Starting phenix.real_space_refine
on Thu Feb 13 03:19:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rx5_24725/02_2025/7rx5_24725.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rx5_24725/02_2025/7rx5_24725.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/7rx5_24725/02_2025/7rx5_24725.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rx5_24725/02_2025/7rx5_24725.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rx5_24725/02_2025/7rx5_24725.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rx5_24725/02_2025/7rx5_24725.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
-------------------------------------------------------------------------------
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=   0.003 sd=   0.068
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    5640      2.51       5
     N    1720      2.21       5
     O    1760      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: 9120
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "1"
      Number of atoms: 228
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 228
          Classifications: {'peptide': 29}
          Link IDs: {'TRANS': 28}
  Restraints were copied for chains:
    0, 3, 2, 5, 4, 7, 6, 9, 8, A, C, B, E, D, G, F, I, H, K, J, M, L,
    O, N, Q, P, S, R, U, T, W, V, Y, X, Z, a, c, b, d
  Time building chain proxies: 2.13, per 1000 atoms: 0.23
  Number of scatterers: 9120
  At special positions: 0
  Unit cell: (89.64, 89.64, 105.84, 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    1760      8.00
     N    1720      7.00
     C    5640      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: 2.17
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2320

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 0 sheets defined
      100.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA A   7 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1 through 29
      removed outlier: 3.912A  pdb=" N   ALA B   7 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1 through 29
      removed outlier: 3.912A  pdb=" N   ALA C   7 " --> pdb=" O   GLU C   3 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1 through 29
      removed outlier: 3.912A  pdb=" N   ALA D   7 " --> pdb=" O   GLU D   3 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1 through 29
      removed outlier: 3.912A  pdb=" N   ALA E   7 " --> pdb=" O   GLU E   3 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1 through 29
      removed outlier: 3.912A  pdb=" N   ALA F   7 " --> pdb=" O   GLU F   3 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1 through 29
      removed outlier: 3.912A  pdb=" N   ALA G   7 " --> pdb=" O   GLU G   3 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA H   7 " --> pdb=" O   GLU H   3 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA I   7 " --> pdb=" O   GLU I   3 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 1 through 29
      removed outlier: 3.912A  pdb=" N   ALA J   7 " --> pdb=" O   GLU J   3 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1 through 29
      removed outlier: 3.912A  pdb=" N   ALA K   7 " --> pdb=" O   GLU K   3 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA L   7 " --> pdb=" O   GLU L   3 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA M   7 " --> pdb=" O   GLU M   3 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA N   7 " --> pdb=" O   GLU N   3 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA O   7 " --> pdb=" O   GLU O   3 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA P   7 " --> pdb=" O   GLU P   3 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA Q   7 " --> pdb=" O   GLU Q   3 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA R   7 " --> pdb=" O   GLU R   3 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA S   7 " --> pdb=" O   GLU S   3 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA T   7 " --> pdb=" O   GLU T   3 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA U   7 " --> pdb=" O   GLU U   3 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA V   7 " --> pdb=" O   GLU V   3 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 1 through 29
      removed outlier: 3.912A  pdb=" N   ALA W   7 " --> pdb=" O   GLU W   3 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 1 through 29
      removed outlier: 3.912A  pdb=" N   ALA X   7 " --> pdb=" O   GLU X   3 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 1 through 29
      removed outlier: 3.912A  pdb=" N   ALA Y   7 " --> pdb=" O   GLU Y   3 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 1 through 29
      removed outlier: 3.912A  pdb=" N   ALA Z   7 " --> pdb=" O   GLU Z   3 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA 0   7 " --> pdb=" O   GLU 0   3 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA 1   7 " --> pdb=" O   GLU 1   3 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA 2   7 " --> pdb=" O   GLU 2   3 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA 3   7 " --> pdb=" O   GLU 3   3 " (cutoff:3.500A)
    Processing helix  chain '4' and resid 1 through 29
      removed outlier: 3.912A  pdb=" N   ALA 4   7 " --> pdb=" O   GLU 4   3 " (cutoff:3.500A)
    Processing helix  chain '5' and resid 1 through 29
      removed outlier: 3.912A  pdb=" N   ALA 5   7 " --> pdb=" O   GLU 5   3 " (cutoff:3.500A)
    Processing helix  chain '6' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA 6   7 " --> pdb=" O   GLU 6   3 " (cutoff:3.500A)
    Processing helix  chain '7' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA 7   7 " --> pdb=" O   GLU 7   3 " (cutoff:3.500A)
    Processing helix  chain '8' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA 8   7 " --> pdb=" O   GLU 8   3 " (cutoff:3.500A)
    Processing helix  chain '9' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA 9   7 " --> pdb=" O   GLU 9   3 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA a   7 " --> pdb=" O   GLU a   3 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA b   7 " --> pdb=" O   GLU b   3 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA c   7 " --> pdb=" O   GLU c   3 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 1 through 29
      removed outlier: 3.911A  pdb=" N   ALA d   7 " --> pdb=" O   GLU d   3 " (cutoff:3.500A)

    960 hydrogen bonds defined for protein.
    2880 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: 2.73

  Time building geometry restraints manager: 2.48 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 1720
        1.29 -     1.35: 1626
        1.35 -     1.42: 374
        1.42 -     1.48: 1240
        1.48 -     1.54: 4200
  Bond restraints: 9160
  Sorted by residual:
  bond pdb=" N   ILE B  18 "
       pdb=" CA  ILE B  18 "
    ideal  model  delta    sigma   weight residual
    1.461  1.466 -0.005 1.19e-02 7.06e+03 1.74e-01
  bond pdb=" N   ILE C  18 "
       pdb=" CA  ILE C  18 "
    ideal  model  delta    sigma   weight residual
    1.461  1.466 -0.005 1.19e-02 7.06e+03 1.74e-01
  bond pdb=" N   HIS F  22 "
       pdb=" CA  HIS F  22 "
    ideal  model  delta    sigma   weight residual
    1.459  1.464 -0.005 1.21e-02 6.83e+03 1.50e-01
  bond pdb=" N   HIS G  22 "
       pdb=" CA  HIS G  22 "
    ideal  model  delta    sigma   weight residual
    1.459  1.464 -0.005 1.21e-02 6.83e+03 1.50e-01
  bond pdb=" N   ILE N  18 "
       pdb=" CA  ILE N  18 "
    ideal  model  delta    sigma   weight residual
    1.461  1.465 -0.004 1.19e-02 7.06e+03 1.33e-01
  ... (remaining 9155 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.26: 9868
        0.26 -     0.53: 1810
        0.53 -     0.79: 438
        0.79 -     1.05: 124
        1.05 -     1.32: 40
  Bond angle restraints: 12280
  Sorted by residual:
  angle pdb=" C   ILE N  25 "
        pdb=" CA  ILE N  25 "
        pdb=" CB  ILE N  25 "
      ideal   model   delta    sigma   weight residual
     111.97  110.97    1.00 1.28e+00 6.10e-01 6.07e-01
  angle pdb=" C   ILE O  25 "
        pdb=" CA  ILE O  25 "
        pdb=" CB  ILE O  25 "
      ideal   model   delta    sigma   weight residual
     111.97  110.97    1.00 1.28e+00 6.10e-01 6.07e-01
  angle pdb=" C   ILE 8  25 "
        pdb=" CA  ILE 8  25 "
        pdb=" CB  ILE 8  25 "
      ideal   model   delta    sigma   weight residual
     111.97  110.98    0.99 1.28e+00 6.10e-01 5.95e-01
  angle pdb=" C   ILE 9  25 "
        pdb=" CA  ILE 9  25 "
        pdb=" CB  ILE 9  25 "
      ideal   model   delta    sigma   weight residual
     111.97  110.98    0.99 1.28e+00 6.10e-01 5.95e-01
  angle pdb=" C   ILE c  25 "
        pdb=" CA  ILE c  25 "
        pdb=" CB  ILE c  25 "
      ideal   model   delta    sigma   weight residual
     111.97  110.99    0.98 1.28e+00 6.10e-01 5.82e-01
  ... (remaining 12275 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     7.23: 4440
        7.23 -    14.46: 680
       14.46 -    21.68: 320
       21.68 -    28.91: 200
       28.91 -    36.14: 160
  Dihedral angle restraints: 5800
    sinusoidal: 2320
      harmonic: 3480
  Sorted by residual:
  dihedral pdb=" CB  ARG 7  13 "
           pdb=" CG  ARG 7  13 "
           pdb=" CD  ARG 7  13 "
           pdb=" NE  ARG 7  13 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -143.86  -36.14     3      1.50e+01 4.44e-03 6.24e+00
  dihedral pdb=" CB  ARG 6  13 "
           pdb=" CG  ARG 6  13 "
           pdb=" CD  ARG 6  13 "
           pdb=" NE  ARG 6  13 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -143.86  -36.14     3      1.50e+01 4.44e-03 6.24e+00
  dihedral pdb=" CB  ARG C  13 "
           pdb=" CG  ARG C  13 "
           pdb=" CD  ARG C  13 "
           pdb=" NE  ARG C  13 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -143.88  -36.12     3      1.50e+01 4.44e-03 6.23e+00
  ... (remaining 5797 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.017: 782
       0.017 -    0.035: 440
       0.035 -    0.052: 58
       0.052 -    0.070: 40
       0.070 -    0.087: 80
  Chirality restraints: 1400
  Sorted by residual:
  chirality pdb=" CA  ILE H  25 "
            pdb=" N   ILE H  25 "
            pdb=" C   ILE H  25 "
            pdb=" CB  ILE H  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.52   -0.09 2.00e-01 2.50e+01 1.89e-01
  chirality pdb=" CA  ILE I  25 "
            pdb=" N   ILE I  25 "
            pdb=" C   ILE I  25 "
            pdb=" CB  ILE I  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.52   -0.09 2.00e-01 2.50e+01 1.89e-01
  chirality pdb=" CA  ILE O  25 "
            pdb=" N   ILE O  25 "
            pdb=" C   ILE O  25 "
            pdb=" CB  ILE O  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.52   -0.09 2.00e-01 2.50e+01 1.86e-01
  ... (remaining 1397 not shown)

  Planarity restraints: 1640
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS D  22 "    0.003 2.00e-02 2.50e+03   2.68e-03 1.07e-01
        pdb=" CG  HIS D  22 "   -0.006 2.00e-02 2.50e+03
        pdb=" ND1 HIS D  22 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS D  22 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 HIS D  22 "    0.000 2.00e-02 2.50e+03
        pdb=" NE2 HIS D  22 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS E  22 "    0.003 2.00e-02 2.50e+03   2.68e-03 1.07e-01
        pdb=" CG  HIS E  22 "   -0.006 2.00e-02 2.50e+03
        pdb=" ND1 HIS E  22 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS E  22 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 HIS E  22 "    0.000 2.00e-02 2.50e+03
        pdb=" NE2 HIS E  22 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS Y  22 "    0.002 2.00e-02 2.50e+03   2.65e-03 1.05e-01
        pdb=" CG  HIS Y  22 "   -0.006 2.00e-02 2.50e+03
        pdb=" ND1 HIS Y  22 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS Y  22 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 HIS Y  22 "    0.000 2.00e-02 2.50e+03
        pdb=" NE2 HIS Y  22 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1637 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2424
        2.81 -     3.33: 9756
        3.33 -     3.86: 15358
        3.86 -     4.38: 18174
        4.38 -     4.90: 29490
  Nonbonded interactions: 75202
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN Y  29 "
            pdb=" NH1 ARG 0  13 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" OE1 GLN Z  29 "
            pdb=" NH1 ARG 1  13 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" OE1 GLN S  29 "
            pdb=" NH1 ARG U  13 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" OE1 GLN R  29 "
            pdb=" NH1 ARG T  13 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" OE1 GLN U  29 "
            pdb=" NH1 ARG V  13 "
     model   vdw
     2.288 3.120
  ... (remaining 75197 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain '1'
  selection = chain '0'
  selection = chain '3'
  selection = chain '2'
  selection = chain '5'
  selection = chain '4'
  selection = chain '7'
  selection = chain '6'
  selection = chain '9'
  selection = chain '8'
  selection = 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 'K'
  selection = chain 'J'
  selection = chain 'M'
  selection = chain 'L'
  selection = chain 'O'
  selection = chain 'N'
  selection = chain 'Q'
  selection = chain 'P'
  selection = chain 'S'
  selection = chain 'R'
  selection = chain 'U'
  selection = chain 'T'
  selection = chain 'W'
  selection = chain 'V'
  selection = chain 'Y'
  selection = chain 'X'
  selection = chain 'Z'
  selection = chain 'a'
  selection = chain 'c'
  selection = chain 'b'
  selection = chain 'd'
}

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:             1.410
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     18.960
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
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      :  0.002   0.008   9160  Z= 0.117
  Angle     :  0.246   1.318  12280  Z= 0.156
  Chirality :  0.029   0.087   1400
  Planarity :  0.001   0.006   1640
  Dihedral  : 11.982  36.141   3480
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  4.54 (0.24), residues: 1080
  helix:  2.95 (0.15), residues: 1080
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS Y  22 
 TYR   0.002   0.001   TYR T  15 
 ARG   0.001   0.000   ARG P  17 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 1.048 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.4216
  time to fit residues: 40.9895
Evaluate side-chains
  80 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 60 optimal weight:    7.9990
   chunk 33 optimal weight:    0.7980
   chunk 20 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 46 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.4074 r_free = 0.4074 target = 0.172987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.145065 restraints weight = 8710.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 1.10
r_work: 0.2859 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2678 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.1042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   9160  Z= 0.217
  Angle     :  0.338   3.359  12280  Z= 0.191
  Chirality :  0.031   0.101   1400
  Planarity :  0.002   0.014   1640
  Dihedral  :  3.251   6.056   1240
  Min Nonbonded Distance : 2.688

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.20 (0.23), residues: 1080
  helix:  2.74 (0.14), residues: 1080
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS S  22 
 TYR   0.004   0.001   TYR J  15 
 ARG   0.002   0.001   ARG 4  13 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.950 
Fit side-chains
REVERT: D   24 GLU cc_start: 0.8344 (tp30) cc_final: 0.8074 (tp30)
REVERT: E   24 GLU cc_start: 0.8361 (tp30) cc_final: 0.8091 (tp30)
REVERT: N   24 GLU cc_start: 0.8792 (tp30) cc_final: 0.8283 (tp30)
REVERT: O   24 GLU cc_start: 0.8774 (tp30) cc_final: 0.8260 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.4507
  time to fit residues: 39.4344
Evaluate side-chains
  72 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 6 optimal weight:   10.0000
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4052 r_free = 0.4052 target = 0.171158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.141995 restraints weight = 8854.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3022 rms_B_bonded: 1.18
r_work: 0.2871 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2685 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.1036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   9160  Z= 0.145
  Angle     :  0.276   2.421  12280  Z= 0.162
  Chirality :  0.029   0.098   1400
  Planarity :  0.001   0.007   1640
  Dihedral  :  3.145   6.071   1240
  Min Nonbonded Distance : 2.691

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  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:  4.60 (0.22), residues: 1080
  helix:  2.99 (0.14), residues: 1080
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS R  22 
 TYR   0.002   0.000   TYR K  15 
 ARG   0.002   0.000   ARG W  13 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 1.114 
Fit side-chains
REVERT: D   24 GLU cc_start: 0.8440 (tp30) cc_final: 0.8039 (tp30)
REVERT: E   24 GLU cc_start: 0.8475 (tp30) cc_final: 0.8075 (tp30)
REVERT: 6   24 GLU cc_start: 0.8531 (tp30) cc_final: 0.8144 (tp30)
REVERT: 7   24 GLU cc_start: 0.8535 (tp30) cc_final: 0.8145 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.4319
  time to fit residues: 41.3130
Evaluate side-chains
  78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 76 optimal weight:    0.0770
   chunk 68 optimal weight:    0.9980
   chunk 72 optimal weight:    8.9990
   overall best weight:    1.0144

-------------------------------------------------------------------------------
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 = 0.4081 r_free = 0.4081 target = 0.173707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.145795 restraints weight = 8731.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 1.13
r_work: 0.2876 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2692 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.1133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   9160  Z= 0.173
  Angle     :  0.278   2.588  12280  Z= 0.162
  Chirality :  0.030   0.099   1400
  Planarity :  0.002   0.010   1640
  Dihedral  :  3.111   6.071   1240
  Min Nonbonded Distance : 2.691

Molprobity Statistics.
  All-atom Clashscore : 2.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  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:  4.80 (0.22), residues: 1080
  helix:  3.11 (0.13), residues: 1080
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS S  22 
 TYR   0.002   0.001   TYR 8  15 
 ARG   0.002   0.000   ARG X  13 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.927 
Fit side-chains
REVERT: D   24 GLU cc_start: 0.8522 (tp30) cc_final: 0.8072 (tp30)
REVERT: E   24 GLU cc_start: 0.8500 (tp30) cc_final: 0.8057 (tp30)
REVERT: N   24 GLU cc_start: 0.8717 (tp30) cc_final: 0.8256 (tp30)
REVERT: O   24 GLU cc_start: 0.8723 (tp30) cc_final: 0.8272 (tp30)
REVERT: 6   24 GLU cc_start: 0.8429 (tp30) cc_final: 0.7926 (tp30)
REVERT: 7   24 GLU cc_start: 0.8441 (tp30) cc_final: 0.7947 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.4513
  time to fit residues: 40.5613
Evaluate side-chains
  74 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 38 optimal weight:    0.3980
   chunk 60 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 70 optimal weight:    7.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.4085 r_free = 0.4085 target = 0.174129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.146377 restraints weight = 8736.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 1.12
r_work: 0.2880 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2698 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.1150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   9160  Z= 0.167
  Angle     :  0.272   2.680  12280  Z= 0.159
  Chirality :  0.030   0.098   1400
  Planarity :  0.001   0.010   1640
  Dihedral  :  3.101   6.058   1240
  Min Nonbonded Distance : 2.692

Molprobity Statistics.
  All-atom Clashscore : 2.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  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:  5.02 (0.21), residues: 1080
  helix:  3.24 (0.13), residues: 1080
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS S  22 
 TYR   0.002   0.001   TYR 8  15 
 ARG   0.002   0.000   ARG W  13 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.984 
Fit side-chains
REVERT: D   24 GLU cc_start: 0.8533 (tp30) cc_final: 0.8116 (tp30)
REVERT: E   24 GLU cc_start: 0.8521 (tp30) cc_final: 0.8107 (tp30)
REVERT: 6   24 GLU cc_start: 0.8415 (tp30) cc_final: 0.7952 (tp30)
REVERT: 7   24 GLU cc_start: 0.8441 (tp30) cc_final: 0.7973 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.4557
  time to fit residues: 42.0234
Evaluate side-chains
  76 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.4111 r_free = 0.4111 target = 0.176201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.148448 restraints weight = 8656.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 1.13
r_work: 0.2881 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2701 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.1179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   9160  Z= 0.150
  Angle     :  0.263   2.795  12280  Z= 0.155
  Chirality :  0.029   0.097   1400
  Planarity :  0.001   0.008   1640
  Dihedral  :  3.091   6.049   1240
  Min Nonbonded Distance : 2.693

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  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:  5.22 (0.21), residues: 1080
  helix:  3.37 (0.13), residues: 1080
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS R  22 
 TYR   0.002   0.000   TYR 9  15 
 ARG   0.001   0.000   ARG W  13 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.958 
Fit side-chains
REVERT: D   24 GLU cc_start: 0.8517 (tp30) cc_final: 0.8114 (tp30)
REVERT: E   24 GLU cc_start: 0.8541 (tp30) cc_final: 0.8140 (tp30)
REVERT: A   24 GLU cc_start: 0.8591 (tp30) cc_final: 0.8382 (tp30)
REVERT: V   24 GLU cc_start: 0.8607 (tp30) cc_final: 0.8398 (tp30)
REVERT: 6   24 GLU cc_start: 0.8412 (tp30) cc_final: 0.8114 (tp30)
REVERT: 7   24 GLU cc_start: 0.8435 (tp30) cc_final: 0.8130 (tp30)
REVERT: 8   24 GLU cc_start: 0.8481 (tp30) cc_final: 0.8239 (tp30)
REVERT: 9   24 GLU cc_start: 0.8452 (tp30) cc_final: 0.8213 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.4223
  time to fit residues: 40.0920
Evaluate side-chains
  78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 52 optimal weight:    7.9990
   chunk 20 optimal weight:    0.0980
   chunk 25 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 64 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4122 r_free = 0.4122 target = 0.177371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.149699 restraints weight = 8777.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 1.11
r_work: 0.2913 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2735 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.1191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   9160  Z= 0.121
  Angle     :  0.253   2.956  12280  Z= 0.150
  Chirality :  0.029   0.098   1400
  Planarity :  0.001   0.006   1640
  Dihedral  :  3.078   5.981   1240
  Min Nonbonded Distance : 2.692

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.48 (0.21), residues: 1080
  helix:  3.53 (0.13), residues: 1080
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS S  22 
 TYR   0.002   0.000   TYR 9  15 
 ARG   0.001   0.000   ARG 2  13 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 1.147 
Fit side-chains
REVERT: D   24 GLU cc_start: 0.8545 (tp30) cc_final: 0.8142 (tp30)
REVERT: E   24 GLU cc_start: 0.8582 (tp30) cc_final: 0.8174 (tp30)
REVERT: L   24 GLU cc_start: 0.8766 (tp30) cc_final: 0.8530 (tp30)
REVERT: M   24 GLU cc_start: 0.8739 (tp30) cc_final: 0.8505 (tp30)
REVERT: 6   24 GLU cc_start: 0.8389 (tp30) cc_final: 0.8174 (tp30)
REVERT: 7   24 GLU cc_start: 0.8397 (tp30) cc_final: 0.8179 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.4497
  time to fit residues: 42.8137
Evaluate side-chains
  78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 24 optimal weight:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 49 optimal weight:    0.6980
   chunk 59 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 55 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4067 r_free = 0.4067 target = 0.172839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.144944 restraints weight = 8895.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 1.12
r_work: 0.2917 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2730 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.1215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9160  Z= 0.136
  Angle     :  0.279   4.567  12280  Z= 0.162
  Chirality :  0.029   0.097   1400
  Planarity :  0.001   0.007   1640
  Dihedral  :  3.055   5.969   1240
  Min Nonbonded Distance : 2.693

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.58 (0.21), residues: 1080
  helix:  3.59 (0.13), residues: 1080
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS R  22 
 TYR   0.002   0.000   TYR c  15 
 ARG   0.001   0.000   ARG W  13 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.944 
Fit side-chains
REVERT: D   24 GLU cc_start: 0.8536 (tp30) cc_final: 0.8137 (tp30)
REVERT: E   24 GLU cc_start: 0.8590 (tp30) cc_final: 0.8222 (tp30)
REVERT: L   24 GLU cc_start: 0.8745 (tp30) cc_final: 0.8529 (tp30)
REVERT: M   24 GLU cc_start: 0.8724 (tp30) cc_final: 0.8510 (tp30)
REVERT: N   24 GLU cc_start: 0.8649 (tp30) cc_final: 0.8180 (tp30)
REVERT: O   24 GLU cc_start: 0.8679 (tp30) cc_final: 0.8209 (tp30)
REVERT: 6   24 GLU cc_start: 0.8386 (tp30) cc_final: 0.8115 (tp30)
REVERT: 7   24 GLU cc_start: 0.8382 (tp30) cc_final: 0.8124 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.4183
  time to fit residues: 39.7806
Evaluate side-chains
  78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 54 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 8 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 34 optimal weight:    0.7980
   chunk 11 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   overall best weight:    2.0984

-------------------------------------------------------------------------------
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 = 0.4000 r_free = 0.4000 target = 0.166892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.139633 restraints weight = 8779.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 1.10
r_work: 0.2836 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2642 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.1421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   9160  Z= 0.320
  Angle     :  0.359   4.458  12280  Z= 0.202
  Chirality :  0.033   0.099   1400
  Planarity :  0.002   0.019   1640
  Dihedral  :  3.128   6.464   1240
  Min Nonbonded Distance : 2.687

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.67 (0.22), residues: 1080
  helix:  3.03 (0.13), residues: 1080
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS I  22 
 TYR   0.003   0.001   TYR 8  15 
 ARG   0.003   0.000   ARG 5  17 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.995 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.4778
  time to fit residues: 36.9851
Evaluate side-chains
  64 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0770
   chunk 40 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0980
   chunk 79 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 16 optimal weight:   10.0000
   overall best weight:    0.4938

-------------------------------------------------------------------------------
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 = 0.4118 r_free = 0.4118 target = 0.177097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.149693 restraints weight = 8825.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 1.13
r_work: 0.2906 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2727 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9160  Z= 0.117
  Angle     :  0.279   4.314  12280  Z= 0.162
  Chirality :  0.029   0.098   1400
  Planarity :  0.001   0.009   1640
  Dihedral  :  3.149   6.149   1240
  Min Nonbonded Distance : 2.693

Molprobity Statistics.
  All-atom Clashscore : 2.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  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:  5.30 (0.21), residues: 1080
  helix:  3.42 (0.13), residues: 1080
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS Z  22 
 TYR   0.002   0.001   TYR 8  15 
 ARG   0.002   0.000   ARG X  13 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.988 
Fit side-chains
REVERT: D   24 GLU cc_start: 0.8501 (tp30) cc_final: 0.8159 (tp30)
REVERT: E   24 GLU cc_start: 0.8549 (tp30) cc_final: 0.8205 (tp30)
REVERT: F   24 GLU cc_start: 0.8544 (tp30) cc_final: 0.8017 (tp30)
REVERT: G   24 GLU cc_start: 0.8526 (tp30) cc_final: 0.7996 (tp30)
REVERT: L   24 GLU cc_start: 0.8746 (tp30) cc_final: 0.8503 (tp30)
REVERT: M   24 GLU cc_start: 0.8719 (tp30) cc_final: 0.8478 (tp30)
REVERT: R   22 HIS cc_start: 0.8705 (m-70) cc_final: 0.8477 (m170)
REVERT: S   22 HIS cc_start: 0.8711 (m-70) cc_final: 0.8482 (m170)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.4211
  time to fit residues: 41.0427
Evaluate side-chains
  80 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   chunk 64 optimal weight:    0.0270
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.6438

-------------------------------------------------------------------------------
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 = 0.4112 r_free = 0.4112 target = 0.176644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.149018 restraints weight = 8732.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 1.10
r_work: 0.2915 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2733 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9160  Z= 0.139
  Angle     :  0.301   4.590  12280  Z= 0.172
  Chirality :  0.029   0.101   1400
  Planarity :  0.001   0.010   1640
  Dihedral  :  3.061   5.969   1240
  Min Nonbonded Distance : 2.694

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  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:  5.58 (0.21), residues: 1080
  helix:  3.59 (0.13), residues: 1080
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS R  22 
 TYR   0.002   0.000   TYR c  15 
 ARG   0.001   0.000   ARG W  13 

===============================================================================
Job complete
usr+sys time: 3613.47 seconds
wall clock time: 65 minutes 22.97 seconds (3922.97 seconds total)