Starting phenix.real_space_refine
on Tue Feb 11 17:50:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8oq5_17105/02_2025/8oq5_17105.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8oq5_17105/02_2025/8oq5_17105.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8oq5_17105/02_2025/8oq5_17105.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8oq5_17105/02_2025/8oq5_17105.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8oq5_17105/02_2025/8oq5_17105.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8oq5_17105/02_2025/8oq5_17105.cif"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    4128      2.51       5
     N    1044      2.21       5
     O    1320      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 96 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6528
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 544
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 544
          Classifications: {'peptide': 68}
          Link IDs: {'PTRANS': 1, 'TRANS': 66}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, M, L, N
  Time building chain proxies: 2.41, per 1000 atoms: 0.37
  Number of scatterers: 6528
  At special positions: 0
  Unit cell: (117.52, 91.52, 49.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1320      8.00
     N    1044      7.00
     C    4128      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.39
  Conformation dependent library (CDL) restraints added in 911.0 milliseconds
  

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1560

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 14 sheets defined
      0.0% alpha, 23.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7
      removed outlier: 6.681A  pdb=" N   ASP A   6 " --> pdb=" O   MET C   7 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ASP C   6 " --> pdb=" O   MET E   7 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ASP E   6 " --> pdb=" O   MET G   7 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ASP G   6 " --> pdb=" O   MET I   7 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ASP I   6 " --> pdb=" O   MET M   7 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11
      removed outlier: 6.252A  pdb=" N   LEU A  10 " --> pdb=" O   PHE C  11 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   LEU C  10 " --> pdb=" O   PHE E  11 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   LEU E  10 " --> pdb=" O   PHE G  11 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   LEU G  10 " --> pdb=" O   PHE I  11 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   LEU I  10 " --> pdb=" O   PHE M  11 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 21
      removed outlier: 6.092A  pdb=" N   THR A  19 " --> pdb=" O   GLU C  20 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   THR C  19 " --> pdb=" O   GLU E  20 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   THR E  19 " --> pdb=" O   GLU G  20 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   THR G  19 " --> pdb=" O   GLU I  20 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   THR I  19 " --> pdb=" O   GLU M  20 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 25 through 26
    Processing sheet with id=AA5, first strand: chain 'A' and resid 46 through 49
      removed outlier: 8.747A  pdb=" N   GLU A  47 " --> pdb=" O   GLN C  48 " (cutoff:3.500A)
      removed outlier: 8.747A  pdb=" N   GLU C  47 " --> pdb=" O   GLN E  48 " (cutoff:3.500A)
      removed outlier: 8.747A  pdb=" N   GLU E  47 " --> pdb=" O   GLN G  48 " (cutoff:3.500A)
      removed outlier: 8.748A  pdb=" N   GLU G  47 " --> pdb=" O   GLN I  48 " (cutoff:3.500A)
      removed outlier: 8.747A  pdb=" N   GLU I  47 " --> pdb=" O   GLN M  48 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 52 through 54
    Processing sheet with id=AA7, first strand: chain 'A' and resid 60 through 64
    Processing sheet with id=AA8, first strand: chain 'B' and resid 5 through 7
      removed outlier: 6.681A  pdb=" N   ASP B   6 " --> pdb=" O   MET D   7 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ASP D   6 " --> pdb=" O   MET F   7 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ASP F   6 " --> pdb=" O   MET H   7 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ASP H   6 " --> pdb=" O   MET L   7 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ASP L   6 " --> pdb=" O   MET N   7 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 11
      removed outlier: 6.251A  pdb=" N   LEU B  10 " --> pdb=" O   PHE D  11 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   LEU D  10 " --> pdb=" O   PHE F  11 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   LEU F  10 " --> pdb=" O   PHE H  11 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   LEU H  10 " --> pdb=" O   PHE L  11 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   LEU L  10 " --> pdb=" O   PHE N  11 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 18 through 21
      removed outlier: 6.093A  pdb=" N   THR B  19 " --> pdb=" O   GLU D  20 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   THR D  19 " --> pdb=" O   GLU F  20 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   THR F  19 " --> pdb=" O   GLU H  20 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   THR H  19 " --> pdb=" O   GLU L  20 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   THR L  19 " --> pdb=" O   GLU N  20 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 25 through 26
    Processing sheet with id=AB3, first strand: chain 'B' and resid 46 through 49
      removed outlier: 8.746A  pdb=" N   GLU B  47 " --> pdb=" O   GLN D  48 " (cutoff:3.500A)
      removed outlier: 8.748A  pdb=" N   GLU D  47 " --> pdb=" O   GLN F  48 " (cutoff:3.500A)
      removed outlier: 8.746A  pdb=" N   GLU F  47 " --> pdb=" O   GLN H  48 " (cutoff:3.500A)
      removed outlier: 8.746A  pdb=" N   GLU H  47 " --> pdb=" O   GLN L  48 " (cutoff:3.500A)
      removed outlier: 8.748A  pdb=" N   GLU L  47 " --> pdb=" O   GLN N  48 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 52 through 54
    Processing sheet with id=AB5, first strand: chain 'B' and resid 60 through 64

    70 hydrogen bonds defined for protein.
    210 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: 1.56

  Time building geometry restraints manager: 1.66 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1116
        1.29 -     1.42: 1659
        1.42 -     1.56: 3764
        1.56 -     1.69: 25
        1.69 -     1.82: 72
  Bond restraints: 6636
  Sorted by residual:
  bond pdb=" C   TYR I  21 "
       pdb=" O   TYR I  21 "
    ideal  model  delta    sigma   weight residual
    1.233  1.165  0.069 1.17e-02 7.31e+03 3.45e+01
  bond pdb=" C   TYR N  21 "
       pdb=" O   TYR N  21 "
    ideal  model  delta    sigma   weight residual
    1.233  1.165  0.069 1.17e-02 7.31e+03 3.45e+01
  bond pdb=" C   TYR F  21 "
       pdb=" O   TYR F  21 "
    ideal  model  delta    sigma   weight residual
    1.233  1.165  0.069 1.17e-02 7.31e+03 3.44e+01
  bond pdb=" C   TYR H  21 "
       pdb=" O   TYR H  21 "
    ideal  model  delta    sigma   weight residual
    1.233  1.165  0.069 1.17e-02 7.31e+03 3.44e+01
  bond pdb=" C   TYR C  21 "
       pdb=" O   TYR C  21 "
    ideal  model  delta    sigma   weight residual
    1.233  1.165  0.069 1.17e-02 7.31e+03 3.43e+01
  ... (remaining 6631 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 5714
        1.72 -     3.43: 2295
        3.43 -     5.15: 706
        5.15 -     6.86: 177
        6.86 -     8.58: 12
  Bond angle restraints: 8904
  Sorted by residual:
  angle pdb=" N   ILE H  34 "
        pdb=" CA  ILE H  34 "
        pdb=" C   ILE H  34 "
      ideal   model   delta    sigma   weight residual
     107.37  115.95   -8.58 1.48e+00 4.57e-01 3.36e+01
  angle pdb=" N   ILE G  34 "
        pdb=" CA  ILE G  34 "
        pdb=" C   ILE G  34 "
      ideal   model   delta    sigma   weight residual
     107.37  115.95   -8.58 1.48e+00 4.57e-01 3.36e+01
  angle pdb=" N   ILE I  34 "
        pdb=" CA  ILE I  34 "
        pdb=" C   ILE I  34 "
      ideal   model   delta    sigma   weight residual
     107.37  115.95   -8.58 1.48e+00 4.57e-01 3.36e+01
  angle pdb=" N   ILE D  34 "
        pdb=" CA  ILE D  34 "
        pdb=" C   ILE D  34 "
      ideal   model   delta    sigma   weight residual
     107.37  115.94   -8.57 1.48e+00 4.57e-01 3.35e+01
  angle pdb=" N   ILE N  34 "
        pdb=" CA  ILE N  34 "
        pdb=" C   ILE N  34 "
      ideal   model   delta    sigma   weight residual
     107.37  115.93   -8.56 1.48e+00 4.57e-01 3.35e+01
  ... (remaining 8899 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.61: 3252
        9.61 -    19.22: 384
       19.22 -    28.84: 204
       28.84 -    38.45: 96
       38.45 -    48.06: 84
  Dihedral angle restraints: 4020
    sinusoidal: 1620
      harmonic: 2400
  Sorted by residual:
  dihedral pdb=" CA  ALA L  40 "
           pdb=" C   ALA L  40 "
           pdb=" N   TYR L  41 "
           pdb=" CA  TYR L  41 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.37  -27.63     0      5.00e+00 4.00e-02 3.05e+01
  dihedral pdb=" CA  ALA B  40 "
           pdb=" C   ALA B  40 "
           pdb=" N   TYR B  41 "
           pdb=" CA  TYR B  41 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.37  -27.63     0      5.00e+00 4.00e-02 3.05e+01
  dihedral pdb=" CA  ALA C  40 "
           pdb=" C   ALA C  40 "
           pdb=" N   TYR C  41 "
           pdb=" CA  TYR C  41 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.38  -27.62     0      5.00e+00 4.00e-02 3.05e+01
  ... (remaining 4017 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 312
       0.047 -    0.094: 288
       0.094 -    0.141: 237
       0.141 -    0.187: 87
       0.187 -    0.234: 60
  Chirality restraints: 984
  Sorted by residual:
  chirality pdb=" CA  VAL D  61 "
            pdb=" N   VAL D  61 "
            pdb=" C   VAL D  61 "
            pdb=" CB  VAL D  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.68   -0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" CA  VAL L  61 "
            pdb=" N   VAL L  61 "
            pdb=" C   VAL L  61 "
            pdb=" CB  VAL L  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CA  VAL F  61 "
            pdb=" N   VAL F  61 "
            pdb=" C   VAL F  61 "
            pdb=" CB  VAL F  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.23 2.00e-01 2.50e+01 1.36e+00
  ... (remaining 981 not shown)

  Planarity restraints: 1140
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN I  16 "   -0.016 2.00e-02 2.50e+03   3.32e-02 1.10e+01
        pdb=" C   GLN I  16 "    0.057 2.00e-02 2.50e+03
        pdb=" O   GLN I  16 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   SER I  17 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU N  67 "    0.016 2.00e-02 2.50e+03   3.32e-02 1.10e+01
        pdb=" C   LEU N  67 "   -0.057 2.00e-02 2.50e+03
        pdb=" O   LEU N  67 "    0.021 2.00e-02 2.50e+03
        pdb=" N   MET N  68 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN G  16 "   -0.016 2.00e-02 2.50e+03   3.31e-02 1.09e+01
        pdb=" C   GLN G  16 "    0.057 2.00e-02 2.50e+03
        pdb=" O   GLN G  16 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   SER G  17 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1137 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     2.99: 3421
        2.99 -     3.47: 5989
        3.47 -     3.95: 11952
        3.95 -     4.42: 13817
        4.42 -     4.90: 25285
  Nonbonded interactions: 60464
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  66 "
            pdb=" O   PHE D  63 "
     model   vdw
     2.517 3.040
  nonbonded pdb=" OG  SER H  66 "
            pdb=" O   PHE L  63 "
     model   vdw
     2.517 3.040
  nonbonded pdb=" OG  SER C  66 "
            pdb=" O   PHE E  63 "
     model   vdw
     2.518 3.040
  nonbonded pdb=" OG  SER E  66 "
            pdb=" O   PHE G  63 "
     model   vdw
     2.518 3.040
  nonbonded pdb=" OG  SER F  66 "
            pdb=" O   PHE H  63 "
     model   vdw
     2.518 3.040
  ... (remaining 60459 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'M'
  selection = chain 'L'
  selection = chain 'N'
}

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:             2.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     16.410
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
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      :  0.015   0.069   6636  Z= 1.005
  Angle     :  2.049   8.581   8904  Z= 1.453
  Chirality :  0.100   0.234    984
  Planarity :  0.011   0.033   1140
  Dihedral  : 14.254  48.059   2460
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 1.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.16 (0.16), residues: 792
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.93 (0.12), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B  46 
 PHE   0.016   0.005   PHE I  11 
 TYR   0.031   0.006   TYR L  21 
 ARG   0.001   0.000   ARG M  54 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 313
  time to evaluate  : 0.775 
Fit side-chains
REVERT: N   50 THR cc_start: 0.8229 (p) cc_final: 0.8028 (p)
  outliers start: 0
  outliers final: 3
  residues processed: 313
  average time/residue: 1.2282
  time to fit residues: 401.9362
Evaluate side-chains
  242 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 239
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    6 ASP
Chi-restraints excluded: chain F residue    6 ASP
Chi-restraints excluded: chain N residue    6 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    0.2980
   chunk 54 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0870
   chunk 29 optimal weight:    0.7980
   chunk 56 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
A   5 GLN
** B  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   5 GLN
** C  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F   5 GLN
F  35 GLN
** F  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   5 GLN
H  13 GLN
H  35 GLN
** H  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I   5 GLN
I  35 GLN
** I  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   5 GLN
L  35 GLN
N   5 GLN
N  35 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.130516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.120812 restraints weight = 7522.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 1.48
r_work: 0.3698 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3590 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.4262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6636  Z= 0.219
  Angle     :  0.658   8.540   8904  Z= 0.331
  Chirality :  0.043   0.122    984
  Planarity :  0.004   0.046   1140
  Dihedral  :  6.355  23.263    858
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 18.31 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.30 (0.20), residues: 792
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.27 (0.15), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E  46 
 PHE   0.009   0.001   PHE E  11 
 TYR   0.016   0.002   TYR G  21 
 ARG   0.004   0.002   ARG L  54 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 270
  time to evaluate  : 0.824 
Fit side-chains
REVERT: A   69 ASN cc_start: 0.8323 (t0) cc_final: 0.8097 (t0)
REVERT: B   28 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.7995 (mptt)
REVERT: G   30 LYS cc_start: 0.8756 (mtpp) cc_final: 0.8503 (mtpt)
REVERT: I   71 GLU cc_start: 0.7030 (tt0) cc_final: 0.6666 (mt-10)
REVERT: M   30 LYS cc_start: 0.8625 (mtpp) cc_final: 0.8399 (mtpt)
REVERT: N   53 VAL cc_start: 0.9007 (p) cc_final: 0.8803 (p)
  outliers start: 26
  outliers final: 4
  residues processed: 284
  average time/residue: 1.1815
  time to fit residues: 351.7030
Evaluate side-chains
  244 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 239
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain B residue   28 LYS
Chi-restraints excluded: chain C residue   32 SER
Chi-restraints excluded: chain L residue   32 SER
Chi-restraints excluded: chain L residue   52 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0050
   chunk 47 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0770
   chunk 24 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.4552

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   5 GLN
** B  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.122754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.113809 restraints weight = 7510.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3725 rms_B_bonded: 1.40
r_work: 0.3609 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3501 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.5255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6636  Z= 0.211
  Angle     :  0.674   8.719   8904  Z= 0.331
  Chirality :  0.044   0.130    984
  Planarity :  0.004   0.044   1140
  Dihedral  :  6.040  20.542    852
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 19.81 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.06 (0.21), residues: 792
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.09 (0.16), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C  46 
 PHE   0.008   0.001   PHE I  42 
 TYR   0.014   0.002   TYR G  21 
 ARG   0.005   0.002   ARG I  54 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 261
  time to evaluate  : 0.706 
Fit side-chains
REVERT: B   41 TYR cc_start: 0.8724 (m-80) cc_final: 0.8464 (m-80)
REVERT: C   33 GLU cc_start: 0.7904 (tt0) cc_final: 0.7559 (tm-30)
REVERT: E   24 ASP cc_start: 0.8319 (m-30) cc_final: 0.8017 (m-30)
REVERT: G   71 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7457 (mt-10)
REVERT: M   68 MET cc_start: 0.8776 (ttp) cc_final: 0.8535 (ttm)
  outliers start: 20
  outliers final: 7
  residues processed: 268
  average time/residue: 1.3199
  time to fit residues: 370.1190
Evaluate side-chains
  256 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 249
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain E residue   12 THR
Chi-restraints excluded: chain H residue   12 THR
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain L residue   52 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 48 optimal weight:    0.4980
   chunk 39 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  13 GLN
** C  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  13 GLN
** F  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.117054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.108156 restraints weight = 7552.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 1.40
r_work: 0.3534 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.3424 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.5672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6636  Z= 0.295
  Angle     :  0.701   6.852   8904  Z= 0.351
  Chirality :  0.044   0.131    984
  Planarity :  0.005   0.052   1140
  Dihedral  :  6.287  21.950    852
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 21.99 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.73 (0.22), residues: 792
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.83 (0.17), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  46 
 PHE   0.009   0.001   PHE N  42 
 TYR   0.013   0.002   TYR E  21 
 ARG   0.004   0.002   ARG I  54 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 251
  time to evaluate  : 0.836 
Fit side-chains
REVERT: B   41 TYR cc_start: 0.8669 (m-80) cc_final: 0.8411 (m-80)
REVERT: C   33 GLU cc_start: 0.7961 (tt0) cc_final: 0.7640 (tm-30)
REVERT: E   24 ASP cc_start: 0.8573 (m-30) cc_final: 0.8224 (m-30)
REVERT: H    9 SER cc_start: 0.8857 (p) cc_final: 0.8641 (m)
REVERT: L   50 THR cc_start: 0.8868 (m) cc_final: 0.8507 (p)
REVERT: M   18 MET cc_start: 0.9076 (ttm) cc_final: 0.8820 (ttp)
  outliers start: 22
  outliers final: 10
  residues processed: 263
  average time/residue: 1.3217
  time to fit residues: 363.0952
Evaluate side-chains
  256 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 246
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain E residue   52 LEU
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   52 LEU
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain L residue   52 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 18 optimal weight:    0.2980
   chunk 29 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  13 GLN
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.117656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.108698 restraints weight = 7497.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 1.38
r_work: 0.3546 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3436 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.5841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6636  Z= 0.276
  Angle     :  0.690   7.290   8904  Z= 0.345
  Chirality :  0.044   0.129    984
  Planarity :  0.004   0.047   1140
  Dihedral  :  6.131  21.595    852
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 24.59 %
    Favored  : 72.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.57 (0.22), residues: 792
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.71 (0.17), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D  46 
 PHE   0.008   0.001   PHE B  11 
 TYR   0.012   0.002   TYR H  41 
 ARG   0.004   0.001   ARG I  54 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 248
  time to evaluate  : 0.783 
Fit side-chains
REVERT: C   33 GLU cc_start: 0.7948 (tt0) cc_final: 0.7616 (tm-30)
REVERT: E   24 ASP cc_start: 0.8581 (m-30) cc_final: 0.8304 (m-30)
REVERT: G   24 ASP cc_start: 0.8832 (m-30) cc_final: 0.8594 (m-30)
REVERT: H    9 SER cc_start: 0.8887 (p) cc_final: 0.8658 (m)
REVERT: M   18 MET cc_start: 0.9084 (ttm) cc_final: 0.8833 (ttp)
  outliers start: 20
  outliers final: 11
  residues processed: 257
  average time/residue: 1.2961
  time to fit residues: 347.8804
Evaluate side-chains
  256 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 245
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain E residue   52 LEU
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   52 LEU
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue   70 LEU
Chi-restraints excluded: chain N residue   28 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 24 optimal weight:    0.0670
   chunk 48 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
A  37 GLN
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  37 GLN
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  37 GLN
** F  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  37 GLN
** H  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  37 GLN
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.117405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.108441 restraints weight = 7430.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 1.37
r_work: 0.3547 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3438 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.5990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6636  Z= 0.274
  Angle     :  0.687   7.011   8904  Z= 0.344
  Chirality :  0.044   0.127    984
  Planarity :  0.005   0.048   1140
  Dihedral  :  6.042  21.180    852
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 25.55 %
    Favored  : 71.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.53 (0.22), residues: 792
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.68 (0.17), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D  46 
 PHE   0.009   0.001   PHE B  11 
 TYR   0.014   0.002   TYR H  41 
 ARG   0.004   0.001   ARG I  54 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 245
  time to evaluate  : 0.827 
Fit side-chains
REVERT: C   33 GLU cc_start: 0.7956 (tt0) cc_final: 0.7621 (tm-30)
REVERT: E   24 ASP cc_start: 0.8637 (m-30) cc_final: 0.8372 (m-30)
REVERT: F   67 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8116 (tp)
REVERT: G   24 ASP cc_start: 0.8882 (m-30) cc_final: 0.8643 (m-30)
REVERT: H    9 SER cc_start: 0.8886 (p) cc_final: 0.8655 (m)
REVERT: M   18 MET cc_start: 0.9095 (ttm) cc_final: 0.8837 (ttp)
REVERT: N   41 TYR cc_start: 0.8425 (m-80) cc_final: 0.8184 (m-80)
  outliers start: 23
  outliers final: 12
  residues processed: 259
  average time/residue: 1.2951
  time to fit residues: 350.5402
Evaluate side-chains
  256 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 243
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain E residue   52 LEU
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain F residue   12 THR
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   52 LEU
Chi-restraints excluded: chain F residue   67 LEU
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue   70 LEU
Chi-restraints excluded: chain L residue   70 LEU
Chi-restraints excluded: chain N residue   28 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
** B  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  69 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.114637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.105717 restraints weight = 7378.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 1.39
r_work: 0.3499 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.6059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   6636  Z= 0.372
  Angle     :  0.752   7.754   8904  Z= 0.378
  Chirality :  0.046   0.137    984
  Planarity :  0.005   0.062   1140
  Dihedral  :  6.366  22.556    852
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 26.09 %
    Favored  : 71.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.54 (0.21), residues: 792
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.16), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D  46 
 PHE   0.009   0.002   PHE B  11 
 TYR   0.013   0.002   TYR H  41 
 ARG   0.004   0.001   ARG H  54 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 244
  time to evaluate  : 0.749 
Fit side-chains
REVERT: B   33 GLU cc_start: 0.8070 (tt0) cc_final: 0.7785 (tt0)
REVERT: C   33 GLU cc_start: 0.7971 (tt0) cc_final: 0.7641 (tm-30)
REVERT: E   24 ASP cc_start: 0.8718 (m-30) cc_final: 0.8464 (m-30)
REVERT: I   71 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7606 (mt-10)
REVERT: M   18 MET cc_start: 0.9098 (ttm) cc_final: 0.8850 (ttp)
REVERT: N   41 TYR cc_start: 0.8492 (m-80) cc_final: 0.8177 (m-80)
  outliers start: 21
  outliers final: 11
  residues processed: 258
  average time/residue: 1.2825
  time to fit residues: 345.6356
Evaluate side-chains
  251 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 240
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain D residue   44 LYS
Chi-restraints excluded: chain E residue   12 THR
Chi-restraints excluded: chain E residue   52 LEU
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain F residue   12 THR
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue   70 LEU
Chi-restraints excluded: chain N residue   28 LYS
Chi-restraints excluded: chain N residue   70 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** B  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.115544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.106518 restraints weight = 7456.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 1.38
r_work: 0.3506 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3394 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.6103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6636  Z= 0.343
  Angle     :  0.741   7.903   8904  Z= 0.372
  Chirality :  0.045   0.135    984
  Planarity :  0.005   0.058   1140
  Dihedral  :  6.293  22.382    852
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 27.46 %
    Favored  : 70.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.60 (0.21), residues: 792
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.73 (0.16), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  46 
 PHE   0.008   0.001   PHE E  11 
 TYR   0.014   0.002   TYR M  41 
 ARG   0.003   0.001   ARG M  54 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 243
  time to evaluate  : 0.781 
Fit side-chains
REVERT: B   33 GLU cc_start: 0.8046 (tt0) cc_final: 0.7766 (tt0)
REVERT: C   33 GLU cc_start: 0.7918 (tt0) cc_final: 0.7601 (tm-30)
REVERT: E   24 ASP cc_start: 0.8670 (m-30) cc_final: 0.8375 (m-30)
REVERT: I   71 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7571 (mt-10)
REVERT: M   18 MET cc_start: 0.9104 (ttm) cc_final: 0.8862 (ttp)
REVERT: N   41 TYR cc_start: 0.8471 (m-80) cc_final: 0.8147 (m-80)
REVERT: N   71 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7932 (mt-10)
  outliers start: 16
  outliers final: 10
  residues processed: 253
  average time/residue: 1.3029
  time to fit residues: 344.0467
Evaluate side-chains
  251 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 241
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain E residue   12 THR
Chi-restraints excluded: chain E residue   52 LEU
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain F residue   12 THR
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue   70 LEU
Chi-restraints excluded: chain N residue   28 LYS
Chi-restraints excluded: chain N residue   70 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.116606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.107410 restraints weight = 7492.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 1.42
r_work: 0.3523 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.3409 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.6121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6636  Z= 0.292
  Angle     :  0.712   7.159   8904  Z= 0.357
  Chirality :  0.045   0.132    984
  Planarity :  0.005   0.051   1140
  Dihedral  :  6.129  21.359    852
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 27.73 %
    Favored  : 70.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.64 (0.21), residues: 792
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.16), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  46 
 PHE   0.009   0.001   PHE B  11 
 TYR   0.015   0.002   TYR M  41 
 ARG   0.004   0.001   ARG I  54 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 242
  time to evaluate  : 0.839 
Fit side-chains
REVERT: B   33 GLU cc_start: 0.8076 (tt0) cc_final: 0.7764 (tt0)
REVERT: C   33 GLU cc_start: 0.7927 (tt0) cc_final: 0.7600 (tm-30)
REVERT: E   24 ASP cc_start: 0.8634 (m-30) cc_final: 0.8322 (m-30)
REVERT: I   71 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7466 (mt-10)
REVERT: L   28 LYS cc_start: 0.8903 (mttt) cc_final: 0.8702 (mttp)
REVERT: M   18 MET cc_start: 0.9105 (ttm) cc_final: 0.8883 (ttp)
REVERT: N   41 TYR cc_start: 0.8465 (m-80) cc_final: 0.8192 (m-80)
  outliers start: 14
  outliers final: 10
  residues processed: 249
  average time/residue: 1.2847
  time to fit residues: 334.0896
Evaluate side-chains
  247 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 237
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain E residue   12 THR
Chi-restraints excluded: chain E residue   52 LEU
Chi-restraints excluded: chain F residue   12 THR
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue   28 LYS
Chi-restraints excluded: chain I residue   70 LEU
Chi-restraints excluded: chain N residue   28 LYS
Chi-restraints excluded: chain N residue   70 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 55 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 62 optimal weight:    0.1980
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.116699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.107608 restraints weight = 7510.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 1.39
r_work: 0.3528 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3416 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.6136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6636  Z= 0.286
  Angle     :  0.717   6.985   8904  Z= 0.357
  Chirality :  0.044   0.131    984
  Planarity :  0.005   0.051   1140
  Dihedral  :  6.084  21.219    852
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 27.60 %
    Favored  : 70.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.69 (0.21), residues: 792
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.80 (0.16), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  46 
 PHE   0.009   0.001   PHE B  11 
 TYR   0.015   0.002   TYR M  41 
 ARG   0.004   0.001   ARG I  54 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 237
  time to evaluate  : 0.865 
Fit side-chains
REVERT: B   33 GLU cc_start: 0.8065 (tt0) cc_final: 0.7748 (tt0)
REVERT: C   33 GLU cc_start: 0.7922 (tt0) cc_final: 0.7589 (tm-30)
REVERT: E   24 ASP cc_start: 0.8621 (m-30) cc_final: 0.8321 (m-30)
REVERT: I   71 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7441 (mt-10)
REVERT: L   28 LYS cc_start: 0.8901 (mttt) cc_final: 0.8698 (mttp)
REVERT: M   18 MET cc_start: 0.9098 (ttm) cc_final: 0.8876 (ttp)
REVERT: N   41 TYR cc_start: 0.8432 (m-80) cc_final: 0.8145 (m-80)
  outliers start: 13
  outliers final: 9
  residues processed: 243
  average time/residue: 1.2927
  time to fit residues: 328.1490
Evaluate side-chains
  244 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 235
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain E residue   12 THR
Chi-restraints excluded: chain E residue   52 LEU
Chi-restraints excluded: chain F residue   12 THR
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue   28 LYS
Chi-restraints excluded: chain I residue   70 LEU
Chi-restraints excluded: chain N residue   28 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 59 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 55 optimal weight:    0.5980
   chunk 66 optimal weight:    0.4980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** B  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.117408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.108272 restraints weight = 7574.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 1.40
r_work: 0.3540 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3428 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.6152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6636  Z= 0.263
  Angle     :  0.698   6.842   8904  Z= 0.350
  Chirality :  0.044   0.131    984
  Planarity :  0.005   0.050   1140
  Dihedral  :  5.984  20.776    852
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 28.01 %
    Favored  : 70.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.70 (0.21), residues: 792
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.82 (0.16), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D  46 
 PHE   0.009   0.001   PHE B  11 
 TYR   0.014   0.002   TYR M  41 
 ARG   0.004   0.001   ARG I  54 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6929.96 seconds
wall clock time: 122 minutes 31.28 seconds (7351.28 seconds total)