Starting phenix.real_space_refine
on Fri Aug 22 20:26:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fai_28957/08_2025/8fai_28957.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fai_28957/08_2025/8fai_28957.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/8fai_28957/08_2025/8fai_28957.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fai_28957/08_2025/8fai_28957.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fai_28957/08_2025/8fai_28957.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fai_28957/08_2025/8fai_28957.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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      15      5.49       5
     S      60      5.16       5
     C    5250      2.51       5
     N    1140      2.21       5
     O    1380      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7845
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 472
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 472
          Classifications: {'peptide': 68}
          Link IDs: {'PTRANS': 2, 'TRANS': 65}
    Chain: "F"
      Number of atoms: 472
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 472
          Classifications: {'peptide': 68}
          Link IDs: {'PTRANS': 2, 'TRANS': 65}
    Chain: "K"
      Number of atoms: 472
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 472
          Classifications: {'peptide': 68}
          Link IDs: {'PTRANS': 2, 'TRANS': 65}
    Chain: "F"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 51
          Unusual residues: {'XL0': 1}
          Classifications: {'undetermined': 1}
    Chain: "K"
      Number of atoms: 102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 102
          Unusual residues: {'XL0': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B, C, D, E, G, H, I, J, L, M, N, O
  Time building chain proxies: 1.16, per 1000 atoms: 0.15
  Number of scatterers: 7845
  At special positions: 0
  Unit cell: (87.36, 89.024, 93.184, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      60     16.00
     P      15     15.00
     O    1380      8.00
     N    1140      7.00
     C    5250      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  64 " - pdb=" SG  CYS B  64 " distance=0.00
    Simple disulfide: pdb=" SG  CYS C  64 " - pdb=" SG  CYS C  64 " distance=0.00

  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=10, symmetry=0
  Number of additional bonds: simple=10, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 441.8 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1620

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 0 sheets defined
      91.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 55 through 68
    Processing helix  chain 'A' and resid 69 through 89
    Processing helix  chain 'A' and resid 93 through 109
      removed outlier: 3.751A  pdb=" N   VAL A  97 " --> pdb=" O   SER A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 118
    Processing helix  chain 'B' and resid 55 through 68
    Processing helix  chain 'B' and resid 69 through 89
    Processing helix  chain 'B' and resid 93 through 109
      removed outlier: 3.751A  pdb=" N   VAL B  97 " --> pdb=" O   SER B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 118
    Processing helix  chain 'C' and resid 55 through 68
    Processing helix  chain 'C' and resid 69 through 89
    Processing helix  chain 'C' and resid 93 through 109
      removed outlier: 3.751A  pdb=" N   VAL C  97 " --> pdb=" O   SER C  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 109 through 118
    Processing helix  chain 'D' and resid 55 through 68
    Processing helix  chain 'D' and resid 69 through 89
    Processing helix  chain 'D' and resid 93 through 109
      removed outlier: 3.751A  pdb=" N   VAL D  97 " --> pdb=" O   SER D  93 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 118
    Processing helix  chain 'E' and resid 55 through 68
    Processing helix  chain 'E' and resid 69 through 89
    Processing helix  chain 'E' and resid 93 through 109
      removed outlier: 3.751A  pdb=" N   VAL E  97 " --> pdb=" O   SER E  93 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 109 through 118
    Processing helix  chain 'F' and resid 55 through 68
    Processing helix  chain 'F' and resid 69 through 89
    Processing helix  chain 'F' and resid 93 through 109
      removed outlier: 3.751A  pdb=" N   VAL F  97 " --> pdb=" O   SER F  93 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 109 through 118
    Processing helix  chain 'G' and resid 55 through 68
    Processing helix  chain 'G' and resid 69 through 89
    Processing helix  chain 'G' and resid 93 through 109
      removed outlier: 3.752A  pdb=" N   VAL G  97 " --> pdb=" O   SER G  93 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 109 through 118
    Processing helix  chain 'H' and resid 55 through 68
    Processing helix  chain 'H' and resid 69 through 89
    Processing helix  chain 'H' and resid 93 through 109
      removed outlier: 3.751A  pdb=" N   VAL H  97 " --> pdb=" O   SER H  93 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 109 through 118
    Processing helix  chain 'I' and resid 55 through 68
    Processing helix  chain 'I' and resid 69 through 89
    Processing helix  chain 'I' and resid 93 through 109
      removed outlier: 3.751A  pdb=" N   VAL I  97 " --> pdb=" O   SER I  93 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 109 through 118
    Processing helix  chain 'J' and resid 55 through 68
    Processing helix  chain 'J' and resid 69 through 89
    Processing helix  chain 'J' and resid 93 through 109
      removed outlier: 3.752A  pdb=" N   VAL J  97 " --> pdb=" O   SER J  93 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 109 through 118
    Processing helix  chain 'K' and resid 55 through 68
    Processing helix  chain 'K' and resid 69 through 89
    Processing helix  chain 'K' and resid 93 through 109
      removed outlier: 3.751A  pdb=" N   VAL K  97 " --> pdb=" O   SER K  93 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 109 through 118
    Processing helix  chain 'L' and resid 55 through 68
    Processing helix  chain 'L' and resid 69 through 89
    Processing helix  chain 'L' and resid 93 through 109
      removed outlier: 3.751A  pdb=" N   VAL L  97 " --> pdb=" O   SER L  93 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 109 through 118
    Processing helix  chain 'M' and resid 55 through 68
    Processing helix  chain 'M' and resid 69 through 89
    Processing helix  chain 'M' and resid 93 through 109
      removed outlier: 3.751A  pdb=" N   VAL M  97 " --> pdb=" O   SER M  93 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 109 through 118
    Processing helix  chain 'N' and resid 55 through 68
    Processing helix  chain 'N' and resid 69 through 89
    Processing helix  chain 'N' and resid 93 through 109
      removed outlier: 3.751A  pdb=" N   VAL N  97 " --> pdb=" O   SER N  93 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 109 through 118
    Processing helix  chain 'O' and resid 55 through 68
    Processing helix  chain 'O' and resid 69 through 89
    Processing helix  chain 'O' and resid 93 through 109
      removed outlier: 3.751A  pdb=" N   VAL O  97 " --> pdb=" O   SER O  93 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 109 through 118

    675 hydrogen bonds defined for protein.
    2025 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.31

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1125
        1.31 -     1.43: 1909
        1.43 -     1.56: 4631
        1.56 -     1.68: 180
        1.68 -     1.81: 105
  Bond restraints: 7950
  Sorted by residual:
  bond pdb=" C31 XL0 L 202 "
       pdb=" O31 XL0 L 202 "
    ideal  model  delta    sigma   weight residual
    1.333  1.440 -0.107 2.00e-02 2.50e+03 2.86e+01
  bond pdb=" C31 XL0 I 200 "
       pdb=" O31 XL0 I 200 "
    ideal  model  delta    sigma   weight residual
    1.333  1.440 -0.107 2.00e-02 2.50e+03 2.85e+01
  bond pdb=" C31 XL0 M 202 "
       pdb=" O31 XL0 M 202 "
    ideal  model  delta    sigma   weight residual
    1.333  1.440 -0.107 2.00e-02 2.50e+03 2.84e+01
  bond pdb=" C31 XL0 N 202 "
       pdb=" O31 XL0 N 202 "
    ideal  model  delta    sigma   weight residual
    1.333  1.440 -0.107 2.00e-02 2.50e+03 2.84e+01
  bond pdb=" C31 XL0 N 201 "
       pdb=" O31 XL0 N 201 "
    ideal  model  delta    sigma   weight residual
    1.333  1.440 -0.107 2.00e-02 2.50e+03 2.84e+01
  ... (remaining 7945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.47: 10249
        4.47 -     8.94: 311
        8.94 -    13.41: 15
       13.41 -    17.88: 0
       17.88 -    22.36: 15
  Bond angle restraints: 10590
  Sorted by residual:
  angle pdb=" O13 XL0 M 202 "
        pdb=" P   XL0 M 202 "
        pdb=" O14 XL0 M 202 "
      ideal   model   delta    sigma   weight residual
     123.28  100.92   22.36 3.00e+00 1.11e-01 5.55e+01
  angle pdb=" O13 XL0 K 202 "
        pdb=" P   XL0 K 202 "
        pdb=" O14 XL0 K 202 "
      ideal   model   delta    sigma   weight residual
     123.28  100.93   22.35 3.00e+00 1.11e-01 5.55e+01
  angle pdb=" O13 XL0 K 201 "
        pdb=" P   XL0 K 201 "
        pdb=" O14 XL0 K 201 "
      ideal   model   delta    sigma   weight residual
     123.28  100.94   22.34 3.00e+00 1.11e-01 5.54e+01
  angle pdb=" O13 XL0 H 200 "
        pdb=" P   XL0 H 200 "
        pdb=" O14 XL0 H 200 "
      ideal   model   delta    sigma   weight residual
     123.28  100.94   22.34 3.00e+00 1.11e-01 5.54e+01
  angle pdb=" O13 XL0 N 202 "
        pdb=" P   XL0 N 202 "
        pdb=" O14 XL0 N 202 "
      ideal   model   delta    sigma   weight residual
     123.28  100.95   22.33 3.00e+00 1.11e-01 5.54e+01
  ... (remaining 10585 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.75: 3655
       10.75 -    21.50: 481
       21.50 -    32.26: 443
       32.26 -    43.01: 150
       43.01 -    53.76: 45
  Dihedral angle restraints: 4774
    sinusoidal: 2149
      harmonic: 2625
  Sorted by residual:
  dihedral pdb=" CB  MET N  59 "
           pdb=" CG  MET N  59 "
           pdb=" SD  MET N  59 "
           pdb=" CE  MET N  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  141.01   38.99     3      1.50e+01 4.44e-03 6.89e+00
  dihedral pdb=" CB  MET B  59 "
           pdb=" CG  MET B  59 "
           pdb=" SD  MET B  59 "
           pdb=" CE  MET B  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  141.01   38.99     3      1.50e+01 4.44e-03 6.89e+00
  dihedral pdb=" CB  MET I  59 "
           pdb=" CG  MET I  59 "
           pdb=" SD  MET I  59 "
           pdb=" CE  MET I  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  141.02   38.98     3      1.50e+01 4.44e-03 6.89e+00
  ... (remaining 4771 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 705
       0.027 -    0.053: 284
       0.053 -    0.080: 211
       0.080 -    0.106: 15
       0.106 -    0.133: 15
  Chirality restraints: 1230
  Sorted by residual:
  chirality pdb=" C12 XL0 L 201 "
            pdb=" C11 XL0 L 201 "
            pdb=" C13 XL0 L 201 "
            pdb=" OC2 XL0 L 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.38   -2.52    0.13 2.00e-01 2.50e+01 4.40e-01
  chirality pdb=" C12 XL0 F 200 "
            pdb=" C11 XL0 F 200 "
            pdb=" C13 XL0 F 200 "
            pdb=" OC2 XL0 F 200 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.38   -2.52    0.13 2.00e-01 2.50e+01 4.33e-01
  chirality pdb=" C12 XL0 O 201 "
            pdb=" C11 XL0 O 201 "
            pdb=" C13 XL0 O 201 "
            pdb=" OC2 XL0 O 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.38   -2.51    0.13 2.00e-01 2.50e+01 4.23e-01
  ... (remaining 1227 not shown)

  Planarity restraints: 1260
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C38 XL0 L 202 "   -0.012 2.00e-02 2.50e+03   2.12e-02 4.51e+00
        pdb=" C39 XL0 L 202 "    0.027 2.00e-02 2.50e+03
        pdb="C310 XL0 L 202 "   -0.027 2.00e-02 2.50e+03
        pdb="C311 XL0 L 202 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C38 XL0 N 201 "    0.012 2.00e-02 2.50e+03   2.12e-02 4.49e+00
        pdb=" C39 XL0 N 201 "   -0.027 2.00e-02 2.50e+03
        pdb="C310 XL0 N 201 "    0.027 2.00e-02 2.50e+03
        pdb="C311 XL0 N 201 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C38 XL0 G 200 "   -0.012 2.00e-02 2.50e+03   2.08e-02 4.32e+00
        pdb=" C39 XL0 G 200 "    0.027 2.00e-02 2.50e+03
        pdb="C310 XL0 G 200 "   -0.027 2.00e-02 2.50e+03
        pdb="C311 XL0 G 200 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1257 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 2815
        2.90 -     3.40: 8045
        3.40 -     3.90: 13421
        3.90 -     4.40: 15033
        4.40 -     4.90: 23836
  Nonbonded interactions: 63150
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 117 "
            pdb=" OG1 THR B 118 "
     model   vdw
     2.395 3.040
  nonbonded pdb=" O   LEU N 117 "
            pdb=" OG1 THR N 118 "
     model   vdw
     2.395 3.040
  nonbonded pdb=" O   LEU G 117 "
            pdb=" OG1 THR G 118 "
     model   vdw
     2.396 3.040
  nonbonded pdb=" O   LEU A 117 "
            pdb=" OG1 THR A 118 "
     model   vdw
     2.396 3.040
  nonbonded pdb=" O   LEU K 117 "
            pdb=" OG1 THR K 118 "
     model   vdw
     2.396 3.040
  ... (remaining 63145 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
}

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:             1.790
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.220
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  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:6.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
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   0.107   7960  Z= 0.553
  Angle     :  1.627  22.356  10592  Z= 0.588
  Chirality :  0.038   0.133   1230
  Planarity :  0.004   0.022   1260
  Dihedral  : 15.884  53.761   3150
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 4.13
  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 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:  3.16 (0.27), residues: 990
  helix:  2.50 (0.17), residues: 885
  sheet:  None (None), residues: 0
  loop : -1.82 (0.48), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG O  91 
 PHE   0.007   0.001   PHE D  71 
 TRP   0.002   0.001   TRP N  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.01111 ( 7950)
  covalent geometry    : angle       1.62692 (10590)
  SS BOND              : angle       0.00000 (    2)
  hydrogen bonds       : bond        0.13819 (  675)
  hydrogen bonds       : angle       5.78682 ( 2025)
  Misc. bond           : bond        0.00104 (   10)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 271
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A   74 SER cc_start: 0.8716 (m) cc_final: 0.8398 (p)
REVERT: B   74 SER cc_start: 0.8818 (m) cc_final: 0.8539 (p)
REVERT: B   94 LEU cc_start: 0.8697 (tp) cc_final: 0.8410 (tp)
REVERT: C   74 SER cc_start: 0.8697 (m) cc_final: 0.8425 (p)
REVERT: D   74 SER cc_start: 0.8707 (m) cc_final: 0.8443 (p)
REVERT: E   74 SER cc_start: 0.8792 (m) cc_final: 0.8483 (p)
REVERT: F   74 SER cc_start: 0.8656 (m) cc_final: 0.8425 (p)
REVERT: H   74 SER cc_start: 0.8705 (m) cc_final: 0.8496 (p)
  outliers start: 0
  outliers final: 1
  residues processed: 271
  average time/residue: 0.3495
  time to fit residues: 103.2236
Evaluate side-chains
  189 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 188
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  107 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3444 r_free = 0.3444 target = 0.123757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.114480 restraints weight = 10846.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 1.27
r_work: 0.3212 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.2611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7960  Z= 0.158
  Angle     :  0.662   8.624  10592  Z= 0.322
  Chirality :  0.038   0.205   1230
  Planarity :  0.005   0.054   1260
  Dihedral  : 12.691  48.342   1818
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Rotamer:
    Outliers :  6.81 %
    Allowed  : 22.22 %
    Favored  : 70.97 %
  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:  3.73 (0.26), residues: 990
  helix:  2.86 (0.17), residues: 885
  sheet:  None (None), residues: 0
  loop : -1.39 (0.45), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.003   ARG N  91 
 PHE   0.012   0.001   PHE L 112 
 TRP   0.005   0.001   TRP L  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 7950)
  covalent geometry    : angle       0.66209 (10590)
  SS BOND              : angle       0.00000 (    2)
  hydrogen bonds       : bond        0.03653 (  675)
  hydrogen bonds       : angle       4.42313 ( 2025)
  Misc. bond           : bond        0.00543 (   10)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 203
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A   54 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.7984 (t)
REVERT: A   91 ARG cc_start: 0.6714 (ppt170) cc_final: 0.6496 (ppt170)
REVERT: B   74 SER cc_start: 0.8968 (m) cc_final: 0.8501 (p)
REVERT: C   54 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.8000 (t)
REVERT: D   74 SER cc_start: 0.8985 (m) cc_final: 0.8611 (p)
REVERT: F   54 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8095 (t)
REVERT: G   54 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.7962 (t)
REVERT: H   54 THR cc_start: 0.8256 (p) cc_final: 0.7883 (t)
REVERT: J   54 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.7949 (t)
REVERT: K   54 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7876 (t)
REVERT: L   54 THR cc_start: 0.8238 (p) cc_final: 0.7940 (t)
REVERT: M   54 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7968 (t)
REVERT: M  106 ILE cc_start: 0.8563 (mt) cc_final: 0.8309 (mt)
REVERT: N   54 THR cc_start: 0.8061 (OUTLIER) cc_final: 0.7836 (t)
REVERT: N   60 VAL cc_start: 0.8537 (t) cc_final: 0.7837 (m)
REVERT: O   54 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7939 (t)
  outliers start: 49
  outliers final: 28
  residues processed: 224
  average time/residue: 0.2403
  time to fit residues: 59.9915
Evaluate side-chains
  210 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 173
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   67 ILE
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   93 SER
Chi-restraints excluded: chain H residue   93 SER
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   97 VAL
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   67 ILE
Chi-restraints excluded: chain K residue   93 SER
Chi-restraints excluded: chain K residue   97 VAL
Chi-restraints excluded: chain L residue   97 VAL
Chi-restraints excluded: chain M residue   54 THR
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain N residue   54 THR
Chi-restraints excluded: chain N residue   93 SER
Chi-restraints excluded: chain N residue   97 VAL
Chi-restraints excluded: chain O residue   54 THR
Chi-restraints excluded: chain O residue   67 ILE
Chi-restraints excluded: chain O residue   97 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 55 optimal weight:    0.2980
   chunk 38 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0570
   chunk 81 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
H  62 ASN
L  61 ASN
L  62 ASN
M  62 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.125275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.115938 restraints weight = 10701.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 1.25
r_work: 0.3241 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7960  Z= 0.127
  Angle     :  0.551   7.763  10592  Z= 0.273
  Chirality :  0.036   0.185   1230
  Planarity :  0.003   0.027   1260
  Dihedral  : 11.052  43.553   1815
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  6.53 %
    Allowed  : 25.28 %
    Favored  : 68.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  3.95 (0.25), residues: 990
  helix:  3.01 (0.16), residues: 885
  sheet:  None (None), residues: 0
  loop : -1.47 (0.37), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.002   ARG N  91 
 PHE   0.010   0.001   PHE K 112 
 TRP   0.004   0.001   TRP K  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7950)
  covalent geometry    : angle       0.55107 (10590)
  SS BOND              : angle       0.00000 (    2)
  hydrogen bonds       : bond        0.03347 (  675)
  hydrogen bonds       : angle       4.13399 ( 2025)
  Misc. bond           : bond        0.00315 (   10)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 168
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A   54 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.7973 (t)
REVERT: B   54 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.7888 (t)
REVERT: E   59 MET cc_start: 0.7955 (mtt) cc_final: 0.7746 (mtt)
REVERT: E   94 LEU cc_start: 0.8836 (tp) cc_final: 0.8573 (tp)
REVERT: E  115 LYS cc_start: 0.7858 (ttmm) cc_final: 0.7554 (mttm)
REVERT: F   54 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8180 (t)
REVERT: G   54 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8016 (t)
REVERT: G   88 MET cc_start: 0.7691 (ttm) cc_final: 0.7480 (ttp)
REVERT: H   54 THR cc_start: 0.8285 (p) cc_final: 0.7923 (t)
REVERT: H   74 SER cc_start: 0.8852 (m) cc_final: 0.8596 (p)
REVERT: J   54 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8105 (t)
REVERT: K   54 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8182 (t)
REVERT: L   54 THR cc_start: 0.8313 (p) cc_final: 0.8061 (t)
REVERT: M   54 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.7958 (t)
REVERT: M   60 VAL cc_start: 0.8563 (t) cc_final: 0.7898 (m)
REVERT: N   54 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.8042 (t)
REVERT: N   60 VAL cc_start: 0.8432 (t) cc_final: 0.8045 (m)
REVERT: O   54 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.8043 (t)
  outliers start: 47
  outliers final: 26
  residues processed: 188
  average time/residue: 0.2893
  time to fit residues: 60.0362
Evaluate side-chains
  199 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 164
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   67 ILE
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   97 VAL
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   67 ILE
Chi-restraints excluded: chain K residue   97 VAL
Chi-restraints excluded: chain L residue   97 VAL
Chi-restraints excluded: chain M residue   54 THR
Chi-restraints excluded: chain M residue   86 SER
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain M residue  111 SER
Chi-restraints excluded: chain N residue   54 THR
Chi-restraints excluded: chain N residue   97 VAL
Chi-restraints excluded: chain O residue   54 THR
Chi-restraints excluded: chain O residue   67 ILE
Chi-restraints excluded: chain O residue   97 VAL
Chi-restraints excluded: chain O residue  111 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 54 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 65 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 78 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
L  62 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.123302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.113920 restraints weight = 10923.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 1.27
r_work: 0.3208 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.3042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7960  Z= 0.143
  Angle     :  0.577   8.892  10592  Z= 0.280
  Chirality :  0.036   0.155   1230
  Planarity :  0.003   0.024   1260
  Dihedral  : 11.747  51.821   1815
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  7.50 %
    Allowed  : 26.53 %
    Favored  : 65.97 %
  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:  3.89 (0.25), residues: 990
  helix:  2.99 (0.16), residues: 885
  sheet:  None (None), residues: 0
  loop : -1.61 (0.31), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.002   ARG N  91 
 PHE   0.009   0.001   PHE M 112 
 TRP   0.004   0.001   TRP H  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 7950)
  covalent geometry    : angle       0.57715 (10590)
  SS BOND              : angle       0.00000 (    2)
  hydrogen bonds       : bond        0.03520 (  675)
  hydrogen bonds       : angle       4.21424 ( 2025)
  Misc. bond           : bond        0.00273 (   10)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 174
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: B   54 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8012 (t)
REVERT: D   65 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8171 (p)
REVERT: E   59 MET cc_start: 0.8019 (mtt) cc_final: 0.7748 (mtp)
REVERT: E   94 LEU cc_start: 0.8896 (tp) cc_final: 0.8659 (tp)
REVERT: G   54 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.7981 (t)
REVERT: I   60 VAL cc_start: 0.8513 (m) cc_final: 0.8312 (t)
REVERT: K   54 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8212 (t)
REVERT: L   54 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.8038 (t)
REVERT: M   54 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.7962 (t)
REVERT: N   54 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8088 (t)
REVERT: N   60 VAL cc_start: 0.8519 (t) cc_final: 0.8116 (m)
REVERT: O   54 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8044 (t)
  outliers start: 54
  outliers final: 35
  residues processed: 199
  average time/residue: 0.2579
  time to fit residues: 57.0905
Evaluate side-chains
  207 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 164
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   65 THR
Chi-restraints excluded: chain E residue   67 ILE
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   67 ILE
Chi-restraints excluded: chain J residue   67 ILE
Chi-restraints excluded: chain J residue   97 VAL
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   67 ILE
Chi-restraints excluded: chain K residue   93 SER
Chi-restraints excluded: chain K residue   97 VAL
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   67 ILE
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain L residue   97 VAL
Chi-restraints excluded: chain M residue   54 THR
Chi-restraints excluded: chain M residue   67 ILE
Chi-restraints excluded: chain M residue   86 SER
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain N residue   54 THR
Chi-restraints excluded: chain N residue   93 SER
Chi-restraints excluded: chain N residue   97 VAL
Chi-restraints excluded: chain O residue   54 THR
Chi-restraints excluded: chain O residue   67 ILE
Chi-restraints excluded: chain O residue   97 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0050
   chunk 41 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.7596

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

Flipped N/Q/H residues before XYZ refinement:
B  62 ASN
G  62 ASN
J  62 ASN
L  62 ASN
M  62 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.123401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.114794 restraints weight = 10770.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 1.16
r_work: 0.3236 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7960  Z= 0.133
  Angle     :  0.546   8.487  10592  Z= 0.268
  Chirality :  0.035   0.118   1230
  Planarity :  0.003   0.021   1260
  Dihedral  : 11.477  51.276   1815
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Rotamer:
    Outliers :  9.44 %
    Allowed  : 26.39 %
    Favored  : 64.17 %
  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:  3.90 (0.24), residues: 990
  helix:  3.01 (0.16), residues: 885
  sheet:  None (None), residues: 0
  loop : -1.79 (0.28), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG N  91 
 PHE   0.009   0.001   PHE O 112 
 TRP   0.004   0.001   TRP F  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 7950)
  covalent geometry    : angle       0.54602 (10590)
  SS BOND              : angle       0.00000 (    2)
  hydrogen bonds       : bond        0.03351 (  675)
  hydrogen bonds       : angle       4.12446 ( 2025)
  Misc. bond           : bond        0.00227 (   10)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 180
  time to evaluate  : 0.215 
Fit side-chains
REVERT: E   94 LEU cc_start: 0.8856 (tp) cc_final: 0.8625 (tp)
REVERT: E  115 LYS cc_start: 0.7792 (ttmm) cc_final: 0.7500 (mttp)
REVERT: G   54 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8002 (t)
REVERT: H   74 SER cc_start: 0.8873 (m) cc_final: 0.8636 (p)
REVERT: L   54 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.8004 (t)
REVERT: M   54 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.7965 (t)
REVERT: N   54 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8081 (t)
REVERT: N   60 VAL cc_start: 0.8494 (t) cc_final: 0.7961 (m)
  outliers start: 68
  outliers final: 37
  residues processed: 219
  average time/residue: 0.3409
  time to fit residues: 81.0207
Evaluate side-chains
  205 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 164
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   65 THR
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   93 SER
Chi-restraints excluded: chain F residue   97 VAL
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain H residue   93 SER
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   97 VAL
Chi-restraints excluded: chain J residue   97 VAL
Chi-restraints excluded: chain K residue   67 ILE
Chi-restraints excluded: chain K residue   93 SER
Chi-restraints excluded: chain K residue   97 VAL
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   67 ILE
Chi-restraints excluded: chain L residue   97 VAL
Chi-restraints excluded: chain M residue   54 THR
Chi-restraints excluded: chain M residue   86 SER
Chi-restraints excluded: chain M residue   93 SER
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain N residue   54 THR
Chi-restraints excluded: chain N residue   93 SER
Chi-restraints excluded: chain N residue   97 VAL
Chi-restraints excluded: chain O residue   67 ILE
Chi-restraints excluded: chain O residue   97 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   chunk 46 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 42 optimal weight:    7.9990
   chunk 83 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  62 ASN
L  62 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.123617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.114353 restraints weight = 10829.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 1.24
r_work: 0.3220 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7960  Z= 0.161
  Angle     :  0.660   9.316  10592  Z= 0.317
  Chirality :  0.037   0.104   1230
  Planarity :  0.006   0.088   1260
  Dihedral  : 12.498  53.637   1815
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  7.64 %
    Allowed  : 28.61 %
    Favored  : 63.75 %
  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:  3.77 (0.24), residues: 990
  helix:  2.94 (0.16), residues: 885
  sheet:  None (None), residues: 0
  loop : -1.95 (0.26), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.005   ARG O  91 
 PHE   0.010   0.001   PHE F  89 
 TRP   0.005   0.001   TRP H  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 7950)
  covalent geometry    : angle       0.66010 (10590)
  SS BOND              : angle       0.00000 (    2)
  hydrogen bonds       : bond        0.03512 (  675)
  hydrogen bonds       : angle       4.22080 ( 2025)
  Misc. bond           : bond        0.00643 (   10)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 171
  time to evaluate  : 0.296 
Fit side-chains
REVERT: D   65 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8209 (p)
REVERT: E   94 LEU cc_start: 0.8848 (tp) cc_final: 0.8628 (tp)
REVERT: G   54 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.7997 (t)
REVERT: H   74 SER cc_start: 0.8891 (m) cc_final: 0.8617 (p)
REVERT: L   54 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.8003 (t)
REVERT: N   54 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.8067 (t)
REVERT: N   60 VAL cc_start: 0.8494 (t) cc_final: 0.8096 (m)
  outliers start: 55
  outliers final: 44
  residues processed: 201
  average time/residue: 0.2455
  time to fit residues: 54.9687
Evaluate side-chains
  213 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 165
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   65 THR
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   93 SER
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   83 ILE
Chi-restraints excluded: chain G residue   93 SER
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain H residue   93 SER
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   97 VAL
Chi-restraints excluded: chain J residue   67 ILE
Chi-restraints excluded: chain J residue   97 VAL
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   67 ILE
Chi-restraints excluded: chain K residue   93 SER
Chi-restraints excluded: chain K residue   97 VAL
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   67 ILE
Chi-restraints excluded: chain L residue   97 VAL
Chi-restraints excluded: chain M residue   86 SER
Chi-restraints excluded: chain M residue   93 SER
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain N residue   54 THR
Chi-restraints excluded: chain N residue   93 SER
Chi-restraints excluded: chain N residue   97 VAL
Chi-restraints excluded: chain O residue   67 ILE
Chi-restraints excluded: chain O residue   97 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 21 optimal weight:    0.2980
   chunk 10 optimal weight:    0.9980
   chunk 42 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C  62 ASN
E  62 ASN
F  62 ASN
L  62 ASN
M  62 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.125132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.115828 restraints weight = 10780.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 1.25
r_work: 0.3241 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7960  Z= 0.141
  Angle     :  0.604   8.490  10592  Z= 0.295
  Chirality :  0.036   0.094   1230
  Planarity :  0.004   0.048   1260
  Dihedral  : 11.854  51.655   1815
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  7.36 %
    Allowed  : 30.14 %
    Favored  : 62.50 %
  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:  3.89 (0.24), residues: 990
  helix:  3.03 (0.16), residues: 885
  sheet:  None (None), residues: 0
  loop : -2.02 (0.26), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.003   ARG O  91 
 PHE   0.008   0.001   PHE O 112 
 TRP   0.004   0.001   TRP F  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 7950)
  covalent geometry    : angle       0.60405 (10590)
  SS BOND              : angle       0.00000 (    2)
  hydrogen bonds       : bond        0.03293 (  675)
  hydrogen bonds       : angle       4.10870 ( 2025)
  Misc. bond           : bond        0.00500 (   10)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 168
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A   65 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.8089 (p)
REVERT: D   65 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8211 (p)
REVERT: E   94 LEU cc_start: 0.8838 (tp) cc_final: 0.8616 (tp)
REVERT: G   54 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.7986 (t)
REVERT: H   74 SER cc_start: 0.8867 (m) cc_final: 0.8641 (p)
REVERT: J   59 MET cc_start: 0.8266 (mtt) cc_final: 0.8010 (mtp)
REVERT: N   54 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.8094 (t)
REVERT: N   60 VAL cc_start: 0.8482 (t) cc_final: 0.8093 (m)
  outliers start: 53
  outliers final: 40
  residues processed: 198
  average time/residue: 0.2486
  time to fit residues: 54.6332
Evaluate side-chains
  206 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 162
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   65 THR
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   97 VAL
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain H residue   93 SER
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   97 VAL
Chi-restraints excluded: chain J residue   67 ILE
Chi-restraints excluded: chain J residue   97 VAL
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   67 ILE
Chi-restraints excluded: chain K residue   93 SER
Chi-restraints excluded: chain K residue   97 VAL
Chi-restraints excluded: chain L residue   67 ILE
Chi-restraints excluded: chain L residue   97 VAL
Chi-restraints excluded: chain M residue   67 ILE
Chi-restraints excluded: chain M residue   86 SER
Chi-restraints excluded: chain M residue   93 SER
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain N residue   54 THR
Chi-restraints excluded: chain N residue   93 SER
Chi-restraints excluded: chain N residue   97 VAL
Chi-restraints excluded: chain O residue   67 ILE
Chi-restraints excluded: chain O residue   97 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 18 optimal weight:    8.9990
   chunk 24 optimal weight:    9.9990
   chunk 36 optimal weight:    6.9990
   chunk 9 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
L  62 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.120144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.111140 restraints weight = 10695.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 1.25
r_work: 0.3163 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.3344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   7960  Z= 0.203
  Angle     :  0.738  10.749  10592  Z= 0.349
  Chirality :  0.041   0.132   1230
  Planarity :  0.004   0.047   1260
  Dihedral  : 14.031  54.848   1815
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  8.06 %
    Allowed  : 29.86 %
    Favored  : 62.08 %
  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:  3.36 (0.24), residues: 990
  helix:  2.67 (0.16), residues: 885
  sheet:  None (None), residues: 0
  loop : -2.04 (0.26), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.003   ARG O  91 
 PHE   0.012   0.002   PHE B 108 
 TRP   0.008   0.002   TRP F  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 7950)
  covalent geometry    : angle       0.73765 (10590)
  SS BOND              : angle       0.00000 (    2)
  hydrogen bonds       : bond        0.04225 (  675)
  hydrogen bonds       : angle       4.49397 ( 2025)
  Misc. bond           : bond        0.00536 (   10)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 157
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
REVERT: D   65 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8182 (p)
REVERT: E   94 LEU cc_start: 0.8898 (tp) cc_final: 0.8667 (tp)
REVERT: G   54 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8034 (t)
REVERT: H   74 SER cc_start: 0.9014 (m) cc_final: 0.8696 (p)
REVERT: N   54 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8090 (t)
  outliers start: 58
  outliers final: 47
  residues processed: 198
  average time/residue: 0.2664
  time to fit residues: 58.1512
Evaluate side-chains
  201 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 151
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   65 THR
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   93 SER
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   83 ILE
Chi-restraints excluded: chain G residue   91 ARG
Chi-restraints excluded: chain G residue   93 SER
Chi-restraints excluded: chain G residue   97 VAL
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain H residue   93 SER
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   97 VAL
Chi-restraints excluded: chain J residue   67 ILE
Chi-restraints excluded: chain J residue   97 VAL
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   67 ILE
Chi-restraints excluded: chain K residue   93 SER
Chi-restraints excluded: chain K residue   97 VAL
Chi-restraints excluded: chain L residue   97 VAL
Chi-restraints excluded: chain M residue   54 THR
Chi-restraints excluded: chain M residue   67 ILE
Chi-restraints excluded: chain M residue   86 SER
Chi-restraints excluded: chain M residue   93 SER
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain N residue   54 THR
Chi-restraints excluded: chain N residue   86 SER
Chi-restraints excluded: chain N residue   93 SER
Chi-restraints excluded: chain N residue   97 VAL
Chi-restraints excluded: chain O residue   67 ILE
Chi-restraints excluded: chain O residue   97 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 50 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
L  62 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.123847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.114783 restraints weight = 10652.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 1.24
r_work: 0.3226 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.3425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7960  Z= 0.143
  Angle     :  0.615   8.846  10592  Z= 0.301
  Chirality :  0.036   0.122   1230
  Planarity :  0.004   0.042   1260
  Dihedral  : 12.411  52.599   1815
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 31.67 %
    Favored  : 61.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  3.71 (0.24), residues: 990
  helix:  2.91 (0.16), residues: 885
  sheet:  None (None), residues: 0
  loop : -2.09 (0.25), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.003   ARG O  91 
 PHE   0.008   0.001   PHE D 108 
 TRP   0.006   0.001   TRP H  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 7950)
  covalent geometry    : angle       0.61537 (10590)
  SS BOND              : angle       0.00000 (    2)
  hydrogen bonds       : bond        0.03370 (  675)
  hydrogen bonds       : angle       4.17384 ( 2025)
  Misc. bond           : bond        0.00422 (   10)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 165
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A   65 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8095 (p)
REVERT: D   65 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8235 (p)
REVERT: E   94 LEU cc_start: 0.8875 (tp) cc_final: 0.8640 (tp)
REVERT: G   54 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.7997 (t)
REVERT: H   74 SER cc_start: 0.8868 (m) cc_final: 0.8649 (p)
REVERT: N   54 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.8075 (t)
REVERT: N   60 VAL cc_start: 0.8497 (t) cc_final: 0.8100 (m)
  outliers start: 48
  outliers final: 42
  residues processed: 196
  average time/residue: 0.2755
  time to fit residues: 60.1495
Evaluate side-chains
  205 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 159
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   65 THR
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   93 SER
Chi-restraints excluded: chain F residue   97 VAL
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   83 ILE
Chi-restraints excluded: chain G residue   93 SER
Chi-restraints excluded: chain G residue   97 VAL
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain H residue   93 SER
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   97 VAL
Chi-restraints excluded: chain J residue   97 VAL
Chi-restraints excluded: chain K residue   67 ILE
Chi-restraints excluded: chain K residue   93 SER
Chi-restraints excluded: chain K residue   97 VAL
Chi-restraints excluded: chain L residue   97 VAL
Chi-restraints excluded: chain M residue   54 THR
Chi-restraints excluded: chain M residue   67 ILE
Chi-restraints excluded: chain M residue   86 SER
Chi-restraints excluded: chain M residue   93 SER
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain N residue   54 THR
Chi-restraints excluded: chain N residue   97 VAL
Chi-restraints excluded: chain O residue   67 ILE
Chi-restraints excluded: chain O residue   97 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 84 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 70 optimal weight:    4.9990
   chunk 87 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.7180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.123371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.114735 restraints weight = 10818.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 1.23
r_work: 0.3228 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.3480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7960  Z= 0.143
  Angle     :  0.617   8.878  10592  Z= 0.302
  Chirality :  0.036   0.139   1230
  Planarity :  0.003   0.037   1260
  Dihedral  : 12.166  52.148   1815
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Rotamer:
    Outliers :  6.39 %
    Allowed  : 31.67 %
    Favored  : 61.94 %
  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:  3.81 (0.24), residues: 990
  helix:  2.98 (0.16), residues: 885
  sheet:  None (None), residues: 0
  loop : -2.13 (0.25), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.002   ARG O  91 
 PHE   0.008   0.001   PHE D 108 
 TRP   0.005   0.001   TRP H  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 7950)
  covalent geometry    : angle       0.61716 (10590)
  SS BOND              : angle       0.00000 (    2)
  hydrogen bonds       : bond        0.03410 (  675)
  hydrogen bonds       : angle       4.15328 ( 2025)
  Misc. bond           : bond        0.00401 (   10)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 161
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A   65 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8153 (p)
REVERT: C  108 PHE cc_start: 0.8792 (m-80) cc_final: 0.8591 (m-80)
REVERT: D   65 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8228 (p)
REVERT: E   94 LEU cc_start: 0.8828 (tp) cc_final: 0.8624 (tp)
REVERT: G   54 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.7995 (t)
REVERT: H   74 SER cc_start: 0.8831 (m) cc_final: 0.8595 (p)
REVERT: J   59 MET cc_start: 0.8192 (mtt) cc_final: 0.7952 (mtp)
REVERT: N   60 VAL cc_start: 0.8499 (t) cc_final: 0.8107 (m)
  outliers start: 46
  outliers final: 42
  residues processed: 191
  average time/residue: 0.2858
  time to fit residues: 60.4808
Evaluate side-chains
  203 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 158
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   65 THR
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   93 SER
Chi-restraints excluded: chain F residue   97 VAL
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   83 ILE
Chi-restraints excluded: chain G residue   97 VAL
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain H residue   93 SER
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   97 VAL
Chi-restraints excluded: chain J residue   97 VAL
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   67 ILE
Chi-restraints excluded: chain K residue   93 SER
Chi-restraints excluded: chain K residue   97 VAL
Chi-restraints excluded: chain L residue   97 VAL
Chi-restraints excluded: chain M residue   54 THR
Chi-restraints excluded: chain M residue   67 ILE
Chi-restraints excluded: chain M residue   86 SER
Chi-restraints excluded: chain M residue   93 SER
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain N residue   97 VAL
Chi-restraints excluded: chain O residue   67 ILE
Chi-restraints excluded: chain O residue   97 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 82 optimal weight:    0.0470
   chunk 16 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0040
   chunk 75 optimal weight:    0.5980
   overall best weight:    0.4090

-------------------------------------------------------------------------------
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 = 0.3483 r_free = 0.3483 target = 0.126614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.118003 restraints weight = 10943.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.24
r_work: 0.3274 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   7960  Z= 0.124
  Angle     :  0.573   9.728  10592  Z= 0.282
  Chirality :  0.036   0.157   1230
  Planarity :  0.003   0.031   1260
  Dihedral  : 11.272  51.862   1815
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 32.64 %
    Favored  : 61.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  4.03 (0.24), residues: 990
  helix:  3.13 (0.16), residues: 885
  sheet:  None (None), residues: 0
  loop : -2.08 (0.26), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.002   ARG O  91 
 PHE   0.007   0.001   PHE N 112 
 TRP   0.004   0.001   TRP N  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7950)
  covalent geometry    : angle       0.57285 (10590)
  SS BOND              : angle       0.00000 (    2)
  hydrogen bonds       : bond        0.03051 (  675)
  hydrogen bonds       : angle       3.96559 ( 2025)
  Misc. bond           : bond        0.00333 (   10)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2118.47 seconds
wall clock time: 36 minutes 57.84 seconds (2217.84 seconds total)