Starting phenix.real_space_refine
on Tue Mar  3 13:02:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6sst_10305/03_2026/6sst_10305.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6sst_10305/03_2026/6sst_10305.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6sst_10305/03_2026/6sst_10305.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6sst_10305/03_2026/6sst_10305.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6sst_10305/03_2026/6sst_10305.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6sst_10305/03_2026/6sst_10305.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    3050      2.51       5
     N     860      2.21       5
     O     990      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4900
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 490
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 490
          Classifications: {'peptide': 73}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'TRANS': 72}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J
  Time building chain proxies: 0.56, per 1000 atoms: 0.11
  Number of scatterers: 4900
  At special positions: 0
  Unit cell: (97.495, 122.655, 44.03, 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     990      8.00
     N     860      7.00
     C    3050      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: 0.32
  Conformation dependent library (CDL) restraints added in 334.8 milliseconds
  

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1220

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 14 sheets defined
      0.0% alpha, 56.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 23
    Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 49
      removed outlier: 6.861A  pdb=" N   LEU B  38 " --> pdb=" O   VAL A  37 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   TYR A  39 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   VAL B  40 " --> pdb=" O   TYR A  39 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   GLY A  41 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   SER B  42 " --> pdb=" O   GLY A  41 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   LYS A  43 " --> pdb=" O   SER B  42 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   THR B  44 " --> pdb=" O   LYS A  43 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   LYS A  45 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   GLU B  46 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 9.135A  pdb=" N   VAL B  37 " --> pdb=" O   LEU C  38 " (cutoff:3.500A)
      removed outlier: 10.129A  pdb=" N   VAL C  40 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
      removed outlier: 9.155A  pdb=" N   TYR B  39 " --> pdb=" O   VAL C  40 " (cutoff:3.500A)
      removed outlier: 9.929A  pdb=" N   SER C  42 " --> pdb=" O   TYR B  39 " (cutoff:3.500A)
      removed outlier: 8.884A  pdb=" N   GLY B  41 " --> pdb=" O   SER C  42 " (cutoff:3.500A)
      removed outlier: 9.966A  pdb=" N   THR C  44 " --> pdb=" O   GLY B  41 " (cutoff:3.500A)
      removed outlier: 8.978A  pdb=" N   LYS B  43 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 10.575A  pdb=" N   GLU C  46 " --> pdb=" O   LYS B  43 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   LYS B  45 " --> pdb=" O   GLU C  46 " (cutoff:3.500A)
      removed outlier: 8.925A  pdb=" N   VAL C  48 " --> pdb=" O   LYS B  45 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   GLY B  47 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 9.069A  pdb=" N   VAL C  37 " --> pdb=" O   LEU D  38 " (cutoff:3.500A)
      removed outlier: 10.068A  pdb=" N   VAL D  40 " --> pdb=" O   VAL C  37 " (cutoff:3.500A)
      removed outlier: 9.097A  pdb=" N   TYR C  39 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
      removed outlier: 9.877A  pdb=" N   SER D  42 " --> pdb=" O   TYR C  39 " (cutoff:3.500A)
      removed outlier: 8.836A  pdb=" N   GLY C  41 " --> pdb=" O   SER D  42 " (cutoff:3.500A)
      removed outlier: 9.919A  pdb=" N   THR D  44 " --> pdb=" O   GLY C  41 " (cutoff:3.500A)
      removed outlier: 8.941A  pdb=" N   LYS C  43 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 10.540A  pdb=" N   GLU D  46 " --> pdb=" O   LYS C  43 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   LYS C  45 " --> pdb=" O   GLU D  46 " (cutoff:3.500A)
      removed outlier: 8.923A  pdb=" N   VAL D  48 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   GLY C  47 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 8.998A  pdb=" N   VAL D  37 " --> pdb=" O   LEU E  38 " (cutoff:3.500A)
      removed outlier: 10.007A  pdb=" N   VAL E  40 " --> pdb=" O   VAL D  37 " (cutoff:3.500A)
      removed outlier: 9.031A  pdb=" N   TYR D  39 " --> pdb=" O   VAL E  40 " (cutoff:3.500A)
      removed outlier: 9.817A  pdb=" N   SER E  42 " --> pdb=" O   TYR D  39 " (cutoff:3.500A)
      removed outlier: 8.770A  pdb=" N   GLY D  41 " --> pdb=" O   SER E  42 " (cutoff:3.500A)
      removed outlier: 9.869A  pdb=" N   THR E  44 " --> pdb=" O   GLY D  41 " (cutoff:3.500A)
      removed outlier: 8.881A  pdb=" N   LYS D  43 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
      removed outlier: 10.492A  pdb=" N   GLU E  46 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   LYS D  45 " --> pdb=" O   GLU E  46 " (cutoff:3.500A)
      removed outlier: 8.857A  pdb=" N   VAL E  48 " --> pdb=" O   LYS D  45 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   GLY D  47 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 57
    Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 66
    Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 71
    Processing sheet with id=AA6, first strand: chain 'A' and resid 75 through 79
    Processing sheet with id=AA7, first strand: chain 'A' and resid 86 through 91
      removed outlier: 6.491A  pdb=" N   SER A  87 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   ALA B  90 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   ALA A  89 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   SER B  87 " --> pdb=" O   ILE C  88 " (cutoff:3.500A)
      removed outlier: 7.680A  pdb=" N   ALA C  90 " --> pdb=" O   SER B  87 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   ALA B  89 " --> pdb=" O   ALA C  90 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   SER C  87 " --> pdb=" O   ILE D  88 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   ALA D  90 " --> pdb=" O   SER C  87 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   ALA C  89 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   SER D  87 " --> pdb=" O   ILE E  88 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   ALA E  90 " --> pdb=" O   SER D  87 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   ALA D  89 " --> pdb=" O   ALA E  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'F' and resid 15 through 23
    Processing sheet with id=AA9, first strand: chain 'F' and resid 37 through 49
      removed outlier: 6.823A  pdb=" N   LEU G  38 " --> pdb=" O   VAL F  37 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   TYR F  39 " --> pdb=" O   LEU G  38 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   VAL G  40 " --> pdb=" O   TYR F  39 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   GLY F  41 " --> pdb=" O   VAL G  40 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   SER G  42 " --> pdb=" O   GLY F  41 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LYS F  43 " --> pdb=" O   SER G  42 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   THR G  44 " --> pdb=" O   LYS F  43 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   LYS F  45 " --> pdb=" O   THR G  44 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   GLU G  46 " --> pdb=" O   LYS F  45 " (cutoff:3.500A)
      removed outlier: 9.112A  pdb=" N   VAL G  37 " --> pdb=" O   LEU H  38 " (cutoff:3.500A)
      removed outlier: 10.099A  pdb=" N   VAL H  40 " --> pdb=" O   VAL G  37 " (cutoff:3.500A)
      removed outlier: 9.127A  pdb=" N   TYR G  39 " --> pdb=" O   VAL H  40 " (cutoff:3.500A)
      removed outlier: 9.895A  pdb=" N   SER H  42 " --> pdb=" O   TYR G  39 " (cutoff:3.500A)
      removed outlier: 8.851A  pdb=" N   GLY G  41 " --> pdb=" O   SER H  42 " (cutoff:3.500A)
      removed outlier: 9.930A  pdb=" N   THR H  44 " --> pdb=" O   GLY G  41 " (cutoff:3.500A)
      removed outlier: 8.945A  pdb=" N   LYS G  43 " --> pdb=" O   THR H  44 " (cutoff:3.500A)
      removed outlier: 10.541A  pdb=" N   GLU H  46 " --> pdb=" O   LYS G  43 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   LYS G  45 " --> pdb=" O   GLU H  46 " (cutoff:3.500A)
      removed outlier: 8.917A  pdb=" N   VAL H  48 " --> pdb=" O   LYS G  45 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   GLY G  47 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 9.114A  pdb=" N   VAL H  37 " --> pdb=" O   LEU I  38 " (cutoff:3.500A)
      removed outlier: 10.108A  pdb=" N   VAL I  40 " --> pdb=" O   VAL H  37 " (cutoff:3.500A)
      removed outlier: 9.136A  pdb=" N   TYR H  39 " --> pdb=" O   VAL I  40 " (cutoff:3.500A)
      removed outlier: 9.909A  pdb=" N   SER I  42 " --> pdb=" O   TYR H  39 " (cutoff:3.500A)
      removed outlier: 8.866A  pdb=" N   GLY H  41 " --> pdb=" O   SER I  42 " (cutoff:3.500A)
      removed outlier: 9.947A  pdb=" N   THR I  44 " --> pdb=" O   GLY H  41 " (cutoff:3.500A)
      removed outlier: 8.963A  pdb=" N   LYS H  43 " --> pdb=" O   THR I  44 " (cutoff:3.500A)
      removed outlier: 10.560A  pdb=" N   GLU I  46 " --> pdb=" O   LYS H  43 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   LYS H  45 " --> pdb=" O   GLU I  46 " (cutoff:3.500A)
      removed outlier: 8.925A  pdb=" N   VAL I  48 " --> pdb=" O   LYS H  45 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   GLY H  47 " --> pdb=" O   VAL I  48 " (cutoff:3.500A)
      removed outlier: 9.055A  pdb=" N   VAL I  37 " --> pdb=" O   LEU J  38 " (cutoff:3.500A)
      removed outlier: 10.059A  pdb=" N   VAL J  40 " --> pdb=" O   VAL I  37 " (cutoff:3.500A)
      removed outlier: 9.090A  pdb=" N   TYR I  39 " --> pdb=" O   VAL J  40 " (cutoff:3.500A)
      removed outlier: 9.875A  pdb=" N   SER J  42 " --> pdb=" O   TYR I  39 " (cutoff:3.500A)
      removed outlier: 8.836A  pdb=" N   GLY I  41 " --> pdb=" O   SER J  42 " (cutoff:3.500A)
      removed outlier: 9.923A  pdb=" N   THR J  44 " --> pdb=" O   GLY I  41 " (cutoff:3.500A)
      removed outlier: 8.947A  pdb=" N   LYS I  43 " --> pdb=" O   THR J  44 " (cutoff:3.500A)
      removed outlier: 10.546A  pdb=" N   GLU J  46 " --> pdb=" O   LYS I  43 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   LYS I  45 " --> pdb=" O   GLU J  46 " (cutoff:3.500A)
      removed outlier: 8.920A  pdb=" N   VAL J  48 " --> pdb=" O   LYS I  45 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   GLY I  47 " --> pdb=" O   VAL J  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 52 through 57
    Processing sheet with id=AB2, first strand: chain 'F' and resid 61 through 66
    Processing sheet with id=AB3, first strand: chain 'F' and resid 69 through 71
    Processing sheet with id=AB4, first strand: chain 'F' and resid 75 through 79
    Processing sheet with id=AB5, first strand: chain 'F' and resid 86 through 91
      removed outlier: 6.496A  pdb=" N   SER F  87 " --> pdb=" O   ILE G  88 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   ALA G  90 " --> pdb=" O   SER F  87 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   ALA F  89 " --> pdb=" O   ALA G  90 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   SER G  87 " --> pdb=" O   ILE H  88 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   ALA H  90 " --> pdb=" O   SER G  87 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   ALA G  89 " --> pdb=" O   ALA H  90 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   SER H  87 " --> pdb=" O   ILE I  88 " (cutoff:3.500A)
      removed outlier: 7.688A  pdb=" N   ALA I  90 " --> pdb=" O   SER H  87 " (cutoff:3.500A)
      removed outlier: 6.066A  pdb=" N   ALA H  89 " --> pdb=" O   ALA I  90 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   SER I  87 " --> pdb=" O   ILE J  88 " (cutoff:3.500A)
      removed outlier: 7.651A  pdb=" N   ALA J  90 " --> pdb=" O   SER I  87 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   ALA I  89 " --> pdb=" O   ALA J  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5

    198 hydrogen bonds defined for protein.
    594 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: 0.70

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 870
        1.29 -     1.35: 770
        1.35 -     1.41: 177
        1.41 -     1.48: 833
        1.48 -     1.54: 2260
  Bond restraints: 4910
  Sorted by residual:
  bond pdb=" CB  THR D  44 "
       pdb=" CG2 THR D  44 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.90e+00
  bond pdb=" CB  THR I  44 "
       pdb=" CG2 THR I  44 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.88e+00
  bond pdb=" CB  THR C  44 "
       pdb=" CG2 THR C  44 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.86e+00
  bond pdb=" CB  THR H  44 "
       pdb=" CG2 THR H  44 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.85e+00
  bond pdb=" CB  THR A  44 "
       pdb=" CG2 THR A  44 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.85e+00
  ... (remaining 4905 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.95: 5286
        0.95 -     1.89: 894
        1.89 -     2.84: 330
        2.84 -     3.79: 69
        3.79 -     4.73: 51
  Bond angle restraints: 6630
  Sorted by residual:
  angle pdb=" C   GLY C  84 "
        pdb=" N   ALA C  85 "
        pdb=" CA  ALA C  85 "
      ideal   model   delta    sigma   weight residual
     122.68  126.37   -3.69 1.47e+00 4.63e-01 6.30e+00
  angle pdb=" C   GLY D  84 "
        pdb=" N   ALA D  85 "
        pdb=" CA  ALA D  85 "
      ideal   model   delta    sigma   weight residual
     122.68  126.35   -3.67 1.47e+00 4.63e-01 6.23e+00
  angle pdb=" C   GLY F  84 "
        pdb=" N   ALA F  85 "
        pdb=" CA  ALA F  85 "
      ideal   model   delta    sigma   weight residual
     122.68  126.35   -3.67 1.47e+00 4.63e-01 6.22e+00
  angle pdb=" C   GLY J  84 "
        pdb=" N   ALA J  85 "
        pdb=" CA  ALA J  85 "
      ideal   model   delta    sigma   weight residual
     122.68  126.34   -3.66 1.47e+00 4.63e-01 6.20e+00
  angle pdb=" C   GLY I  84 "
        pdb=" N   ALA I  85 "
        pdb=" CA  ALA I  85 "
      ideal   model   delta    sigma   weight residual
     122.68  126.34   -3.66 1.47e+00 4.63e-01 6.20e+00
  ... (remaining 6625 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 2530
       17.13 -    34.27: 230
       34.27 -    51.40: 40
       51.40 -    68.53: 30
       68.53 -    85.66: 10
  Dihedral angle restraints: 2840
    sinusoidal: 900
      harmonic: 1940
  Sorted by residual:
  dihedral pdb=" CA  GLY F  73 "
           pdb=" C   GLY F  73 "
           pdb=" N   VAL F  74 "
           pdb=" CA  VAL F  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.41   29.59     0      5.00e+00 4.00e-02 3.50e+01
  dihedral pdb=" CA  GLY D  73 "
           pdb=" C   GLY D  73 "
           pdb=" N   VAL D  74 "
           pdb=" CA  VAL D  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.42   29.58     0      5.00e+00 4.00e-02 3.50e+01
  dihedral pdb=" CA  GLY G  73 "
           pdb=" C   GLY G  73 "
           pdb=" N   VAL G  74 "
           pdb=" CA  VAL G  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.43   29.57     0      5.00e+00 4.00e-02 3.50e+01
  ... (remaining 2837 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 506
       0.048 -    0.095: 218
       0.095 -    0.142: 136
       0.142 -    0.190: 0
       0.190 -    0.237: 10
  Chirality restraints: 870
  Sorted by residual:
  chirality pdb=" CB  THR C  44 "
            pdb=" CA  THR C  44 "
            pdb=" OG1 THR C  44 "
            pdb=" CG2 THR C  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CB  THR F  44 "
            pdb=" CA  THR F  44 "
            pdb=" OG1 THR F  44 "
            pdb=" CG2 THR F  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" CB  THR D  44 "
            pdb=" CA  THR D  44 "
            pdb=" OG1 THR D  44 "
            pdb=" CG2 THR D  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.36e+00
  ... (remaining 867 not shown)

  Planarity restraints: 830
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS F  58 "   -0.006 2.00e-02 2.50e+03   1.30e-02 1.70e+00
        pdb=" C   LYS F  58 "    0.023 2.00e-02 2.50e+03
        pdb=" O   LYS F  58 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   THR F  59 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS H  58 "   -0.006 2.00e-02 2.50e+03   1.29e-02 1.67e+00
        pdb=" C   LYS H  58 "    0.022 2.00e-02 2.50e+03
        pdb=" O   LYS H  58 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   THR H  59 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS I  58 "   -0.006 2.00e-02 2.50e+03   1.28e-02 1.64e+00
        pdb=" C   LYS I  58 "    0.022 2.00e-02 2.50e+03
        pdb=" O   LYS I  58 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   THR I  59 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 827 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.92: 2136
        2.92 -     3.42: 4158
        3.42 -     3.91: 8392
        3.91 -     4.41: 8896
        4.41 -     4.90: 17858
  Nonbonded interactions: 41440
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN D  62 "
            pdb=" NE2 GLN E  62 "
     model   vdw
     2.430 3.120
  nonbonded pdb=" OE1 GLN F  62 "
            pdb=" NE2 GLN G  62 "
     model   vdw
     2.432 3.120
  nonbonded pdb=" OE1 GLN A  62 "
            pdb=" NE2 GLN B  62 "
     model   vdw
     2.484 3.120
  nonbonded pdb=" OE1 GLN I  62 "
            pdb=" NE2 GLN J  62 "
     model   vdw
     2.500 3.120
  nonbonded pdb=" OE1 GLN G  62 "
            pdb=" NE2 GLN H  62 "
     model   vdw
     2.502 3.120
  ... (remaining 41435 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 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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:             1.430
  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:             0.020
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     6.030
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
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      :  0.009   0.056   4910  Z= 0.399
  Angle     :  0.941   4.734   6630  Z= 0.559
  Chirality :  0.065   0.237    870
  Planarity :  0.004   0.013    830
  Dihedral  : 16.794  85.661   1620
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 12.77 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.47 (0.26), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.40 (0.20), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.014   0.003   TYR F  39 
 PHE   0.003   0.001   PHE E  94 
 HIS   0.003   0.002   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00891 ( 4910)
  covalent geometry    : angle       0.94068 ( 6630)
  hydrogen bonds       : bond        0.08515 (  198)
  hydrogen bonds       : angle       4.74315 (  594)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 35
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   72 THR cc_start: 0.9388 (m) cc_final: 0.9186 (m)
REVERT: C   58 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6739 (tptp)
REVERT: C   83 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7414 (mt-10)
REVERT: D   58 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.7018 (tptp)
REVERT: D   72 THR cc_start: 0.9573 (m) cc_final: 0.9343 (m)
REVERT: E   58 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6859 (tptp)
REVERT: G   83 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7046 (mt-10)
REVERT: H   83 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7462 (mt-10)
REVERT: I   58 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6478 (ttpt)
REVERT: I   80 LYS cc_start: 0.8344 (mttp) cc_final: 0.7742 (mtpt)
REVERT: J   58 LYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6998 (tppt)
REVERT: J   80 LYS cc_start: 0.8610 (mttp) cc_final: 0.8397 (mttp)
  outliers start: 10
  outliers final: 2
  residues processed: 45
  average time/residue: 0.1299
  time to fit residues: 6.9302
Evaluate side-chains
  35 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 LYS
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain E residue   58 LYS
Chi-restraints excluded: chain G residue   58 LYS
Chi-restraints excluded: chain H residue   58 LYS
Chi-restraints excluded: chain I residue   58 LYS
Chi-restraints excluded: chain J residue   58 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 27 optimal weight:    5.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.136983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.114823 restraints weight = 5925.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3971 rms_B_bonded: 2.11
r_work: 0.3884 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3734 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.1268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   4910  Z= 0.127
  Angle     :  0.573   6.639   6630  Z= 0.330
  Chirality :  0.053   0.129    870
  Planarity :  0.002   0.010    830
  Dihedral  :  9.638  57.199    748
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  :  7.45 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.25 (0.28), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.23 (0.21), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR F  39 
 PHE   0.001   0.001   PHE D  94 
 HIS   0.001   0.000   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 4910)
  covalent geometry    : angle       0.57305 ( 6630)
  hydrogen bonds       : bond        0.01866 (  198)
  hydrogen bonds       : angle       4.38990 (  594)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 26
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
REVERT: B   72 THR cc_start: 0.9382 (m) cc_final: 0.9146 (m)
REVERT: D   58 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6880 (tptp)
REVERT: D   72 THR cc_start: 0.9507 (m) cc_final: 0.9288 (m)
REVERT: D   80 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7943 (mtmm)
REVERT: E   58 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.7112 (tptp)
REVERT: F   83 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7499 (mt-10)
REVERT: G   58 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6692 (tptp)
REVERT: I   58 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.6764 (tptp)
REVERT: J   58 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7111 (tptp)
  outliers start: 25
  outliers final: 7
  residues processed: 50
  average time/residue: 0.0805
  time to fit residues: 5.2643
Evaluate side-chains
  39 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 26
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   80 LYS
Chi-restraints excluded: chain E residue   58 LYS
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   58 LYS
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain I residue   58 LYS
Chi-restraints excluded: chain J residue   58 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 53 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   chunk 57 optimal weight:    6.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.125517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.104141 restraints weight = 6400.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3784 rms_B_bonded: 2.05
r_work: 0.3695 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3549 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.042   4910  Z= 0.412
  Angle     :  0.731   5.490   6630  Z= 0.429
  Chirality :  0.059   0.131    870
  Planarity :  0.003   0.011    830
  Dihedral  :  8.578  57.254    740
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.06 %
    Favored  : 85.94 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 11.70 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.68 (0.24), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.56 (0.18), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.019   0.004   TYR F  39 
 PHE   0.006   0.001   PHE A  94 
 HIS   0.002   0.000   HIS J  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00905 ( 4910)
  covalent geometry    : angle       0.73128 ( 6630)
  hydrogen bonds       : bond        0.02575 (  198)
  hydrogen bonds       : angle       5.07358 (  594)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 30
  time to evaluate  : 0.121 
Fit side-chains
REVERT: D   83 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7628 (mt-10)
REVERT: F   61 GLU cc_start: 0.8024 (mp0) cc_final: 0.7350 (mp0)
REVERT: G   58 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.6807 (mmmt)
REVERT: G   83 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7582 (mt-10)
  outliers start: 16
  outliers final: 13
  residues processed: 44
  average time/residue: 0.0460
  time to fit residues: 2.8968
Evaluate side-chains
  40 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 26
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   58 LYS
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain I residue   59 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 49 optimal weight:    6.9990
   chunk 64 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    7.9990
   chunk 45 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   chunk 7 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.130270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.108970 restraints weight = 6172.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 2.06
r_work: 0.3811 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3669 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   4910  Z= 0.168
  Angle     :  0.600   5.762   6630  Z= 0.347
  Chirality :  0.054   0.126    870
  Planarity :  0.002   0.010    830
  Dihedral  :  6.705  56.396    724
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.13 %
    Favored  : 90.87 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  :  9.15 %
    Favored  : 86.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.51 (0.25), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.43 (0.19), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR H  39 
 PHE   0.003   0.001   PHE A  94 
 HIS   0.002   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 4910)
  covalent geometry    : angle       0.59997 ( 6630)
  hydrogen bonds       : bond        0.01744 (  198)
  hydrogen bonds       : angle       4.46913 (  594)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 27
  time to evaluate  : 0.119 
Fit side-chains
REVERT: D   83 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7585 (mt-10)
REVERT: J   58 LYS cc_start: 0.7849 (tttp) cc_final: 0.7345 (tptt)
  outliers start: 21
  outliers final: 13
  residues processed: 47
  average time/residue: 0.0543
  time to fit residues: 3.6671
Evaluate side-chains
  40 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 27
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue   59 THR
Chi-restraints excluded: chain J residue   44 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 41 optimal weight:    7.9990
   chunk 46 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   chunk 32 optimal weight:   10.0000
   chunk 64 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.124707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.103253 restraints weight = 6568.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3797 rms_B_bonded: 2.06
r_work: 0.3711 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3565 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.039   4910  Z= 0.387
  Angle     :  0.708   5.380   6630  Z= 0.415
  Chirality :  0.059   0.133    870
  Planarity :  0.003   0.014    830
  Dihedral  :  6.825  23.802    720
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.33 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 12.98 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.98 (0.22), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.79 (0.16), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.017   0.004   TYR C  39 
 PHE   0.005   0.001   PHE A  94 
 HIS   0.002   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00847 ( 4910)
  covalent geometry    : angle       0.70836 ( 6630)
  hydrogen bonds       : bond        0.02339 (  198)
  hydrogen bonds       : angle       5.13159 (  594)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 29
  time to evaluate  : 0.183 
Fit side-chains
REVERT: F   72 THR cc_start: 0.9532 (m) cc_final: 0.9267 (m)
REVERT: J   58 LYS cc_start: 0.7938 (tttp) cc_final: 0.7425 (tptt)
  outliers start: 14
  outliers final: 13
  residues processed: 41
  average time/residue: 0.0587
  time to fit residues: 3.4968
Evaluate side-chains
  41 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 28
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain I residue   59 THR
Chi-restraints excluded: chain J residue   44 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 42 optimal weight:    7.9990
   chunk 68 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 14 optimal weight:    7.9990
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.131608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.110191 restraints weight = 6301.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3927 rms_B_bonded: 2.07
r_work: 0.3844 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3701 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   4910  Z= 0.135
  Angle     :  0.588   5.815   6630  Z= 0.340
  Chirality :  0.054   0.127    870
  Planarity :  0.002   0.012    830
  Dihedral  :  6.099  19.864    720
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.28 %
    Favored  : 90.72 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 13.62 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.65 (0.24), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.54 (0.18), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR H  39 
 PHE   0.002   0.001   PHE G  94 
 HIS   0.002   0.001   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 4910)
  covalent geometry    : angle       0.58783 ( 6630)
  hydrogen bonds       : bond        0.01540 (  198)
  hydrogen bonds       : angle       4.37979 (  594)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 29
  time to evaluate  : 0.110 
Fit side-chains
REVERT: E   58 LYS cc_start: 0.7748 (ttmp) cc_final: 0.7427 (tptt)
REVERT: H   83 GLU cc_start: 0.8221 (mp0) cc_final: 0.7990 (mp0)
REVERT: J   58 LYS cc_start: 0.7912 (tttp) cc_final: 0.7426 (tptt)
REVERT: J   83 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7592 (mp0)
  outliers start: 13
  outliers final: 12
  residues processed: 42
  average time/residue: 0.0554
  time to fit residues: 3.3283
Evaluate side-chains
  40 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 28
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue   59 THR
Chi-restraints excluded: chain J residue   44 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 40 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 66 optimal weight:    0.2980
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.127744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.106100 restraints weight = 6148.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 2.05
r_work: 0.3815 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3670 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   4910  Z= 0.198
  Angle     :  0.587   5.623   6630  Z= 0.342
  Chirality :  0.054   0.134    870
  Planarity :  0.002   0.011    830
  Dihedral  :  6.113  20.570    720
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.46 %
    Favored  : 87.54 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 14.04 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.69 (0.24), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.57 (0.18), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.002   TYR H  39 
 PHE   0.002   0.000   PHE A  94 
 HIS   0.002   0.001   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 4910)
  covalent geometry    : angle       0.58726 ( 6630)
  hydrogen bonds       : bond        0.01716 (  198)
  hydrogen bonds       : angle       4.44121 (  594)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 28
  time to evaluate  : 0.175 
Fit side-chains
REVERT: E   58 LYS cc_start: 0.7759 (ttmp) cc_final: 0.7427 (tptt)
REVERT: I   83 GLU cc_start: 0.8261 (mp0) cc_final: 0.7899 (mp0)
REVERT: J   58 LYS cc_start: 0.7992 (tttp) cc_final: 0.7465 (tptt)
  outliers start: 15
  outliers final: 12
  residues processed: 42
  average time/residue: 0.0615
  time to fit residues: 3.6251
Evaluate side-chains
  40 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 28
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain I residue   59 THR
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 10 optimal weight:    7.9990
   chunk 20 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.125759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.104241 restraints weight = 6401.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3856 rms_B_bonded: 2.04
r_work: 0.3773 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3628 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.027   4910  Z= 0.260
  Angle     :  0.630   5.321   6630  Z= 0.366
  Chirality :  0.056   0.136    870
  Planarity :  0.003   0.013    830
  Dihedral  :  6.385  21.652    720
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.88 %
    Favored  : 88.12 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 14.26 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.82 (0.23), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.67 (0.17), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.012   0.003   TYR H  39 
 PHE   0.003   0.001   PHE A  94 
 HIS   0.003   0.001   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 ( 4910)
  covalent geometry    : angle       0.63034 ( 6630)
  hydrogen bonds       : bond        0.01889 (  198)
  hydrogen bonds       : angle       4.70937 (  594)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 28
  time to evaluate  : 0.169 
Fit side-chains
REVERT: E   58 LYS cc_start: 0.7727 (ttmp) cc_final: 0.7356 (tptt)
REVERT: F   72 THR cc_start: 0.9478 (m) cc_final: 0.9167 (m)
REVERT: H   83 GLU cc_start: 0.8335 (mp0) cc_final: 0.8086 (mp0)
REVERT: J   58 LYS cc_start: 0.8014 (tttp) cc_final: 0.7430 (tptt)
  outliers start: 15
  outliers final: 15
  residues processed: 42
  average time/residue: 0.0601
  time to fit residues: 3.6250
Evaluate side-chains
  43 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 28
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain I residue   59 THR
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 17 optimal weight:    6.9990
   chunk 66 optimal weight:    6.9990
   chunk 63 optimal weight:    9.9990
   chunk 27 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 57 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.127622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.106053 restraints weight = 6212.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3911 rms_B_bonded: 2.05
r_work: 0.3825 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3680 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   4910  Z= 0.178
  Angle     :  0.593   5.610   6630  Z= 0.343
  Chirality :  0.054   0.134    870
  Planarity :  0.002   0.014    830
  Dihedral  :  6.095  20.421    720
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.48 %
    Favored  : 86.52 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.32 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.73 (0.24), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.60 (0.18), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR H  39 
 PHE   0.002   0.000   PHE A  94 
 HIS   0.003   0.001   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 4910)
  covalent geometry    : angle       0.59269 ( 6630)
  hydrogen bonds       : bond        0.01669 (  198)
  hydrogen bonds       : angle       4.45948 (  594)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 28
  time to evaluate  : 0.156 
Fit side-chains
REVERT: D   58 LYS cc_start: 0.7796 (ttmp) cc_final: 0.7217 (tptt)
REVERT: E   58 LYS cc_start: 0.7733 (ttmp) cc_final: 0.7392 (tptt)
REVERT: I   83 GLU cc_start: 0.8308 (mp0) cc_final: 0.8006 (mp0)
REVERT: J   58 LYS cc_start: 0.8021 (tttp) cc_final: 0.7476 (tptt)
REVERT: J   83 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7686 (mp0)
  outliers start: 12
  outliers final: 11
  residues processed: 40
  average time/residue: 0.0552
  time to fit residues: 3.0886
Evaluate side-chains
  39 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 28
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain I residue   59 THR
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   chunk 32 optimal weight:   10.0000
   chunk 42 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9990
   chunk 17 optimal weight:    8.9990
   chunk 58 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.123145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.101139 restraints weight = 6407.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 2.15
r_work: 0.3722 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3571 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.2564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.033   4910  Z= 0.302
  Angle     :  0.660   5.191   6630  Z= 0.384
  Chirality :  0.057   0.136    870
  Planarity :  0.003   0.015    830
  Dihedral  :  6.426  21.101    720
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.91 %
    Favored  : 86.09 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 15.11 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.97 (0.22), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.78 (0.17), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.003   TYR H  39 
 PHE   0.003   0.001   PHE A  94 
 HIS   0.003   0.001   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00659 ( 4910)
  covalent geometry    : angle       0.65986 ( 6630)
  hydrogen bonds       : bond        0.02028 (  198)
  hydrogen bonds       : angle       4.85457 (  594)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 30
  time to evaluate  : 0.119 
Fit side-chains
REVERT: C   58 LYS cc_start: 0.7735 (tttt) cc_final: 0.6797 (tptp)
REVERT: E   58 LYS cc_start: 0.7751 (ttmp) cc_final: 0.7376 (tptt)
REVERT: F   72 THR cc_start: 0.9498 (m) cc_final: 0.9169 (m)
REVERT: H   83 GLU cc_start: 0.8369 (mp0) cc_final: 0.8120 (mp0)
REVERT: I   83 GLU cc_start: 0.8247 (mp0) cc_final: 0.7879 (mp0)
REVERT: J   58 LYS cc_start: 0.8063 (tttp) cc_final: 0.7447 (tptt)
REVERT: J   83 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7619 (mp0)
  outliers start: 14
  outliers final: 14
  residues processed: 43
  average time/residue: 0.0630
  time to fit residues: 3.7477
Evaluate side-chains
  43 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 29
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain I residue   59 THR
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 61 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 68 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.128181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.106704 restraints weight = 6408.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 2.07
r_work: 0.3808 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3666 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   4910  Z= 0.195
  Angle     :  0.614   5.459   6630  Z= 0.354
  Chirality :  0.055   0.132    870
  Planarity :  0.002   0.014    830
  Dihedral  :  6.176  20.437    720
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.88 %
    Favored  : 88.12 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 15.74 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.85 (0.23), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.69 (0.17), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR H  39 
 PHE   0.002   0.001   PHE A  94 
 HIS   0.003   0.001   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 4910)
  covalent geometry    : angle       0.61399 ( 6630)
  hydrogen bonds       : bond        0.01732 (  198)
  hydrogen bonds       : angle       4.58213 (  594)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1223.60 seconds
wall clock time: 21 minutes 45.99 seconds (1305.99 seconds total)