Starting phenix.real_space_refine
on Tue Feb 11 07:54:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6sst_10305/02_2025/6sst_10305.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6sst_10305/02_2025/6sst_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_10305/02_2025/6sst_10305.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6sst_10305/02_2025/6sst_10305.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6sst_10305/02_2025/6sst_10305.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6sst_10305/02_2025/6sst_10305.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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:
    C, B, E, D, G, F, I, H, J
  Time building chain proxies: 2.02, per 1000 atoms: 0.41
  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: 1.09
  Conformation dependent library (CDL) restraints added in 630.1 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: 0.73
  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: 1.36

  Time building geometry restraints manager: 1.28 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  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:             1.780
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.170
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.220
-------------------------------------------------------------------------------
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= 0.598
  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 (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: -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
 HIS   0.003   0.002   HIS E  50 
 PHE   0.003   0.001   PHE E  94 
 TYR   0.014   0.003   TYR F  39 

*********************** 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  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   72 THR cc_start: 0.9387 (m) cc_final: 0.9186 (m)
REVERT: C   58 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6738 (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: 0.2645
  time to fit residues: 14.3763
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  : 0.508 
-------------------------------------------------------------------------------
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 59 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 35 optimal weight:    8.9990
   chunk 28 optimal weight:   20.0000
   chunk 54 optimal weight:    0.8980
   chunk 21 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 63 optimal weight:   10.0000
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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**
** 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 = 0.4221 r_free = 0.4221 target = 0.134946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.112849 restraints weight = 5943.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 2.09
r_work: 0.3861 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3719 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.1225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4910  Z= 0.222
  Angle     :  0.584   6.437   6630  Z= 0.336
  Chirality :  0.053   0.129    870
  Planarity :  0.002   0.010    830
  Dihedral  :  9.610  56.873    748
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  :  7.87 %
    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 (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: -4.28 (0.27), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.26 (0.21), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS G  50 
 PHE   0.002   0.000   PHE D  94 
 TYR   0.006   0.001   TYR F  39 

*********************** 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
  50 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 27
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 THR cc_start: 0.9482 (m) cc_final: 0.9245 (m)
REVERT: B   72 THR cc_start: 0.9410 (m) cc_final: 0.9185 (m)
REVERT: D   58 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.7014 (tptp)
REVERT: D   72 THR cc_start: 0.9526 (m) cc_final: 0.9289 (m)
REVERT: D   83 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7446 (mt-10)
REVERT: E   58 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7236 (tptp)
REVERT: F   83 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7400 (mt-10)
REVERT: G   58 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6762 (tptp)
REVERT: H   58 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6386 (tptp)
REVERT: I   58 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.6891 (tptp)
REVERT: J   58 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7228 (tptp)
  outliers start: 23
  outliers final: 7
  residues processed: 49
  average time/residue: 0.1828
  time to fit residues: 11.7385
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  : 0.485 
-------------------------------------------------------------------------------
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 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 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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 59 optimal weight:    8.9990
   chunk 50 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 58 optimal weight:    5.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
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**
** C  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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.129019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.106813 restraints weight = 6118.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 2.20
r_work: 0.3802 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3657 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   4910  Z= 0.349
  Angle     :  0.619   5.979   6630  Z= 0.360
  Chirality :  0.054   0.131    870
  Planarity :  0.002   0.009    830
  Dihedral  :  8.583  59.829    744
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.75 %
    Favored  : 87.25 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  :  9.57 %
    Favored  : 85.74 %
  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: -4.46 (0.26), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.39 (0.20), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J  50 
 PHE   0.004   0.001   PHE A  94 
 TYR   0.013   0.003   TYR F  39 

*********************** 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
  52 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 30
  time to evaluate  : 0.496 
Fit side-chains
REVERT: D   83 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7662 (mt-10)
REVERT: F   61 GLU cc_start: 0.7974 (mp0) cc_final: 0.7421 (mp0)
REVERT: F   72 THR cc_start: 0.9458 (m) cc_final: 0.9244 (m)
REVERT: F   83 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7113 (mt-10)
REVERT: G   58 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6725 (tptp)
REVERT: G   83 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7386 (mt-10)
REVERT: J   58 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7333 (tptt)
REVERT: J   83 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8056 (mt-10)
  outliers start: 22
  outliers final: 14
  residues processed: 50
  average time/residue: 0.1444
  time to fit residues: 10.1041
Evaluate side-chains
  44 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 28
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
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 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   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
Chi-restraints excluded: chain J residue   58 LYS
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 17 optimal weight:    0.5980
   chunk 21 optimal weight:    9.9990
   chunk 12 optimal weight:    0.6980
   chunk 33 optimal weight:    0.3980
   chunk 14 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 46 optimal weight:    4.9990
   chunk 56 optimal weight:    8.9990
   chunk 26 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.4204 r_free = 0.4204 target = 0.132260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.110720 restraints weight = 6127.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3925 rms_B_bonded: 2.10
r_work: 0.3839 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3693 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.1849

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= 0.205
  Angle     :  0.570   5.686   6630  Z= 0.330
  Chirality :  0.053   0.127    870
  Planarity :  0.002   0.010    830
  Dihedral  :  6.874  59.858    728
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  :  9.36 %
    Favored  : 86.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.38 (0.26), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.33 (0.20), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS H  50 
 PHE   0.002   0.000   PHE A  94 
 TYR   0.005   0.001   TYR F  39 

*********************** 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
  46 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 27
  time to evaluate  : 0.485 
Fit side-chains
REVERT: F   83 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7205 (mt-10)
REVERT: G   83 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7396 (mt-10)
REVERT: J   58 LYS cc_start: 0.7839 (ttmp) cc_final: 0.7358 (tptt)
REVERT: J   83 GLU cc_start: 0.8236 (mt-10) cc_final: 0.8029 (mt-10)
  outliers start: 19
  outliers final: 13
  residues processed: 45
  average time/residue: 0.1149
  time to fit residues: 7.7828
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  : 0.499 
-------------------------------------------------------------------------------
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 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   44 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 49 optimal weight:   10.0000
   chunk 6 optimal weight:    0.2980
   chunk 39 optimal weight:    4.9990
   chunk 32 optimal weight:   10.0000
   chunk 63 optimal weight:    9.9990
   chunk 36 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    2.6588

-------------------------------------------------------------------------------
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 = 0.4152 r_free = 0.4152 target = 0.128307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.106530 restraints weight = 6280.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 2.08
r_work: 0.3778 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3632 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.028   4910  Z= 0.405
  Angle     :  0.621   5.192   6630  Z= 0.362
  Chirality :  0.056   0.132    870
  Planarity :  0.003   0.014    830
  Dihedral  :  6.380  23.059    720
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.90 %
    Favored  : 87.10 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 11.28 %
    Favored  : 85.74 %
  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: -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
 HIS   0.002   0.001   HIS H  50 
 PHE   0.004   0.001   PHE A  94 
 TYR   0.013   0.003   TYR F  39 

*********************** 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
  42 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 28
  time to evaluate  : 0.463 
Fit side-chains
REVERT: F   72 THR cc_start: 0.9462 (m) cc_final: 0.9193 (m)
REVERT: F   83 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7128 (mt-10)
REVERT: G   83 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7388 (mt-10)
REVERT: J   58 LYS cc_start: 0.7926 (ttmp) cc_final: 0.7454 (tptt)
  outliers start: 14
  outliers final: 13
  residues processed: 41
  average time/residue: 0.1289
  time to fit residues: 7.6898
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  : 0.456 
-------------------------------------------------------------------------------
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 8 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 35 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 47 optimal weight:    0.6980
   chunk 7 optimal weight:   10.0000
   chunk 58 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    2.6986

-------------------------------------------------------------------------------
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  50 HIS
** 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  50 HIS
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  50 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.127351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.105613 restraints weight = 6368.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3847 rms_B_bonded: 2.08
r_work: 0.3765 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3619 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.029   4910  Z= 0.402
  Angle     :  0.633   5.393   6630  Z= 0.369
  Chirality :  0.056   0.134    870
  Planarity :  0.003   0.012    830
  Dihedral  :  6.460  20.931    720
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 11.91 %
    Favored  : 84.47 %
  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: -4.78 (0.23), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.64 (0.17), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C  50 
 PHE   0.004   0.001   PHE A  94 
 TYR   0.012   0.003   TYR F  39 

*********************** 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
  43 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 26
  time to evaluate  : 0.467 
Fit side-chains
REVERT: D   83 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7571 (mt-10)
REVERT: F   72 THR cc_start: 0.9476 (m) cc_final: 0.9209 (m)
REVERT: F   83 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7346 (mt-10)
REVERT: G   83 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7532 (mt-10)
REVERT: J   58 LYS cc_start: 0.7963 (ttmp) cc_final: 0.7435 (tptt)
  outliers start: 17
  outliers final: 16
  residues processed: 41
  average time/residue: 0.1341
  time to fit residues: 7.8594
Evaluate side-chains
  42 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 26
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
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 C residue   83 GLU
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   44 THR
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0770
   chunk 64 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 69 optimal weight:    0.5980
   overall best weight:    1.3342

-------------------------------------------------------------------------------
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 = 0.4194 r_free = 0.4194 target = 0.130360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.108715 restraints weight = 6196.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3902 rms_B_bonded: 2.09
r_work: 0.3817 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3671 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
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   0.020   4910  Z= 0.233
  Angle     :  0.580   5.889   6630  Z= 0.336
  Chirality :  0.054   0.130    870
  Planarity :  0.002   0.017    830
  Dihedral  :  6.053  20.264    720
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.32 %
    Favored  : 87.68 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 13.19 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.64 (0.24), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.53 (0.18), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E  50 
 PHE   0.002   0.000   PHE A  94 
 TYR   0.006   0.001   TYR H  39 

*********************** 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
  42 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 26
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
REVERT: E   58 LYS cc_start: 0.7718 (ttmp) cc_final: 0.7397 (tptt)
REVERT: F   83 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7426 (mt-10)
REVERT: H   83 GLU cc_start: 0.8215 (mp0) cc_final: 0.7901 (mp0)
REVERT: J   58 LYS cc_start: 0.7969 (ttmp) cc_final: 0.7431 (tptt)
  outliers start: 16
  outliers final: 13
  residues processed: 41
  average time/residue: 0.1253
  time to fit residues: 7.5390
Evaluate side-chains
  38 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 25
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
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   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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   chunk 66 optimal weight:    6.9990
   chunk 27 optimal weight:    8.9990
   chunk 13 optimal weight:    6.9990
   chunk 30 optimal weight:    0.3980
   chunk 40 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 69 optimal weight:    1.9990
   chunk 42 optimal weight:    9.9990
   overall best weight:    2.8788

-------------------------------------------------------------------------------
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  50 HIS
** 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**
** I  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.126019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.104182 restraints weight = 6354.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3813 rms_B_bonded: 2.09
r_work: 0.3724 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3573 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.030   4910  Z= 0.418
  Angle     :  0.638   5.062   6630  Z= 0.372
  Chirality :  0.056   0.137    870
  Planarity :  0.003   0.013    830
  Dihedral  :  6.397  20.432    720
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.46 %
    Favored  : 87.54 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 14.68 %
    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 (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: -4.87 (0.22), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.70 (0.17), residues: 690

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

*********************** 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  : 0.568 
Fit side-chains
   revert: symmetry clash
REVERT: B   83 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7646 (mp0)
REVERT: E   58 LYS cc_start: 0.7749 (ttmp) cc_final: 0.7351 (tptt)
REVERT: F   72 THR cc_start: 0.9487 (m) cc_final: 0.9203 (m)
REVERT: F   83 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7020 (mt-10)
REVERT: G   83 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7591 (mt-10)
REVERT: H   83 GLU cc_start: 0.8273 (mp0) cc_final: 0.7967 (mp0)
REVERT: I   58 LYS cc_start: 0.7876 (tttp) cc_final: 0.7091 (tptt)
REVERT: J   58 LYS cc_start: 0.7959 (ttmp) cc_final: 0.7378 (tptt)
  outliers start: 15
  outliers final: 13
  residues processed: 41
  average time/residue: 0.1535
  time to fit residues: 8.7369
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  : 0.469 
-------------------------------------------------------------------------------
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 H residue   59 THR
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain I residue   59 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 20 optimal weight:    0.4980
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 24 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.4212 r_free = 0.4212 target = 0.131648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.110274 restraints weight = 6133.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 2.07
r_work: 0.3849 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3705 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   4910  Z= 0.200
  Angle     :  0.572   5.632   6630  Z= 0.330
  Chirality :  0.054   0.131    870
  Planarity :  0.002   0.016    830
  Dihedral  :  5.925  20.004    720
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.01 %
    Favored  : 88.99 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.11 %
    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 (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: -4.63 (0.24), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.52 (0.19), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E  50 
 PHE   0.002   0.000   PHE A  94 
 TYR   0.005   0.001   TYR H  39 

*********************** 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
  42 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 29
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
REVERT: B   83 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7565 (mp0)
REVERT: D   58 LYS cc_start: 0.7776 (ttmp) cc_final: 0.7205 (tptt)
REVERT: E   58 LYS cc_start: 0.7698 (ttmp) cc_final: 0.7493 (tptp)
REVERT: F   83 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7083 (mt-10)
REVERT: G   83 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7448 (mt-10)
REVERT: I   58 LYS cc_start: 0.7928 (tttp) cc_final: 0.7155 (tptt)
REVERT: J   58 LYS cc_start: 0.8019 (ttmp) cc_final: 0.7526 (tptt)
REVERT: J   83 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7629 (mp0)
  outliers start: 13
  outliers final: 13
  residues processed: 42
  average time/residue: 0.1532
  time to fit residues: 8.9898
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  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   59 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   59 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 9 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 55 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   chunk 7 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
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**
E  50 HIS
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.128304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.106585 restraints weight = 6250.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3878 rms_B_bonded: 2.08
r_work: 0.3795 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3649 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.024   4910  Z= 0.326
  Angle     :  0.591   5.174   6630  Z= 0.345
  Chirality :  0.055   0.134    870
  Planarity :  0.002   0.012    830
  Dihedral  :  6.077  19.901    720
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.17 %
    Favored  : 87.83 %
  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 (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: -4.73 (0.23), 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
 HIS   0.002   0.001   HIS C  50 
 PHE   0.002   0.001   PHE A  94 
 TYR   0.010   0.002   TYR H  39 

********************** 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
  43 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 29
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
REVERT: B   83 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7657 (mp0)
REVERT: D   58 LYS cc_start: 0.7740 (ttmp) cc_final: 0.7115 (tptt)
REVERT: E   58 LYS cc_start: 0.7695 (ttmp) cc_final: 0.7357 (tptt)
REVERT: F   83 GLU cc_start: 0.7845 (mt-10) cc_final: 0.6976 (mt-10)
REVERT: G   83 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7517 (mt-10)
REVERT: H   83 GLU cc_start: 0.8265 (mp0) cc_final: 0.7932 (mp0)
REVERT: I   58 LYS cc_start: 0.7921 (tttp) cc_final: 0.7112 (tptt)
REVERT: J   58 LYS cc_start: 0.8035 (ttmp) cc_final: 0.7488 (tptt)
  outliers start: 14
  outliers final: 14
  residues processed: 42
  average time/residue: 0.1626
  time to fit residues: 9.3406
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  : 0.512 
-------------------------------------------------------------------------------
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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 63 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 = 0.4195 r_free = 0.4195 target = 0.129577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.108165 restraints weight = 6215.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3906 rms_B_bonded: 2.05
r_work: 0.3825 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3679 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.2536

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= 0.253
  Angle     :  0.580   5.361   6630  Z= 0.336
  Chirality :  0.054   0.134    870
  Planarity :  0.002   0.017    830
  Dihedral  :  6.009  20.360    720
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.16 %
    Favored  : 88.84 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 14.68 %
    Favored  : 82.34 %
  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: -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
 HIS   0.002   0.001   HIS E  50 
 PHE   0.002   0.000   PHE A  94 
 TYR   0.008   0.002   TYR H  39 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2365.64 seconds
wall clock time: 42 minutes 58.25 seconds (2578.25 seconds total)