Starting phenix.real_space_refine
on Wed Sep 17 03:07:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zwi_60528/09_2025/8zwi_60528.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zwi_60528/09_2025/8zwi_60528.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zwi_60528/09_2025/8zwi_60528.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zwi_60528/09_2025/8zwi_60528.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zwi_60528/09_2025/8zwi_60528.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zwi_60528/09_2025/8zwi_60528.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    1590      2.51       5
     N     438      2.21       5
     O     498      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2526
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
  Restraints were copied for chains:
    D, E, F, B, C
  Time building chain proxies: 0.58, per 1000 atoms: 0.23
  Number of scatterers: 2526
  At special positions: 0
  Unit cell: (97.11, 73.87, 30.71, 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     498      8.00
     N     438      7.00
     C    1590      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: 0.17
  Conformation dependent library (CDL) restraints added in 107.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  624

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 51.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 38 through 40
      removed outlier: 6.549A  pdb=" N   TYR A  39 " --> pdb=" O   VAL E  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 46 through 58
      removed outlier: 6.792A  pdb=" N   VAL D  48 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   VAL A  49 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   HIS D  50 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   GLY A  51 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 8.308A  pdb=" N   GLU A  46 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   VAL E  49 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 9.113A  pdb=" N   VAL A  48 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 10.281A  pdb=" N   GLY E  51 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   HIS A  50 " --> pdb=" O   GLY E  51 " (cutoff:3.500A)
      removed outlier: 9.175A  pdb=" N   ALA E  53 " --> pdb=" O   HIS A  50 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   VAL A  52 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 8.158A  pdb=" N   VAL E  55 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   THR A  54 " --> pdb=" O   VAL E  55 " (cutoff:3.500A)
      removed outlier: 8.129A  pdb=" N   GLU E  57 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   ALA A  56 " --> pdb=" O   GLU E  57 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 62 through 64
      removed outlier: 6.435A  pdb=" N   VAL A  63 " --> pdb=" O   THR E  64 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   VAL E  66 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   ASN A  65 " --> pdb=" O   VAL E  66 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 70 through 72
      removed outlier: 6.342A  pdb=" N   VAL A  70 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 75 through 82
      removed outlier: 5.710A  pdb=" N   THR A  75 " --> pdb=" O   ALA D  76 " (cutoff:3.500A)
      removed outlier: 8.633A  pdb=" N   ALA D  78 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   VAL A  77 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
      removed outlier: 8.572A  pdb=" N   LYS D  80 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   GLN A  79 " --> pdb=" O   LYS D  80 " (cutoff:3.500A)
      removed outlier: 8.393A  pdb=" N   VAL D  82 " --> pdb=" O   GLN A  79 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   THR A  81 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   ALA A  76 " --> pdb=" O   THR E  75 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 87 through 92
      removed outlier: 6.900A  pdb=" N   ILE D  88 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
      removed outlier: 5.659A  pdb=" N   ILE A  88 " --> pdb=" O   ALA E  89 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   ALA E  91 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   ALA A  90 " --> pdb=" O   ALA E  91 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 40
      removed outlier: 6.549A  pdb=" N   TYR F  39 " --> pdb=" O   VAL C  40 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 58
      removed outlier: 6.791A  pdb=" N   VAL B  48 " --> pdb=" O   GLY F  47 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   VAL F  49 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   HIS B  50 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   GLY F  51 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
      removed outlier: 8.307A  pdb=" N   GLU F  46 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   VAL C  49 " --> pdb=" O   GLU F  46 " (cutoff:3.500A)
      removed outlier: 9.112A  pdb=" N   VAL F  48 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 10.280A  pdb=" N   GLY C  51 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   HIS F  50 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
      removed outlier: 9.175A  pdb=" N   ALA C  53 " --> pdb=" O   HIS F  50 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   VAL F  52 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 8.158A  pdb=" N   VAL C  55 " --> pdb=" O   VAL F  52 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   THR F  54 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 8.128A  pdb=" N   GLU C  57 " --> pdb=" O   THR F  54 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   ALA F  56 " --> pdb=" O   GLU C  57 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 62 through 64
      removed outlier: 6.435A  pdb=" N   VAL F  63 " --> pdb=" O   THR C  64 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   VAL C  66 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ASN F  65 " --> pdb=" O   VAL C  66 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 70 through 72
      removed outlier: 6.343A  pdb=" N   VAL F  70 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 75 through 82
      removed outlier: 5.711A  pdb=" N   THR F  75 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 8.632A  pdb=" N   ALA B  78 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   VAL F  77 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 8.572A  pdb=" N   LYS B  80 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   GLN F  79 " --> pdb=" O   LYS B  80 " (cutoff:3.500A)
      removed outlier: 8.393A  pdb=" N   VAL B  82 " --> pdb=" O   GLN F  79 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   THR F  81 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   ALA F  76 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 87 through 92
      removed outlier: 6.900A  pdb=" N   ILE B  88 " --> pdb=" O   SER F  87 " (cutoff:3.500A)
      removed outlier: 5.659A  pdb=" N   ILE F  88 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   ALA C  91 " --> pdb=" O   ILE F  88 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   ALA F  90 " --> pdb=" O   ALA C  91 " (cutoff:3.500A)

    48 hydrogen bonds defined for protein.
    144 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: 0.31

  Time building geometry restraints manager: 0.24 seconds

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

  Histogram of bond lengths:
        1.22 -     1.28: 432
        1.28 -     1.35: 390
        1.35 -     1.41: 101
        1.41 -     1.48: 451
        1.48 -     1.54: 1164
  Bond restraints: 2538
  Sorted by residual:
  bond pdb=" C   ILE F  88 "
       pdb=" N   ALA F  89 "
    ideal  model  delta    sigma   weight residual
    1.331  1.311  0.020 1.29e-02 6.01e+03 2.34e+00
  bond pdb=" C   ILE A  88 "
       pdb=" N   ALA A  89 "
    ideal  model  delta    sigma   weight residual
    1.331  1.311  0.019 1.29e-02 6.01e+03 2.25e+00
  bond pdb=" CB  GLN C  79 "
       pdb=" CG  GLN C  79 "
    ideal  model  delta    sigma   weight residual
    1.520  1.475  0.045 3.00e-02 1.11e+03 2.24e+00
  bond pdb=" CB  GLN D  79 "
       pdb=" CG  GLN D  79 "
    ideal  model  delta    sigma   weight residual
    1.520  1.475  0.045 3.00e-02 1.11e+03 2.24e+00
  bond pdb=" C   ILE D  88 "
       pdb=" N   ALA D  89 "
    ideal  model  delta    sigma   weight residual
    1.331  1.311  0.019 1.29e-02 6.01e+03 2.22e+00
  ... (remaining 2533 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.18: 3019
        1.18 -     2.35: 324
        2.35 -     3.53: 77
        3.53 -     4.71: 0
        4.71 -     5.88: 12
  Bond angle restraints: 3432
  Sorted by residual:
  angle pdb=" OG1 THR E  44 "
        pdb=" CB  THR E  44 "
        pdb=" CG2 THR E  44 "
      ideal   model   delta    sigma   weight residual
     109.30  103.98    5.32 2.00e+00 2.50e-01 7.09e+00
  angle pdb=" OG1 THR F  44 "
        pdb=" CB  THR F  44 "
        pdb=" CG2 THR F  44 "
      ideal   model   delta    sigma   weight residual
     109.30  103.99    5.31 2.00e+00 2.50e-01 7.05e+00
  angle pdb=" OG1 THR A  44 "
        pdb=" CB  THR A  44 "
        pdb=" CG2 THR A  44 "
      ideal   model   delta    sigma   weight residual
     109.30  104.00    5.30 2.00e+00 2.50e-01 7.03e+00
  angle pdb=" OG1 THR D  44 "
        pdb=" CB  THR D  44 "
        pdb=" CG2 THR D  44 "
      ideal   model   delta    sigma   weight residual
     109.30  104.02    5.28 2.00e+00 2.50e-01 6.96e+00
  angle pdb=" OG1 THR C  44 "
        pdb=" CB  THR C  44 "
        pdb=" CG2 THR C  44 "
      ideal   model   delta    sigma   weight residual
     109.30  104.03    5.27 2.00e+00 2.50e-01 6.95e+00
  ... (remaining 3427 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.96: 1209
        8.96 -    17.92: 171
       17.92 -    26.88: 72
       26.88 -    35.84: 24
       35.84 -    44.79: 6
  Dihedral angle restraints: 1482
    sinusoidal: 492
      harmonic: 990
  Sorted by residual:
  dihedral pdb=" CA  LYS C  80 "
           pdb=" CB  LYS C  80 "
           pdb=" CG  LYS C  80 "
           pdb=" CD  LYS C  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  145.26   34.74     3      1.50e+01 4.44e-03 5.91e+00
  dihedral pdb=" CA  LYS B  80 "
           pdb=" CB  LYS B  80 "
           pdb=" CG  LYS B  80 "
           pdb=" CD  LYS B  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  145.26   34.74     3      1.50e+01 4.44e-03 5.90e+00
  dihedral pdb=" CA  LYS E  80 "
           pdb=" CB  LYS E  80 "
           pdb=" CG  LYS E  80 "
           pdb=" CD  LYS E  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  145.27   34.73     3      1.50e+01 4.44e-03 5.90e+00
  ... (remaining 1479 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 212
       0.037 -    0.074: 104
       0.074 -    0.111: 115
       0.111 -    0.148: 17
       0.148 -    0.186: 8
  Chirality restraints: 456
  Sorted by residual:
  chirality pdb=" CB  THR F  75 "
            pdb=" CA  THR F  75 "
            pdb=" OG1 THR F  75 "
            pdb=" CG2 THR F  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.19 2.00e-01 2.50e+01 8.60e-01
  chirality pdb=" CB  THR D  75 "
            pdb=" CA  THR D  75 "
            pdb=" OG1 THR D  75 "
            pdb=" CG2 THR D  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 8.53e-01
  chirality pdb=" CB  THR E  75 "
            pdb=" CA  THR E  75 "
            pdb=" OG1 THR E  75 "
            pdb=" CG2 THR E  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 8.51e-01
  ... (remaining 453 not shown)

  Planarity restraints: 420
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS C  50 "   -0.012 2.00e-02 2.50e+03   1.08e-02 1.76e+00
        pdb=" CG  HIS C  50 "    0.023 2.00e-02 2.50e+03
        pdb=" ND1 HIS C  50 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS C  50 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 HIS C  50 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE2 HIS C  50 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS F  50 "   -0.012 2.00e-02 2.50e+03   1.08e-02 1.74e+00
        pdb=" CG  HIS F  50 "    0.023 2.00e-02 2.50e+03
        pdb=" ND1 HIS F  50 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS F  50 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 HIS F  50 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE2 HIS F  50 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B  50 "   -0.012 2.00e-02 2.50e+03   1.08e-02 1.73e+00
        pdb=" CG  HIS B  50 "    0.023 2.00e-02 2.50e+03
        pdb=" ND1 HIS B  50 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS B  50 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 HIS B  50 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE2 HIS B  50 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 417 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 537
        2.79 -     3.32: 2199
        3.32 -     3.84: 3791
        3.84 -     4.37: 4168
        4.37 -     4.90: 8897
  Nonbonded interactions: 19592
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU C  46 "
            pdb=" NZ  LYS C  80 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" OE1 GLU E  46 "
            pdb=" NZ  LYS E  80 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" OE1 GLU D  46 "
            pdb=" NZ  LYS D  80 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" OE1 GLU B  46 "
            pdb=" NZ  LYS B  80 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" OE1 GLU A  46 "
            pdb=" NZ  LYS A  80 "
     model   vdw
     2.262 3.120
  ... (remaining 19587 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'B'
  selection = chain 'C'
}

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:             3.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     4.110
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
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      :  0.011   0.048   2538  Z= 0.489
  Angle     :  0.859   5.881   3432  Z= 0.499
  Chirality :  0.065   0.186    456
  Planarity :  0.003   0.011    420
  Dihedral  : 11.260  44.795    858
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.70 (0.34), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.81 (0.26), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.002   TYR C  39 
 PHE   0.013   0.004   PHE B  94 
 HIS   0.009   0.006   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.01122 ( 2538)
  covalent geometry    : angle       0.85926 ( 3432)
  hydrogen bonds       : bond        0.19604 (   48)
  hydrogen bonds       : angle       9.21006 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.102 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.6756
  time to fit residues: 26.1967
Evaluate side-chains
  22 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0870
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.8162

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 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 = 0.4322 r_free = 0.4322 target = 0.170097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.143049 restraints weight = 2863.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 2.28
r_work: 0.3974 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3869 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.011   2538  Z= 0.092
  Angle     :  0.449   4.713   3432  Z= 0.246
  Chirality :  0.052   0.126    456
  Planarity :  0.001   0.006    420
  Dihedral  :  3.479   9.480    366
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  8.91 %
    Favored  : 90.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.79 (0.38), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.29), residues: 354

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 ( 2538)
  covalent geometry    : angle       0.44885 ( 3432)
  hydrogen bonds       : bond        0.02346 (   48)
  hydrogen bonds       : angle       6.66873 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 29
  time to evaluate  : 0.057 
Fit side-chains
REVERT: F   75 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8332 (t)
REVERT: B   83 GLU cc_start: 0.8289 (tt0) cc_final: 0.8040 (tt0)
REVERT: C   60 LYS cc_start: 0.8229 (tttt) cc_final: 0.8018 (tttp)
  outliers start: 2
  outliers final: 1
  residues processed: 30
  average time/residue: 0.5991
  time to fit residues: 18.4104
Evaluate side-chains
  24 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain F residue   75 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 24 optimal weight:    9.9990
   chunk 4 optimal weight:    7.9990
   chunk 5 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 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 = 0.4230 r_free = 0.4230 target = 0.163587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.135042 restraints weight = 2859.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3964 rms_B_bonded: 2.40
r_work: 0.3846 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3711 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.023   2538  Z= 0.215
  Angle     :  0.510   3.135   3432  Z= 0.292
  Chirality :  0.051   0.124    456
  Planarity :  0.002   0.007    420
  Dihedral  :  3.981  11.228    366
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 12.79 %
    Favored  : 85.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.55 (0.38), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR A  39 
 PHE   0.008   0.002   PHE A  94 
 HIS   0.007   0.004   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 2538)
  covalent geometry    : angle       0.51050 ( 3432)
  hydrogen bonds       : bond        0.02806 (   48)
  hydrogen bonds       : angle       6.39904 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.098 
Fit side-chains
REVERT: F   75 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8320 (t)
REVERT: B   75 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8280 (t)
REVERT: B   83 GLU cc_start: 0.8376 (tt0) cc_final: 0.8174 (tt0)
REVERT: C   60 LYS cc_start: 0.8247 (tttt) cc_final: 0.7970 (tttp)
  outliers start: 5
  outliers final: 1
  residues processed: 26
  average time/residue: 0.4137
  time to fit residues: 11.1487
Evaluate side-chains
  26 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 6 optimal weight:    8.9990
   chunk 10 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   overall best weight:    1.1182

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.169105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.141427 restraints weight = 2808.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.4035 rms_B_bonded: 2.36
r_work: 0.3921 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3783 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   2538  Z= 0.101
  Angle     :  0.407   2.845   3432  Z= 0.233
  Chirality :  0.050   0.122    456
  Planarity :  0.001   0.005    420
  Dihedral  :  3.433   9.407    366
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 12.40 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.17 (0.40), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.65 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR A  39 
 PHE   0.006   0.002   PHE A  94 
 HIS   0.004   0.002   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 2538)
  covalent geometry    : angle       0.40716 ( 3432)
  hydrogen bonds       : bond        0.02150 (   48)
  hydrogen bonds       : angle       5.97118 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.091 
Fit side-chains
REVERT: F   75 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8285 (t)
REVERT: B   75 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8241 (t)
REVERT: C   60 LYS cc_start: 0.8205 (tttt) cc_final: 0.7941 (tttp)
  outliers start: 5
  outliers final: 1
  residues processed: 25
  average time/residue: 0.5389
  time to fit residues: 13.8418
Evaluate side-chains
  24 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 19 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 30 optimal weight:    0.0000
   chunk 7 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    2.5992

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.165355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.136867 restraints weight = 2859.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3966 rms_B_bonded: 2.37
r_work: 0.3847 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3711 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.022   2538  Z= 0.204
  Angle     :  0.492   3.872   3432  Z= 0.285
  Chirality :  0.051   0.121    456
  Planarity :  0.002   0.007    420
  Dihedral  :  3.847  10.510    366
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.89 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.13 (0.40), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.61 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR A  39 
 PHE   0.009   0.002   PHE A  94 
 HIS   0.006   0.003   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 2538)
  covalent geometry    : angle       0.49240 ( 3432)
  hydrogen bonds       : bond        0.02532 (   48)
  hydrogen bonds       : angle       6.10806 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.148 
Fit side-chains
REVERT: F   75 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8322 (t)
REVERT: B   75 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8241 (t)
REVERT: C   60 LYS cc_start: 0.8315 (tttt) cc_final: 0.7990 (tttp)
  outliers start: 4
  outliers final: 1
  residues processed: 24
  average time/residue: 0.4006
  time to fit residues: 9.9427
Evaluate side-chains
  26 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 31 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    3.3588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.165436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.136442 restraints weight = 2887.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3956 rms_B_bonded: 2.36
r_work: 0.3840 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3708 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.028   2538  Z= 0.255
  Angle     :  0.542   2.935   3432  Z= 0.313
  Chirality :  0.051   0.123    456
  Planarity :  0.002   0.007    420
  Dihedral  :  4.184  10.330    366
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 15.12 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.14 (0.40), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.63 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR A  39 
 PHE   0.010   0.003   PHE A  94 
 HIS   0.007   0.004   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00597 ( 2538)
  covalent geometry    : angle       0.54234 ( 3432)
  hydrogen bonds       : bond        0.02739 (   48)
  hydrogen bonds       : angle       6.24035 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 0.087 
Fit side-chains
REVERT: D   83 GLU cc_start: 0.8321 (tt0) cc_final: 0.8054 (tt0)
REVERT: F   75 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8365 (t)
REVERT: B   75 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8300 (t)
REVERT: C   60 LYS cc_start: 0.8312 (tttt) cc_final: 0.7991 (tttp)
  outliers start: 5
  outliers final: 1
  residues processed: 27
  average time/residue: 0.5180
  time to fit residues: 14.3319
Evaluate side-chains
  29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 35 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   chunk 8 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    1.7786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.168955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.140439 restraints weight = 2825.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.4010 rms_B_bonded: 2.33
r_work: 0.3889 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3752 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   2538  Z= 0.145
  Angle     :  0.443   2.439   3432  Z= 0.256
  Chirality :  0.050   0.123    456
  Planarity :  0.001   0.005    420
  Dihedral  :  3.751  10.136    366
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 17.05 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.99 (0.41), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.51 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR A  39 
 PHE   0.007   0.002   PHE A  94 
 HIS   0.005   0.003   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 2538)
  covalent geometry    : angle       0.44307 ( 3432)
  hydrogen bonds       : bond        0.02311 (   48)
  hydrogen bonds       : angle       5.94493 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.089 
Fit side-chains
REVERT: D   83 GLU cc_start: 0.8292 (tt0) cc_final: 0.7995 (tt0)
REVERT: E   60 LYS cc_start: 0.8305 (tttp) cc_final: 0.7960 (tttp)
REVERT: F   75 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8351 (t)
REVERT: B   75 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8304 (t)
REVERT: C   60 LYS cc_start: 0.8294 (tttt) cc_final: 0.8000 (tttp)
  outliers start: 3
  outliers final: 1
  residues processed: 23
  average time/residue: 0.4489
  time to fit residues: 10.6109
Evaluate side-chains
  24 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 35 optimal weight:    6.9990
   chunk 11 optimal weight:   10.0000
   chunk 33 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 28 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    2.9788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.166327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.136804 restraints weight = 2893.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3955 rms_B_bonded: 2.44
r_work: 0.3836 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3701 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.2126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   2538  Z= 0.229
  Angle     :  0.518   2.776   3432  Z= 0.299
  Chirality :  0.051   0.123    456
  Planarity :  0.002   0.007    420
  Dihedral  :  4.036  10.694    366
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 18.60 %
    Favored  : 80.23 %
  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 aren not related in a simple way.
  whole: -2.03 (0.41), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.54 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR A  39 
 PHE   0.010   0.002   PHE A  94 
 HIS   0.007   0.004   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 ( 2538)
  covalent geometry    : angle       0.51794 ( 3432)
  hydrogen bonds       : bond        0.02617 (   48)
  hydrogen bonds       : angle       6.10434 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.115 
Fit side-chains
REVERT: D   83 GLU cc_start: 0.8279 (tt0) cc_final: 0.7965 (tt0)
REVERT: E   60 LYS cc_start: 0.8323 (tttp) cc_final: 0.8110 (tttm)
REVERT: F   75 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8257 (t)
REVERT: B   75 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8273 (t)
REVERT: C   60 LYS cc_start: 0.8242 (tttt) cc_final: 0.7919 (tttp)
  outliers start: 3
  outliers final: 1
  residues processed: 25
  average time/residue: 0.5349
  time to fit residues: 13.8217
Evaluate side-chains
  27 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 1 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 14 optimal weight:    0.3980
   chunk 2 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.6982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.171382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.143556 restraints weight = 2918.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.4080 rms_B_bonded: 2.37
r_work: 0.3986 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3878 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.013   2538  Z= 0.079
  Angle     :  0.399   2.742   3432  Z= 0.228
  Chirality :  0.050   0.121    456
  Planarity :  0.001   0.004    420
  Dihedral  :  3.368  10.078    366
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 17.05 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.73 (0.43), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.31 (0.33), residues: 354

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00170 ( 2538)
  covalent geometry    : angle       0.39876 ( 3432)
  hydrogen bonds       : bond        0.01943 (   48)
  hydrogen bonds       : angle       5.62903 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.095 
Fit side-chains
REVERT: D   83 GLU cc_start: 0.8219 (tt0) cc_final: 0.7917 (tt0)
REVERT: F   75 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8235 (t)
REVERT: B   75 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8296 (t)
REVERT: C   60 LYS cc_start: 0.8191 (tttt) cc_final: 0.7780 (tttp)
  outliers start: 3
  outliers final: 1
  residues processed: 23
  average time/residue: 0.5674
  time to fit residues: 13.3985
Evaluate side-chains
  24 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 35 optimal weight:    9.9990
   chunk 30 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   overall best weight:    2.7588

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.166855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.137841 restraints weight = 2934.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 2.38
r_work: 0.3854 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3718 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.025   2538  Z= 0.214
  Angle     :  0.522   4.104   3432  Z= 0.298
  Chirality :  0.051   0.122    456
  Planarity :  0.002   0.007    420
  Dihedral  :  3.947  11.726    366
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 17.83 %
    Favored  : 80.23 %
  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 aren not related in a simple way.
  whole: -1.90 (0.42), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.44 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR A  39 
 PHE   0.009   0.002   PHE A  94 
 HIS   0.006   0.003   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 2538)
  covalent geometry    : angle       0.52173 ( 3432)
  hydrogen bonds       : bond        0.02547 (   48)
  hydrogen bonds       : angle       5.87730 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.119 
Fit side-chains
REVERT: D   62 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7805 (mp-120)
REVERT: D   83 GLU cc_start: 0.8268 (tt0) cc_final: 0.7976 (tt0)
REVERT: E   60 LYS cc_start: 0.8457 (tptm) cc_final: 0.8247 (tptm)
REVERT: F   75 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8306 (t)
REVERT: B   75 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8287 (t)
REVERT: C   60 LYS cc_start: 0.8262 (tttt) cc_final: 0.7962 (tttp)
  outliers start: 5
  outliers final: 1
  residues processed: 24
  average time/residue: 0.5071
  time to fit residues: 12.5359
Evaluate side-chains
  27 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   62 GLN
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 21 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0070
   chunk 12 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   overall best weight:    2.8004

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

Flipped N/Q/H residues before XYZ refinement:
** B  62 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 = 0.4280 r_free = 0.4280 target = 0.166743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.137640 restraints weight = 2931.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3967 rms_B_bonded: 2.41
r_work: 0.3850 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3714 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.210   2538  Z= 0.425
  Angle     :  1.518  59.199   3432  Z= 0.892
  Chirality :  0.055   0.455    456
  Planarity :  0.002   0.018    420
  Dihedral  :  3.947  11.725    366
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 17.83 %
    Favored  : 80.62 %
  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 aren not related in a simple way.
  whole: -1.91 (0.42), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.45 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR A  39 
 PHE   0.009   0.002   PHE A  94 
 HIS   0.006   0.003   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00877 ( 2538)
  covalent geometry    : angle       1.51842 ( 3432)
  hydrogen bonds       : bond        0.02568 (   48)
  hydrogen bonds       : angle       5.85777 (  144)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1029.00 seconds
wall clock time: 18 minutes 19.86 seconds (1099.86 seconds total)