REVERT: B   57 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8087 (mt-10)
REVERT: B   62 GLN cc_start: 0.7200 (tm-30) cc_final: 0.6760 (tm-30)
  outliers start: 11
  outliers final: 6
  residues processed: 50
  average time/residue: 1.2274
  time to fit residues: 62.8627
Evaluate side-chains
  50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   60 LYS
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain B residue   46 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 19 optimal weight:    0.5980
   chunk 29 optimal weight:   10.0000
   chunk 22 optimal weight:    0.1980
   chunk 28 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 21 optimal weight:    8.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4923 r_free = 0.4923 target = 0.229036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.184564 restraints weight = 2631.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.4464 rms_B_bonded: 2.32
r_work: 0.4355 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.4241 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.4241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   2640  Z= 0.093
  Angle     :  0.440   3.091   3570  Z= 0.251
  Chirality :  0.049   0.130    468
  Planarity :  0.001   0.007    444
  Dihedral  :  4.330  11.648    378
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 19.26 %
    Favored  : 77.04 %
  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: -2.66 (0.40), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS F  50 
 PHE   0.009   0.002   PHE F  94 
 TYR   0.002   0.001   TYR F  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01850 (   30)
  hydrogen bonds       : angle       4.62222 (   90)
  covalent geometry    : bond        0.00204 ( 2640)
  covalent geometry    : angle       0.44011 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.268 
Fit side-chains
REVERT: D   46 GLU cc_start: 0.8076 (pt0) cc_final: 0.7793 (pt0)
REVERT: D   60 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7519 (tttp)
REVERT: E   43 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7372 (mptp)
REVERT: E   62 GLN cc_start: 0.6788 (tt0) cc_final: 0.6325 (tp40)
REVERT: A   60 LYS cc_start: 0.7768 (tttm) cc_final: 0.7550 (tttm)
REVERT: A   62 GLN cc_start: 0.7129 (tt0) cc_final: 0.6728 (tp40)
REVERT: F   83 GLU cc_start: 0.7318 (tm-30) cc_final: 0.7075 (tm-30)
REVERT: B   57 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8323 (mt-10)
REVERT: B   62 GLN cc_start: 0.7468 (tm-30) cc_final: 0.7091 (tm-30)
  outliers start: 10
  outliers final: 5
  residues processed: 49
  average time/residue: 1.2990
  time to fit residues: 65.1202
Evaluate side-chains
  50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   60 LYS
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain B residue   46 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 22 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
D  79 GLN
E  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4846 r_free = 0.4846 target = 0.217248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.166154 restraints weight = 2610.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.4376 rms_B_bonded: 2.71
r_work: 0.4256 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.4256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.2366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2640  Z= 0.180
  Angle     :  0.540   3.288   3570  Z= 0.311
  Chirality :  0.051   0.129    468
  Planarity :  0.002   0.008    444
  Dihedral  :  5.034  14.289    378
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.38 %
    Favored  : 89.62 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 19.63 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.68 (0.40), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.04 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.004   HIS D  50 
 PHE   0.017   0.004   PHE B  94 
 TYR   0.003   0.001   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02336 (   30)
  hydrogen bonds       : angle       4.69194 (   90)
  covalent geometry    : bond        0.00398 ( 2640)
  covalent geometry    : angle       0.53974 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.289 
Fit side-chains
REVERT: C   46 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7676 (pt0)
REVERT: C   80 LYS cc_start: 0.7993 (tttm) cc_final: 0.7601 (tttp)
REVERT: D   60 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7339 (tttt)
REVERT: E   43 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7433 (mptp)
REVERT: A   62 GLN cc_start: 0.7022 (tt0) cc_final: 0.6593 (tp40)
REVERT: F   62 GLN cc_start: 0.6492 (tt0) cc_final: 0.6215 (tp40)
REVERT: F   83 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6994 (tm-30)
REVERT: B   57 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8158 (mt-10)
REVERT: B   62 GLN cc_start: 0.7239 (tm-30) cc_final: 0.6833 (tm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 54
  average time/residue: 1.3073
  time to fit residues: 72.1514
Evaluate side-chains
  57 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   60 LYS
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain B residue   46 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 31 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0270
   chunk 35 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 6 optimal weight:   10.0000
   chunk 3 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0770
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
D  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4954 r_free = 0.4954 target = 0.231375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.186550 restraints weight = 2721.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.4505 rms_B_bonded: 2.36
r_work: 0.4396 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.4281 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.4281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.2705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   2640  Z= 0.079
  Angle     :  0.432   3.363   3570  Z= 0.244
  Chirality :  0.049   0.127    468
  Planarity :  0.001   0.005    444
  Dihedral  :  4.150  11.914    378
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 21.48 %
    Favored  : 75.56 %
  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: -2.56 (0.41), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS B  50 
 PHE   0.008   0.002   PHE F  94 
 TYR   0.002   0.000   TYR F  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01659 (   30)
  hydrogen bonds       : angle       4.62178 (   90)
  covalent geometry    : bond        0.00170 ( 2640)
  covalent geometry    : angle       0.43187 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.288 
Fit side-chains
REVERT: D   60 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7469 (tttp)
REVERT: E   43 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7428 (mptp)
REVERT: E   62 GLN cc_start: 0.6797 (tt0) cc_final: 0.6420 (tp40)
REVERT: A   62 GLN cc_start: 0.7113 (tt0) cc_final: 0.6740 (tm-30)
REVERT: F   83 GLU cc_start: 0.7319 (tm-30) cc_final: 0.7018 (tm-30)
REVERT: B   62 GLN cc_start: 0.7425 (tm-30) cc_final: 0.7043 (tm-30)
  outliers start: 8
  outliers final: 5
  residues processed: 47
  average time/residue: 1.2110
  time to fit residues: 58.3387
Evaluate side-chains
  49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   60 LYS
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain B residue   46 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 6 optimal weight:   10.0000
   chunk 27 optimal weight:    0.8980
   chunk 30 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 22 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 18 optimal weight:    8.9990
   overall best weight:    1.3582

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

Flipped N/Q/H residues before XYZ refinement:
F  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4903 r_free = 0.4903 target = 0.227229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.181947 restraints weight = 2642.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.4448 rms_B_bonded: 2.34
r_work: 0.4315 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.4191 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.4191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2640  Z= 0.118
  Angle     :  0.472   3.840   3570  Z= 0.269
  Chirality :  0.049   0.128    468
  Planarity :  0.001   0.006    444
  Dihedral  :  4.559  13.331    378
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 22.22 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.54 (0.41), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS B  50 
 PHE   0.012   0.003   PHE B  94 
 TYR   0.002   0.001   TYR F  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01832 (   30)
  hydrogen bonds       : angle       4.50700 (   90)
  covalent geometry    : bond        0.00262 ( 2640)
  covalent geometry    : angle       0.47224 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.275 
Fit side-chains
REVERT: D   60 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7468 (tttp)
REVERT: E   43 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7485 (mptp)
REVERT: E   62 GLN cc_start: 0.6894 (tt0) cc_final: 0.6687 (tt0)
REVERT: A   62 GLN cc_start: 0.7103 (tt0) cc_final: 0.6698 (tp40)
REVERT: F   83 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7112 (tm-30)
REVERT: B   62 GLN cc_start: 0.7503 (tm-30) cc_final: 0.7146 (tm-30)
  outliers start: 9
  outliers final: 5
  residues processed: 50
  average time/residue: 1.2115
  time to fit residues: 62.0518
Evaluate side-chains
  51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   60 LYS
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain B residue   46 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 28 optimal weight:    7.9990
   chunk 23 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 30 optimal weight:    8.9990
   chunk 19 optimal weight:    5.9990
   chunk 21 optimal weight:    0.0000
   chunk 34 optimal weight:    3.9990
   overall best weight:    2.3992

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

Flipped N/Q/H residues before XYZ refinement:
F  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4845 r_free = 0.4845 target = 0.217182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.166125 restraints weight = 2615.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.4378 rms_B_bonded: 2.71
r_work: 0.4257 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.4257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.2649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2640  Z= 0.185
  Angle     :  0.555   4.194   3570  Z= 0.318
  Chirality :  0.051   0.130    468
  Planarity :  0.002   0.007    444
  Dihedral  :  5.107  16.129    378
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.48 %
    Favored  : 88.52 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 21.48 %
    Favored  : 75.56 %
  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: -2.59 (0.40), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.004   HIS F  50 
 PHE   0.017   0.004   PHE B  94 
 TYR   0.003   0.001   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02204 (   30)
  hydrogen bonds       : angle       4.69800 (   90)
  covalent geometry    : bond        0.00412 ( 2640)
  covalent geometry    : angle       0.55544 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.298 
Fit side-chains
REVERT: D   60 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7347 (tttt)
REVERT: E   43 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7552 (mptp)
REVERT: A   62 GLN cc_start: 0.7066 (tt0) cc_final: 0.6681 (tp40)
REVERT: F   62 GLN cc_start: 0.6483 (tt0) cc_final: 0.6209 (tp40)
REVERT: F   83 GLU cc_start: 0.7307 (tm-30) cc_final: 0.7029 (tm-30)
REVERT: B   62 GLN cc_start: 0.7226 (tm-30) cc_final: 0.6806 (tm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 51
  average time/residue: 1.1333
  time to fit residues: 59.2693
Evaluate side-chains
  56 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   60 LYS
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain B residue   46 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 28 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 32 optimal weight:    7.9990
   chunk 26 optimal weight:    8.9990
   chunk 11 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 12 optimal weight:   10.0000
   overall best weight:    2.3986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4848 r_free = 0.4848 target = 0.216867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.166038 restraints weight = 2622.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.4371 rms_B_bonded: 2.71
r_work: 0.4251 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.4251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2640  Z= 0.184
  Angle     :  0.572   4.671   3570  Z= 0.325
  Chirality :  0.051   0.132    468
  Planarity :  0.002   0.008    444
  Dihedral  :  5.134  16.338    378
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 21.85 %
    Favored  : 75.19 %
  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: -2.67 (0.40), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.03 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.004   HIS D  50 
 PHE   0.016   0.004   PHE F  94 
 TYR   0.004   0.001   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02228 (   30)
  hydrogen bonds       : angle       4.73605 (   90)
  covalent geometry    : bond        0.00409 ( 2640)
  covalent geometry    : angle       0.57187 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.315 
Fit side-chains
REVERT: D   60 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7345 (tttt)
REVERT: E   43 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7578 (mptp)
REVERT: E   62 GLN cc_start: 0.6755 (tt0) cc_final: 0.6378 (tt0)
REVERT: A   62 GLN cc_start: 0.7067 (tt0) cc_final: 0.6677 (tp40)
REVERT: F   62 GLN cc_start: 0.6411 (tt0) cc_final: 0.6087 (tp40)
REVERT: F   83 GLU cc_start: 0.7333 (tm-30) cc_final: 0.7059 (tm-30)
REVERT: B   62 GLN cc_start: 0.7263 (tm-30) cc_final: 0.6833 (tm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 54
  average time/residue: 1.3082
  time to fit residues: 72.2090
Evaluate side-chains
  59 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   60 LYS
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain B residue   46 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 14 optimal weight:    0.0670
   chunk 5 optimal weight:    8.9990
   chunk 19 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0030
   chunk 17 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 22 optimal weight:    0.0980
   chunk 6 optimal weight:    9.9990
   chunk 23 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    1.8332

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4887 r_free = 0.4887 target = 0.224350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.179465 restraints weight = 2682.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.4412 rms_B_bonded: 2.36
r_work: 0.4298 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.4182 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2640  Z= 0.150
  Angle     :  0.553   5.378   3570  Z= 0.311
  Chirality :  0.050   0.132    468
  Planarity :  0.002   0.009    444
  Dihedral  :  4.933  14.979    378
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.02 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 22.22 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.68 (0.40), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.03 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS F  50 
 PHE   0.013   0.004   PHE F  94 
 TYR   0.003   0.001   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02081 (   30)
  hydrogen bonds       : angle       4.68514 (   90)
  covalent geometry    : bond        0.00339 ( 2640)
  covalent geometry    : angle       0.55256 ( 3570)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2618.09 seconds
wall clock time: 45 minutes 48.31 seconds (2748.31 seconds total)