Starting phenix.real_space_refine
on Wed Sep 17 02:59:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8az0_15728/09_2025/8az0_15728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8az0_15728/09_2025/8az0_15728.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8az0_15728/09_2025/8az0_15728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8az0_15728/09_2025/8az0_15728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8az0_15728/09_2025/8az0_15728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8az0_15728/09_2025/8az0_15728.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    1350      2.51       5
     N     420      2.21       5
     O     410      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2180
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 217
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 28, 210
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
      Conformer: "B"
        Number of residues, atoms: 28, 210
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
          bond proxies already assigned to first conformer: 204
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J
  Time building chain proxies: 0.53, per 1000 atoms: 0.24
  Number of scatterers: 2180
  At special positions: 0
  Unit cell: (63, 73.08, 45.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     410      8.00
     N     420      7.00
     C    1350      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=10, symmetry=0
  Number of additional bonds: simple=10, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.21
  Conformation dependent library (CDL) restraints added in 93.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  520

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 53.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 22
      removed outlier: 6.969A  pdb=" N   ASN A  21 " --> pdb=" O   GLY C  20 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   ASN C  22 " --> pdb=" O   ASN A  21 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   ASN C  21 " --> pdb=" O   GLY E  20 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   ASN E  22 " --> pdb=" O   ASN C  21 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   ASN E  21 " --> pdb=" O   GLY G  20 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   ASN G  22 " --> pdb=" O   ASN E  21 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   ASN G  21 " --> pdb=" O   GLY I  20 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ASN I  22 " --> pdb=" O   ASN G  21 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26
    Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 32
      removed outlier: 6.413A  pdb=" N   SER A  29 " --> pdb=" O   THR C  30 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   VAL C  32 " --> pdb=" O   SER A  29 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   ASN A  31 " --> pdb=" O   VAL C  32 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   SER C  29 " --> pdb=" O   THR E  30 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   VAL E  32 " --> pdb=" O   SER C  29 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   ASN C  31 " --> pdb=" O   VAL E  32 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   SER E  29 " --> pdb=" O   THR G  30 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   VAL G  32 " --> pdb=" O   SER E  29 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   ASN E  31 " --> pdb=" O   VAL G  32 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   SER G  29 " --> pdb=" O   THR I  30 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   VAL I  32 " --> pdb=" O   SER G  29 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   ASN G  31 " --> pdb=" O   VAL I  32 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 22
      removed outlier: 6.991A  pdb=" N   ASN B  21 " --> pdb=" O   GLY D  20 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   ASN D  22 " --> pdb=" O   ASN B  21 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ASN D  21 " --> pdb=" O   GLY F  20 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   ASN F  22 " --> pdb=" O   ASN D  21 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   ASN F  21 " --> pdb=" O   GLY H  20 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   ASN H  22 " --> pdb=" O   ASN F  21 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   ASN H  21 " --> pdb=" O   GLY J  20 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   ASN J  22 " --> pdb=" O   ASN H  21 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 26
    Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32
      removed outlier: 6.397A  pdb=" N   SER B  29 " --> pdb=" O   THR D  30 " (cutoff:3.500A)
      removed outlier: 7.996A  pdb=" N   VAL D  32 " --> pdb=" O   SER B  29 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   ASN B  31 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   SER D  29 " --> pdb=" O   THR F  30 " (cutoff:3.500A)
      removed outlier: 8.046A  pdb=" N   VAL F  32 " --> pdb=" O   SER D  29 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   ASN D  31 " --> pdb=" O   VAL F  32 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   SER F  29 " --> pdb=" O   THR H  30 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   VAL H  32 " --> pdb=" O   SER F  29 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   ASN F  31 " --> pdb=" O   VAL H  32 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   SER H  29 " --> pdb=" O   THR J  30 " (cutoff:3.500A)
      removed outlier: 7.990A  pdb=" N   VAL J  32 " --> pdb=" O   SER H  29 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   ASN H  31 " --> pdb=" O   VAL J  32 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    80 hydrogen bonds defined for protein.
    232 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.18

  Time building geometry restraints manager: 0.24 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 340
        1.29 -     1.35: 400
        1.35 -     1.41: 270
        1.41 -     1.48: 306
        1.48 -     1.54: 904
  Bond restraints: 2220
  Sorted by residual:
  bond pdb=" N   THR G  36 "
       pdb=" CA  THR G  36 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.26e-02 6.30e+03 5.76e+00
  bond pdb=" N   THR J  36 "
       pdb=" CA  THR J  36 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.26e-02 6.30e+03 5.73e+00
  bond pdb=" N   THR B  36 "
       pdb=" CA  THR B  36 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.26e-02 6.30e+03 5.68e+00
  bond pdb=" N   THR H  36 "
       pdb=" CA  THR H  36 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.26e-02 6.30e+03 5.62e+00
  bond pdb=" N   THR E  36 "
       pdb=" CA  THR E  36 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.26e-02 6.30e+03 5.62e+00
  ... (remaining 2215 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.92: 2678
        0.92 -     1.84: 200
        1.84 -     2.76: 102
        2.76 -     3.68: 30
        3.68 -     4.60: 10
  Bond angle restraints: 3020
  Sorted by residual:
  angle pdb=" CA  SER B  34 "
        pdb=" C   SER B  34 "
        pdb=" O   SER B  34 "
      ideal   model   delta    sigma   weight residual
     121.28  117.78    3.50 1.19e+00 7.06e-01 8.64e+00
  angle pdb=" CA  SER A  34 "
        pdb=" C   SER A  34 "
        pdb=" O   SER A  34 "
      ideal   model   delta    sigma   weight residual
     121.28  117.80    3.48 1.19e+00 7.06e-01 8.57e+00
  angle pdb=" CA  SER J  34 "
        pdb=" C   SER J  34 "
        pdb=" O   SER J  34 "
      ideal   model   delta    sigma   weight residual
     121.28  117.81    3.47 1.19e+00 7.06e-01 8.49e+00
  angle pdb=" CA  SER G  34 "
        pdb=" C   SER G  34 "
        pdb=" O   SER G  34 "
      ideal   model   delta    sigma   weight residual
     121.28  117.81    3.47 1.19e+00 7.06e-01 8.49e+00
  angle pdb=" CA  SER D  34 "
        pdb=" C   SER D  34 "
        pdb=" O   SER D  34 "
      ideal   model   delta    sigma   weight residual
     121.28  117.83    3.45 1.19e+00 7.06e-01 8.42e+00
  ... (remaining 3015 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     5.96: 1022
        5.96 -    11.92: 128
       11.92 -    17.87: 72
       17.87 -    23.83: 28
       23.83 -    29.79: 10
  Dihedral angle restraints: 1260
    sinusoidal: 440
      harmonic: 820
  Sorted by residual:
  dihedral pdb=" N   HIS J  18 "
           pdb=" CA AHIS J  18 "
           pdb=" CB AHIS J  18 "
           pdb=" CG AHIS J  18 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -83.02   23.02     3      1.50e+01 4.44e-03 3.05e+00
  dihedral pdb=" N   HIS E  18 "
           pdb=" CA AHIS E  18 "
           pdb=" CB AHIS E  18 "
           pdb=" CG AHIS E  18 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -83.00   23.00     3      1.50e+01 4.44e-03 3.04e+00
  dihedral pdb=" N   HIS D  18 "
           pdb=" CA AHIS D  18 "
           pdb=" CB AHIS D  18 "
           pdb=" CG AHIS D  18 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -82.99   22.99     3      1.50e+01 4.44e-03 3.04e+00
  ... (remaining 1257 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 127
       0.027 -    0.054: 149
       0.054 -    0.080: 24
       0.080 -    0.107: 17
       0.107 -    0.134: 23
  Chirality restraints: 340
  Sorted by residual:
  chirality pdb=" CA  ILE F  26 "
            pdb=" N   ILE F  26 "
            pdb=" C   ILE F  26 "
            pdb=" CB  ILE F  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.48e-01
  chirality pdb=" CA  ILE B  26 "
            pdb=" N   ILE B  26 "
            pdb=" C   ILE B  26 "
            pdb=" CB  ILE B  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.28e-01
  chirality pdb=" CA  ILE I  26 "
            pdb=" N   ILE I  26 "
            pdb=" C   ILE I  26 "
            pdb=" CB  ILE I  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.24e-01
  ... (remaining 337 not shown)

  Planarity restraints: 400
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D  32 "   -0.015 2.00e-02 2.50e+03   2.96e-02 8.77e+00
        pdb=" C   VAL D  32 "    0.051 2.00e-02 2.50e+03
        pdb=" O   VAL D  32 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLY D  33 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  32 "   -0.015 2.00e-02 2.50e+03   2.96e-02 8.76e+00
        pdb=" C   VAL B  32 "    0.051 2.00e-02 2.50e+03
        pdb=" O   VAL B  32 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLY B  33 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL I  32 "    0.014 2.00e-02 2.50e+03   2.94e-02 8.67e+00
        pdb=" C   VAL I  32 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   VAL I  32 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLY I  33 "    0.017 2.00e-02 2.50e+03
  ... (remaining 397 not shown)

  Histogram of nonbonded interaction distances:
        2.61 -     3.07: 1471
        3.07 -     3.53: 1993
        3.53 -     3.98: 3105
        3.98 -     4.44: 3846
        4.44 -     4.90: 7332
  Nonbonded interactions: 17747
  Sorted by model distance:
  nonbonded pdb=" O   SER B  34 "
            pdb=" OG  SER B  34 "
     model   vdw
     2.611 3.040
  nonbonded pdb=" O   SER J  34 "
            pdb=" OG  SER J  34 "
     model   vdw
     2.612 3.040
  nonbonded pdb=" O   SER F  34 "
            pdb=" OG  SER F  34 "
     model   vdw
     2.612 3.040
  nonbonded pdb=" O   SER H  34 "
            pdb=" OG  SER H  34 "
     model   vdw
     2.612 3.040
  nonbonded pdb=" O   SER D  34 "
            pdb=" OG  SER D  34 "
     model   vdw
     2.612 3.040
  ... (remaining 17742 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.97
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:             1.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.260
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.096   2230  Z= 0.729
  Angle     :  0.742   4.601   3020  Z= 0.491
  Chirality :  0.051   0.134    340
  Planarity :  0.005   0.030    400
  Dihedral  :  8.049  29.789    740
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 0.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  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: -4.46 (0.25), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.39 (0.19), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E  11 
 TYR   0.003   0.001   TYR E  37 
 PHE   0.005   0.001   PHE B  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00582 ( 2220)
  covalent geometry    : angle       0.74198 ( 3020)
  hydrogen bonds       : bond        0.16649 (   80)
  hydrogen bonds       : angle       8.05042 (  232)
  Misc. bond           : bond        0.09481 (   10)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.080 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0312
  time to fit residues: 0.6624
Evaluate side-chains
  13 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   chunk 1 optimal weight:    8.9990
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 15 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A  18 HIS    A
A  21 ASN
B  18 HIS    A
B  21 ASN
C  18 HIS    A
C  21 ASN
D  18 HIS    A
D  21 ASN
E  18 HIS    A
E  21 ASN
F  18 HIS    A
F  21 ASN
G  18 HIS    A
G  21 ASN
H  18 HIS    A
H  21 ASN
I  18 HIS    A
I  21 ASN
J  18 HIS    A
J  21 ASN

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.101015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.078927 restraints weight = 14137.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 4.64
r_work: 0.3123 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3098
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3093
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.1443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.012   2230  Z= 0.115
  Angle     :  0.383   2.726   3020  Z= 0.225
  Chirality :  0.043   0.124    340
  Planarity :  0.002   0.005    400
  Dihedral  :  3.577   7.192    310
  Min Nonbonded Distance : 2.687

Molprobity Statistics.
  All-atom Clashscore : 0.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  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: -4.46 (0.28), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.39 (0.21), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG J  11 
 TYR   0.002   0.000   TYR G  37 
 PHE   0.007   0.001   PHE H  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 2220)
  covalent geometry    : angle       0.38313 ( 3020)
  hydrogen bonds       : bond        0.03459 (   80)
  hydrogen bonds       : angle       4.85196 (  232)
  Misc. bond           : bond        0.00026 (   10)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.082 
Fit side-chains
REVERT: G   19 SER cc_start: 0.8713 (t) cc_final: 0.8331 (p)
REVERT: H   19 SER cc_start: 0.8646 (t) cc_final: 0.8311 (p)
REVERT: I   19 SER cc_start: 0.8922 (t) cc_final: 0.8704 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0276
  time to fit residues: 1.0082
Evaluate side-chains
  24 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 19 optimal weight:    8.9990
   chunk 15 optimal weight:    3.9990
   chunk 3 optimal weight:    0.3980
   chunk 11 optimal weight:    8.9990
   chunk 10 optimal weight:    9.9990
   chunk 0 optimal weight:    8.9990
   chunk 7 optimal weight:    0.7980
   chunk 9 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    3.8386

-------------------------------------------------------------------------------
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 = 0.3518 r_free = 0.3518 target = 0.097933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.075402 restraints weight = 19583.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 5.59
r_work: 0.3024 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3026
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3026 r_free = 0.3026    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3026 r_free = 0.3026    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3026
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.023   2230  Z= 0.298
  Angle     :  0.565   6.875   3020  Z= 0.315
  Chirality :  0.046   0.126    340
  Planarity :  0.003   0.009    400
  Dihedral  :  4.276   9.053    310
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 0.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  4.58 %
    Favored  : 95.00 %
  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: -4.89 (0.26), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.72 (0.20), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  11 
 TYR   0.004   0.001   TYR A  37 
 PHE   0.016   0.003   PHE H  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00652 ( 2220)
  covalent geometry    : angle       0.56463 ( 3020)
  hydrogen bonds       : bond        0.04592 (   80)
  hydrogen bonds       : angle       4.83825 (  232)
  Misc. bond           : bond        0.00149 (   10)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.078 
Fit side-chains
REVERT: I   19 SER cc_start: 0.8956 (t) cc_final: 0.8697 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 26
  average time/residue: 0.0265
  time to fit residues: 1.0410
Evaluate side-chains
  26 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   28 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 0 optimal weight:    7.9990
   chunk 6 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 4 optimal weight:    5.9990
   chunk 14 optimal weight:    8.9990
   chunk 8 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.3600 r_free = 0.3600 target = 0.104687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.080595 restraints weight = 20860.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 5.71
r_work: 0.2991 rms_B_bonded: 5.21 restraints_weight: 2.0000
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2994
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2994 r_free = 0.2994    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2994 r_free = 0.2994    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2994
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.027   2230  Z= 0.334
  Angle     :  0.608   6.467   3020  Z= 0.337
  Chirality :  0.047   0.125    340
  Planarity :  0.003   0.008    400
  Dihedral  :  4.377   9.731    310
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.38 %
    Favored  : 89.62 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  :  6.25 %
    Favored  : 91.67 %
  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: -5.09 (0.26), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.87 (0.20), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG D  11 
 TYR   0.006   0.001   TYR I  37 
 PHE   0.018   0.004   PHE G  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00735 ( 2220)
  covalent geometry    : angle       0.60812 ( 3020)
  hydrogen bonds       : bond        0.04775 (   80)
  hydrogen bonds       : angle       4.79991 (  232)
  Misc. bond           : bond        0.00102 (   10)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.114 
Fit side-chains
REVERT: H   35 ASN cc_start: 0.8975 (m-40) cc_final: 0.8744 (m-40)
REVERT: I   11 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7514 (mtm-85)
  outliers start: 5
  outliers final: 5
  residues processed: 38
  average time/residue: 0.0391
  time to fit residues: 1.9440
Evaluate side-chains
  37 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 SER
Chi-restraints excluded: chain F residue   28 SER
Chi-restraints excluded: chain G residue   28 SER
Chi-restraints excluded: chain H residue   28 SER
Chi-restraints excluded: chain I residue   28 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN
I  35 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.109873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.084668 restraints weight = 22314.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 5.94
r_work: 0.3035 rms_B_bonded: 5.58 restraints_weight: 2.0000
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3033
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3033 r_free = 0.3033    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3033 r_free = 0.3033    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3033
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2230  Z= 0.143
  Angle     :  0.458   5.976   3020  Z= 0.249
  Chirality :  0.043   0.124    340
  Planarity :  0.002   0.005    400
  Dihedral  :  3.616   7.772    310
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 0.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.92 %
    Favored  : 87.08 %
  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: -4.94 (0.29), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.76 (0.22), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B  11 
 TYR   0.002   0.001   TYR G  37 
 PHE   0.009   0.002   PHE H  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 2220)
  covalent geometry    : angle       0.45782 ( 3020)
  hydrogen bonds       : bond        0.02962 (   80)
  hydrogen bonds       : angle       4.60365 (  232)
  Misc. bond           : bond        0.00045 (   10)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.129 
Fit side-chains
REVERT: G   19 SER cc_start: 0.8716 (t) cc_final: 0.8277 (p)
REVERT: H   19 SER cc_start: 0.8616 (t) cc_final: 0.8270 (p)
REVERT: I   11 ARG cc_start: 0.8047 (mtt180) cc_final: 0.7597 (mtm-85)
REVERT: J   11 ARG cc_start: 0.8300 (mtt180) cc_final: 0.7837 (ttm110)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0586
  time to fit residues: 2.0964
Evaluate side-chains
  27 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 14 optimal weight:    9.9990
   chunk 18 optimal weight:    2.9990
   chunk 19 optimal weight:    0.4980
   chunk 8 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0770
   chunk 4 optimal weight:    5.9990
   overall best weight:    0.7140

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

Flipped N/Q/H residues before XYZ refinement:
H  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.113045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.087934 restraints weight = 19726.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 5.68
r_work: 0.3117 rms_B_bonded: 5.53 restraints_weight: 2.0000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3110
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3110
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.010   2230  Z= 0.068
  Angle     :  0.390   5.112   3020  Z= 0.214
  Chirality :  0.042   0.122    340
  Planarity :  0.001   0.005    400
  Dihedral  :  3.187   7.341    310
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 0.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 12.50 %
    Favored  : 87.08 %
  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: -4.81 (0.30), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.66 (0.23), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A  11 
 TYR   0.002   0.000   TYR G  37 
 PHE   0.005   0.001   PHE F  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00144 ( 2220)
  covalent geometry    : angle       0.39024 ( 3020)
  hydrogen bonds       : bond        0.01778 (   80)
  hydrogen bonds       : angle       4.26064 (  232)
  Misc. bond           : bond        0.00017 (   10)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.051 
Fit side-chains
REVERT: G   19 SER cc_start: 0.8516 (t) cc_final: 0.8251 (p)
REVERT: H   19 SER cc_start: 0.8474 (t) cc_final: 0.8230 (p)
REVERT: I   11 ARG cc_start: 0.8044 (mtt180) cc_final: 0.7613 (mtm-85)
REVERT: J   11 ARG cc_start: 0.8322 (mtt180) cc_final: 0.7787 (ttm110)
  outliers start: 1
  outliers final: 1
  residues processed: 28
  average time/residue: 0.0520
  time to fit residues: 1.7889
Evaluate side-chains
  28 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   28 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:   10.0000
   chunk 15 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 17 optimal weight:    7.9990
   chunk 6 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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 = 0.3653 r_free = 0.3653 target = 0.107803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.083027 restraints weight = 20056.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 5.64
r_work: 0.3012 rms_B_bonded: 5.30 restraints_weight: 2.0000
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3015
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3014 r_free = 0.3014    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3014
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.024   2230  Z= 0.266
  Angle     :  0.534   5.038   3020  Z= 0.297
  Chirality :  0.044   0.125    340
  Planarity :  0.003   0.007    400
  Dihedral  :  3.967   9.140    310
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 0.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.62 %
    Favored  : 85.38 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 11.67 %
    Favored  : 85.83 %
  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: -4.87 (0.30), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.70 (0.23), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG D  11 
 TYR   0.004   0.001   TYR I  37 
 PHE   0.015   0.003   PHE G  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00583 ( 2220)
  covalent geometry    : angle       0.53443 ( 3020)
  hydrogen bonds       : bond        0.03998 (   80)
  hydrogen bonds       : angle       4.67486 (  232)
  Misc. bond           : bond        0.00081 (   10)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.106 
Fit side-chains
REVERT: G   19 SER cc_start: 0.8654 (t) cc_final: 0.8176 (p)
REVERT: I   11 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7550 (mtm-85)
REVERT: J   11 ARG cc_start: 0.8366 (mtt180) cc_final: 0.7845 (ttm110)
  outliers start: 6
  outliers final: 6
  residues processed: 32
  average time/residue: 0.0542
  time to fit residues: 2.1698
Evaluate side-chains
  37 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 SER
Chi-restraints excluded: chain B residue   28 SER
Chi-restraints excluded: chain C residue   28 SER
Chi-restraints excluded: chain G residue   28 SER
Chi-restraints excluded: chain H residue   28 SER
Chi-restraints excluded: chain I residue   28 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 5 optimal weight:    0.4980
   chunk 12 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    3.2988

-------------------------------------------------------------------------------
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 = 0.3657 r_free = 0.3657 target = 0.108120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.083299 restraints weight = 22364.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 5.79
r_work: 0.3017 rms_B_bonded: 5.39 restraints_weight: 2.0000
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3015
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3015
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.024   2230  Z= 0.256
  Angle     :  0.540   5.216   3020  Z= 0.298
  Chirality :  0.044   0.124    340
  Planarity :  0.003   0.006    400
  Dihedral  :  4.010   8.867    310
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 0.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.62 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 12.50 %
    Favored  : 85.00 %
  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: -4.80 (0.32), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.65 (0.24), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG G  11 
 TYR   0.009   0.001   TYR G  37 
 PHE   0.014   0.003   PHE G  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 ( 2220)
  covalent geometry    : angle       0.54019 ( 3020)
  hydrogen bonds       : bond        0.03994 (   80)
  hydrogen bonds       : angle       4.76852 (  232)
  Misc. bond           : bond        0.00081 (   10)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.061 
Fit side-chains
REVERT: G   19 SER cc_start: 0.8716 (t) cc_final: 0.8214 (p)
REVERT: I   11 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7543 (mtm-85)
REVERT: J   11 ARG cc_start: 0.8320 (mtt180) cc_final: 0.7798 (ttm110)
  outliers start: 6
  outliers final: 6
  residues processed: 34
  average time/residue: 0.0484
  time to fit residues: 2.0410
Evaluate side-chains
  39 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 SER
Chi-restraints excluded: chain B residue   28 SER
Chi-restraints excluded: chain C residue   28 SER
Chi-restraints excluded: chain F residue   28 SER
Chi-restraints excluded: chain G residue   28 SER
Chi-restraints excluded: chain I residue   28 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 13 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 4 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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 = 0.3674 r_free = 0.3674 target = 0.109391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.084558 restraints weight = 19728.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 5.62
r_work: 0.3046 rms_B_bonded: 5.34 restraints_weight: 2.0000
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3044 r_free = 0.3044    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3044
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   2230  Z= 0.139
  Angle     :  0.452   4.961   3020  Z= 0.247
  Chirality :  0.042   0.124    340
  Planarity :  0.002   0.005    400
  Dihedral  :  3.607   7.877    310
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 0.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 12.92 %
    Favored  : 84.58 %
  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: -4.69 (0.33), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.57 (0.25), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG G  11 
 TYR   0.007   0.001   TYR G  37 
 PHE   0.009   0.002   PHE F  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 2220)
  covalent geometry    : angle       0.45178 ( 3020)
  hydrogen bonds       : bond        0.02859 (   80)
  hydrogen bonds       : angle       4.64235 (  232)
  Misc. bond           : bond        0.00044 (   10)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.084 
Fit side-chains
REVERT: G   19 SER cc_start: 0.8583 (t) cc_final: 0.8190 (p)
REVERT: H   19 SER cc_start: 0.8541 (t) cc_final: 0.8177 (p)
REVERT: I   11 ARG cc_start: 0.7978 (mtt180) cc_final: 0.7525 (mtm-85)
REVERT: J   11 ARG cc_start: 0.8295 (mtt180) cc_final: 0.7771 (ttm110)
  outliers start: 6
  outliers final: 6
  residues processed: 34
  average time/residue: 0.0390
  time to fit residues: 1.6759
Evaluate side-chains
  39 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 SER
Chi-restraints excluded: chain C residue   28 SER
Chi-restraints excluded: chain F residue   28 SER
Chi-restraints excluded: chain G residue   28 SER
Chi-restraints excluded: chain H residue   28 SER
Chi-restraints excluded: chain I residue   28 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 17 optimal weight:    0.2980
   chunk 9 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 4 optimal weight:    4.9990
   overall best weight:    1.0186

-------------------------------------------------------------------------------
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 = 0.3705 r_free = 0.3705 target = 0.111466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.086837 restraints weight = 18522.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 5.54
r_work: 0.3080 rms_B_bonded: 5.36 restraints_weight: 2.0000
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.2860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   2230  Z= 0.088
  Angle     :  0.416   5.304   3020  Z= 0.225
  Chirality :  0.042   0.123    340
  Planarity :  0.001   0.004    400
  Dihedral  :  3.361   7.187    310
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 0.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 14.58 %
    Favored  : 84.17 %
  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: -4.57 (0.34), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.47 (0.26), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B  11 
 TYR   0.007   0.001   TYR G  37 
 PHE   0.006   0.001   PHE F  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00196 ( 2220)
  covalent geometry    : angle       0.41611 ( 3020)
  hydrogen bonds       : bond        0.02095 (   80)
  hydrogen bonds       : angle       4.46288 (  232)
  Misc. bond           : bond        0.00027 (   10)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.078 
Fit side-chains
REVERT: G   19 SER cc_start: 0.8498 (t) cc_final: 0.8182 (p)
REVERT: H   19 SER cc_start: 0.8430 (t) cc_final: 0.8136 (p)
REVERT: I   11 ARG cc_start: 0.7999 (mtt180) cc_final: 0.7590 (mtm-85)
REVERT: J   11 ARG cc_start: 0.8290 (mtt180) cc_final: 0.7760 (ttm110)
  outliers start: 3
  outliers final: 3
  residues processed: 32
  average time/residue: 0.0520
  time to fit residues: 2.0728
Evaluate side-chains
  34 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   28 SER
Chi-restraints excluded: chain H residue   28 SER
Chi-restraints excluded: chain I residue   28 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 18 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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 = 0.3680 r_free = 0.3680 target = 0.109883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.085554 restraints weight = 15880.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 5.25
r_work: 0.3066 rms_B_bonded: 5.08 restraints_weight: 2.0000
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3067
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3067 r_free = 0.3067    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3067 r_free = 0.3067    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3067
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   2230  Z= 0.148
  Angle     :  0.454   4.769   3020  Z= 0.249
  Chirality :  0.042   0.124    340
  Planarity :  0.002   0.005    400
  Dihedral  :  3.589   7.710    310
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 0.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 14.17 %
    Favored  : 84.17 %
  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: -4.62 (0.34), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.51 (0.26), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG G  11 
 TYR   0.007   0.001   TYR G  37 
 PHE   0.010   0.002   PHE F  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 2220)
  covalent geometry    : angle       0.45403 ( 3020)
  hydrogen bonds       : bond        0.02902 (   80)
  hydrogen bonds       : angle       4.50276 (  232)
  Misc. bond           : bond        0.00048 (   10)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 777.59 seconds
wall clock time: 14 minutes 46.78 seconds (886.78 seconds total)