Starting phenix.real_space_refine
on Mon Feb 10 19:38:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v4a_31705/02_2025/7v4a_31705.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v4a_31705/02_2025/7v4a_31705.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v4a_31705/02_2025/7v4a_31705.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v4a_31705/02_2025/7v4a_31705.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v4a_31705/02_2025/7v4a_31705.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v4a_31705/02_2025/7v4a_31705.cif"
  }
  resolution = 3.2
  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=   0.003
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    1029      2.51       5
     N     294      2.21       5
     O     330      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 1653
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 551
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 551
          Classifications: {'peptide': 80}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'TRANS': 79}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 1.12, per 1000 atoms: 0.68
  Number of scatterers: 1653
  At special positions: 0
  Unit cell: (67.84, 86.92, 34.98, 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     330      8.00
     N     294      7.00
     C    1029      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: 1.09
  Conformation dependent library (CDL) restraints added in 223.3 milliseconds
  

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  402

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 37.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19
      removed outlier: 6.702A  pdb=" N   ALA A  18 " --> pdb=" O   ALA B  19 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ALA B  18 " --> pdb=" O   ALA C  19 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 23
      removed outlier: 6.620A  pdb=" N   THR A  22 " --> pdb=" O   LYS B  23 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   THR B  22 " --> pdb=" O   LYS C  23 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 37 through 43
    Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55
      removed outlier: 6.604A  pdb=" N   VAL A  48 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   GLY B  51 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 8.517A  pdb=" N   HIS A  50 " --> pdb=" O   GLY B  51 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ALA B  53 " --> pdb=" O   HIS A  50 " (cutoff:3.500A)
      removed outlier: 9.073A  pdb=" N   VAL A  52 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 10.379A  pdb=" N   VAL B  55 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 8.877A  pdb=" N   THR A  54 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL B  48 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 8.023A  pdb=" N   GLY C  51 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 8.505A  pdb=" N   HIS B  50 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ALA C  53 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
      removed outlier: 9.051A  pdb=" N   VAL B  52 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 10.367A  pdb=" N   VAL C  55 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 8.870A  pdb=" N   THR B  54 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 63 through 66
      removed outlier: 6.744A  pdb=" N   VAL A  63 " --> pdb=" O   THR B  64 " (cutoff:3.500A)
      removed outlier: 8.185A  pdb=" N   VAL B  66 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   ASN A  65 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   VAL B  63 " --> pdb=" O   THR C  64 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   VAL C  66 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ASN B  65 " --> pdb=" O   VAL C  66 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 72
      removed outlier: 6.729A  pdb=" N   ALA A  69 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
      removed outlier: 7.819A  pdb=" N   THR B  72 " --> pdb=" O   ALA A  69 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   VAL A  71 " --> pdb=" O   THR B  72 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   ALA B  69 " --> pdb=" O   VAL C  70 " (cutoff:3.500A)
      removed outlier: 7.783A  pdb=" N   THR C  72 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   VAL B  71 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 75 through 79
    Processing sheet with id=AA8, first strand: chain 'A' and resid 86 through 91

    30 hydrogen bonds defined for protein.
    90 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: 0.37

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 291
        1.29 -     1.36: 258
        1.36 -     1.42: 51
        1.42 -     1.48: 270
        1.48 -     1.55: 786
  Bond restraints: 1656
  Sorted by residual:
  bond pdb=" CA  GLU C  83 "
       pdb=" CB  GLU C  83 "
    ideal  model  delta    sigma   weight residual
    1.533  1.549 -0.016 1.63e-02 3.76e+03 9.11e-01
  bond pdb=" CA  GLU B  83 "
       pdb=" CB  GLU B  83 "
    ideal  model  delta    sigma   weight residual
    1.533  1.548 -0.015 1.63e-02 3.76e+03 8.64e-01
  bond pdb=" CA  GLU A  83 "
       pdb=" CB  GLU A  83 "
    ideal  model  delta    sigma   weight residual
    1.533  1.547 -0.014 1.63e-02 3.76e+03 7.79e-01
  bond pdb=" CB  ASP C  98 "
       pdb=" CG  ASP C  98 "
    ideal  model  delta    sigma   weight residual
    1.516  1.502  0.014 2.50e-02 1.60e+03 3.35e-01
  bond pdb=" CA  GLN C  62 "
       pdb=" C   GLN C  62 "
    ideal  model  delta    sigma   weight residual
    1.530  1.524  0.006 1.08e-02 8.57e+03 3.27e-01
  ... (remaining 1651 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.89: 2047
        0.89 -     1.79: 155
        1.79 -     2.68: 12
        2.68 -     3.58: 6
        3.58 -     4.47: 3
  Bond angle restraints: 2223
  Sorted by residual:
  angle pdb=" CA  GLU A  83 "
        pdb=" CB  GLU A  83 "
        pdb=" CG  GLU A  83 "
      ideal   model   delta    sigma   weight residual
     114.10  118.57   -4.47 2.00e+00 2.50e-01 5.00e+00
  angle pdb=" CA  GLU B  83 "
        pdb=" CB  GLU B  83 "
        pdb=" CG  GLU B  83 "
      ideal   model   delta    sigma   weight residual
     114.10  118.57   -4.47 2.00e+00 2.50e-01 4.99e+00
  angle pdb=" CA  GLU C  83 "
        pdb=" CB  GLU C  83 "
        pdb=" CG  GLU C  83 "
      ideal   model   delta    sigma   weight residual
     114.10  118.55   -4.45 2.00e+00 2.50e-01 4.94e+00
  angle pdb=" C   GLU C  83 "
        pdb=" CA  GLU C  83 "
        pdb=" CB  GLU C  83 "
      ideal   model   delta    sigma   weight residual
     110.44  107.32    3.12 1.68e+00 3.54e-01 3.46e+00
  angle pdb=" C   GLU A  83 "
        pdb=" CA  GLU A  83 "
        pdb=" CB  GLU A  83 "
      ideal   model   delta    sigma   weight residual
     110.44  107.33    3.11 1.68e+00 3.54e-01 3.44e+00
  ... (remaining 2218 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 912
       17.48 -    34.95: 45
       34.95 -    52.42: 15
       52.42 -    69.89: 3
       69.89 -    87.37: 3
  Dihedral angle restraints: 978
    sinusoidal: 339
      harmonic: 639
  Sorted by residual:
  dihedral pdb=" CB  GLU B  20 "
           pdb=" CG  GLU B  20 "
           pdb=" CD  GLU B  20 "
           pdb=" OE1 GLU B  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.37  -87.37     1      3.00e+01 1.11e-03 1.02e+01
  dihedral pdb=" CB  GLU C  20 "
           pdb=" CG  GLU C  20 "
           pdb=" CD  GLU C  20 "
           pdb=" OE1 GLU C  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.36  -87.36     1      3.00e+01 1.11e-03 1.02e+01
  dihedral pdb=" CB  GLU A  20 "
           pdb=" CG  GLU A  20 "
           pdb=" CD  GLU A  20 "
           pdb=" OE1 GLU A  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.32  -87.32     1      3.00e+01 1.11e-03 1.02e+01
  ... (remaining 975 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 134
       0.026 -    0.052: 81
       0.052 -    0.077: 22
       0.077 -    0.103: 25
       0.103 -    0.128: 23
  Chirality restraints: 285
  Sorted by residual:
  chirality pdb=" CA  VAL C  15 "
            pdb=" N   VAL C  15 "
            pdb=" C   VAL C  15 "
            pdb=" CB  VAL C  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.11e-01
  chirality pdb=" CA  VAL A  15 "
            pdb=" N   VAL A  15 "
            pdb=" C   VAL A  15 "
            pdb=" CB  VAL A  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.10e-01
  chirality pdb=" CA  ILE B  88 "
            pdb=" N   ILE B  88 "
            pdb=" C   ILE B  88 "
            pdb=" CB  ILE B  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.97e-01
  ... (remaining 282 not shown)

  Planarity restraints: 276
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C  83 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.08e+00
        pdb=" CD  GLU C  83 "   -0.030 2.00e-02 2.50e+03
        pdb=" OE1 GLU C  83 "    0.011 2.00e-02 2.50e+03
        pdb=" OE2 GLU C  83 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A  83 "    0.008 2.00e-02 2.50e+03   1.73e-02 2.99e+00
        pdb=" CD  GLU A  83 "   -0.030 2.00e-02 2.50e+03
        pdb=" OE1 GLU A  83 "    0.011 2.00e-02 2.50e+03
        pdb=" OE2 GLU A  83 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B  83 "    0.008 2.00e-02 2.50e+03   1.73e-02 2.99e+00
        pdb=" CD  GLU B  83 "   -0.030 2.00e-02 2.50e+03
        pdb=" OE1 GLU B  83 "    0.011 2.00e-02 2.50e+03
        pdb=" OE2 GLU B  83 "    0.011 2.00e-02 2.50e+03
  ... (remaining 273 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.92: 667
        2.92 -     3.41: 1441
        3.41 -     3.91: 2358
        3.91 -     4.40: 2385
        4.40 -     4.90: 5063
  Nonbonded interactions: 11914
  Sorted by model distance:
  nonbonded pdb=" N   ASP A  98 "
            pdb=" OD1 ASP A  98 "
     model   vdw
     2.423 3.120
  nonbonded pdb=" N   ASP C  98 "
            pdb=" OD1 ASP C  98 "
     model   vdw
     2.423 3.120
  nonbonded pdb=" N   ASP B  98 "
            pdb=" OD1 ASP B  98 "
     model   vdw
     2.424 3.120
  nonbonded pdb=" N   GLU A  83 "
            pdb=" OE1 GLU A  83 "
     model   vdw
     2.444 3.120
  nonbonded pdb=" N   GLU B  83 "
            pdb=" OE1 GLU B  83 "
     model   vdw
     2.445 3.120
  ... (remaining 11909 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.080
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     10.010
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   1656  Z= 0.152
  Angle     :  0.518   4.471   2223  Z= 0.314
  Chirality :  0.052   0.128    285
  Planarity :  0.002   0.018    276
  Dihedral  : 14.278  87.365    576
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  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: -5.80 (0.26), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.41 (0.20), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS C  50 
 PHE   0.001   0.000   PHE C  94 
 TYR   0.005   0.001   TYR A  39 

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.9387 (tttm) cc_final: 0.9148 (tttt)
REVERT: A   58 LYS cc_start: 0.8216 (ttmm) cc_final: 0.7898 (tptp)
REVERT: A   60 LYS cc_start: 0.8623 (mmtp) cc_final: 0.7923 (mttp)
REVERT: A   80 LYS cc_start: 0.8612 (mttp) cc_final: 0.7335 (pttp)
REVERT: A   97 LYS cc_start: 0.8710 (ptmm) cc_final: 0.7552 (tppt)
REVERT: B   20 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8182 (mt-10)
REVERT: B   46 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6970 (tm-30)
REVERT: B   58 LYS cc_start: 0.8439 (ttmm) cc_final: 0.8094 (tppt)
REVERT: B   59 THR cc_start: 0.9172 (m) cc_final: 0.8882 (t)
REVERT: B   60 LYS cc_start: 0.8228 (mmtp) cc_final: 0.7959 (mmtm)
REVERT: C   23 LYS cc_start: 0.8875 (mtpt) cc_final: 0.8426 (mmmt)
REVERT: C   45 LYS cc_start: 0.8431 (tttp) cc_final: 0.8186 (ttpt)
REVERT: C   46 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7086 (tm-30)
REVERT: C   58 LYS cc_start: 0.8656 (ttmm) cc_final: 0.7995 (pttm)
REVERT: C   60 LYS cc_start: 0.8282 (mmtp) cc_final: 0.7750 (mttm)
REVERT: C   61 GLU cc_start: 0.8071 (mp0) cc_final: 0.7596 (mp0)
REVERT: C   80 LYS cc_start: 0.8339 (mttp) cc_final: 0.7649 (mmtt)
REVERT: C   83 GLU cc_start: 0.5457 (mp0) cc_final: 0.4921 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.2347
  time to fit residues: 18.1719
Evaluate side-chains
  58 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 9 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 14 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.134606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.106807 restraints weight = 2287.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 3.32
r_work: 0.3478 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   1656  Z= 0.438
  Angle     :  0.608   3.796   2223  Z= 0.360
  Chirality :  0.051   0.132    285
  Planarity :  0.003   0.011    276
  Dihedral  :  5.660  19.677    237
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.60 %
    Favored  : 86.40 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 21.21 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -5.34 (0.30), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.06 (0.23), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B  50 
 PHE   0.005   0.001   PHE B  94 
 TYR   0.015   0.002   TYR B  39 

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8828 (mm110) cc_final: 0.8300 (mp10)
REVERT: A   58 LYS cc_start: 0.8577 (ttmm) cc_final: 0.8178 (tptp)
REVERT: A   60 LYS cc_start: 0.8703 (mmtp) cc_final: 0.8263 (mttp)
REVERT: A   80 LYS cc_start: 0.8927 (mttp) cc_final: 0.7579 (pttp)
REVERT: A   97 LYS cc_start: 0.8712 (ptmm) cc_final: 0.7308 (tppt)
REVERT: B   20 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8598 (mt-10)
REVERT: B   46 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7287 (tm-30)
REVERT: C   23 LYS cc_start: 0.9127 (mtpt) cc_final: 0.8506 (mmmt)
REVERT: C   45 LYS cc_start: 0.8441 (tttp) cc_final: 0.8199 (ttpt)
REVERT: C   46 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7446 (tm-30)
REVERT: C   58 LYS cc_start: 0.8646 (ttmm) cc_final: 0.7933 (pttm)
REVERT: C   60 LYS cc_start: 0.8598 (mmtp) cc_final: 0.6563 (pttm)
REVERT: C   61 GLU cc_start: 0.8498 (mp0) cc_final: 0.8020 (mp0)
REVERT: C   80 LYS cc_start: 0.8818 (mttp) cc_final: 0.8086 (mmtt)
  outliers start: 8
  outliers final: 6
  residues processed: 63
  average time/residue: 0.1787
  time to fit residues: 12.3441
Evaluate side-chains
  62 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue   95 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 18 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 9 optimal weight:    9.9990
   chunk 12 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
B  24 GLN
C  24 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.141295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.112423 restraints weight = 2280.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 3.41
r_work: 0.3570 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   1656  Z= 0.211
  Angle     :  0.482   2.709   2223  Z= 0.285
  Chirality :  0.049   0.127    285
  Planarity :  0.002   0.007    276
  Dihedral  :  4.749  15.542    237
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.53 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 19.39 %
    Favored  : 75.15 %
  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: -5.07 (0.33), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.86 (0.25), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS B  50 
 PHE   0.002   0.001   PHE B  94 
 TYR   0.010   0.002   TYR B  39 

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8059 (tptp)
REVERT: A   60 LYS cc_start: 0.8541 (mmtp) cc_final: 0.8112 (mttp)
REVERT: A   61 GLU cc_start: 0.8451 (mp0) cc_final: 0.8152 (mp0)
REVERT: A   97 LYS cc_start: 0.8594 (ptmm) cc_final: 0.7232 (tppt)
REVERT: B   46 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7148 (tm-30)
REVERT: C   23 LYS cc_start: 0.9129 (mtpt) cc_final: 0.8505 (mmmt)
REVERT: C   46 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7644 (tm-30)
REVERT: C   58 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8028 (pttm)
REVERT: C   60 LYS cc_start: 0.8570 (mmtp) cc_final: 0.8120 (mmtm)
REVERT: C   61 GLU cc_start: 0.8418 (mp0) cc_final: 0.7960 (mp0)
REVERT: C   80 LYS cc_start: 0.8780 (mttp) cc_final: 0.7941 (mmtt)
  outliers start: 9
  outliers final: 5
  residues processed: 60
  average time/residue: 0.1695
  time to fit residues: 11.2199
Evaluate side-chains
  57 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   95 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 0 optimal weight:    8.9990
   chunk 20 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 3 optimal weight:    0.6980
   chunk 10 optimal weight:    8.9990
   chunk 18 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   overall best weight:    2.3186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.137152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.108277 restraints weight = 2234.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 3.43
r_work: 0.3567 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   1656  Z= 0.306
  Angle     :  0.509   3.153   2223  Z= 0.301
  Chirality :  0.049   0.128    285
  Planarity :  0.002   0.008    276
  Dihedral  :  5.053  15.354    237
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.72 %
    Favored  : 87.28 %
  Rotamer:
    Outliers : 10.30 %
    Allowed  : 18.18 %
    Favored  : 71.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.87 (0.33), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.70 (0.26), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS B  50 
 PHE   0.004   0.001   PHE B  94 
 TYR   0.012   0.002   TYR B  39 

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 55
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A   23 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8232 (mtpt)
REVERT: A   24 GLN cc_start: 0.8460 (mp10) cc_final: 0.7906 (mp10)
REVERT: A   58 LYS cc_start: 0.8598 (ttmm) cc_final: 0.7942 (tptt)
REVERT: A   60 LYS cc_start: 0.8600 (mmtp) cc_final: 0.8063 (mttp)
REVERT: A   61 GLU cc_start: 0.8478 (mp0) cc_final: 0.8148 (mp0)
REVERT: A   80 LYS cc_start: 0.8966 (mttp) cc_final: 0.7622 (pttp)
REVERT: A   97 LYS cc_start: 0.8632 (ptmm) cc_final: 0.7258 (tppt)
REVERT: B   46 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7282 (tm-30)
REVERT: B   57 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8104 (pm20)
REVERT: C   23 LYS cc_start: 0.9103 (mtpt) cc_final: 0.8475 (mmmt)
REVERT: C   46 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7728 (tm-30)
REVERT: C   58 LYS cc_start: 0.8562 (ttmm) cc_final: 0.8046 (pttm)
REVERT: C   60 LYS cc_start: 0.8589 (mmtp) cc_final: 0.8099 (mmtm)
REVERT: C   61 GLU cc_start: 0.8481 (mp0) cc_final: 0.8034 (mp0)
REVERT: C   80 LYS cc_start: 0.8838 (mttp) cc_final: 0.8061 (mmtt)
  outliers start: 17
  outliers final: 13
  residues processed: 65
  average time/residue: 0.1684
  time to fit residues: 12.0946
Evaluate side-chains
  68 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue   95 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 9 optimal weight:    9.9990
   chunk 3 optimal weight:    0.0670
   chunk 16 optimal weight:    0.0980
   chunk 21 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 7 optimal weight:    0.1980
   chunk 0 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    1.8722

-------------------------------------------------------------------------------
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 = 0.4058 r_free = 0.4058 target = 0.140713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.112746 restraints weight = 2179.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 3.29
r_work: 0.3566 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   1656  Z= 0.251
  Angle     :  0.488   3.090   2223  Z= 0.288
  Chirality :  0.049   0.128    285
  Planarity :  0.002   0.009    276
  Dihedral  :  4.857  15.197    237
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.84 %
    Favored  : 88.16 %
  Rotamer:
    Outliers :  9.70 %
    Allowed  : 18.79 %
    Favored  : 71.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.77 (0.34), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.63 (0.26), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS C  50 
 PHE   0.003   0.001   PHE B  94 
 TYR   0.011   0.002   TYR B  39 

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.192 
Fit side-chains
REVERT: A   23 LYS cc_start: 0.8856 (mtpt) cc_final: 0.8325 (mtpt)
REVERT: A   24 GLN cc_start: 0.8442 (mp10) cc_final: 0.7964 (mp10)
REVERT: A   58 LYS cc_start: 0.8549 (ttmm) cc_final: 0.7925 (tptt)
REVERT: A   60 LYS cc_start: 0.8561 (mmtp) cc_final: 0.8102 (mttp)
REVERT: A   61 GLU cc_start: 0.8432 (mp0) cc_final: 0.8149 (mp0)
REVERT: A   80 LYS cc_start: 0.8930 (mttp) cc_final: 0.7583 (pttp)
REVERT: A   97 LYS cc_start: 0.8563 (ptmm) cc_final: 0.7235 (tppt)
REVERT: B   46 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7232 (tm-30)
REVERT: B   57 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8105 (pm20)
REVERT: C   23 LYS cc_start: 0.9067 (mtpt) cc_final: 0.8483 (mmmt)
REVERT: C   46 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7590 (tm-30)
REVERT: C   58 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8021 (pttm)
REVERT: C   60 LYS cc_start: 0.8573 (mmtp) cc_final: 0.8088 (mmtm)
REVERT: C   61 GLU cc_start: 0.8369 (mp0) cc_final: 0.7915 (mp0)
REVERT: C   80 LYS cc_start: 0.8817 (mttp) cc_final: 0.8020 (mmtt)
  outliers start: 16
  outliers final: 11
  residues processed: 65
  average time/residue: 0.1689
  time to fit residues: 12.1298
Evaluate side-chains
  67 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue   95 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 15 optimal weight:    8.9990
   chunk 20 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 12 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   chunk 8 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 9 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    2.1386

-------------------------------------------------------------------------------
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 = 0.4030 r_free = 0.4030 target = 0.136795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.108894 restraints weight = 2272.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 3.39
r_work: 0.3564 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   1656  Z= 0.283
  Angle     :  0.498   3.238   2223  Z= 0.295
  Chirality :  0.049   0.129    285
  Planarity :  0.002   0.008    276
  Dihedral  :  4.971  15.460    237
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.72 %
    Favored  : 87.28 %
  Rotamer:
    Outliers : 10.30 %
    Allowed  : 18.18 %
    Favored  : 71.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.68 (0.34), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.56 (0.26), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS B  50 
 PHE   0.004   0.001   PHE B  94 
 TYR   0.011   0.002   TYR B  39 

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 55
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A   23 LYS cc_start: 0.8884 (mtpt) cc_final: 0.8375 (mtpt)
REVERT: A   24 GLN cc_start: 0.8499 (mp10) cc_final: 0.8040 (mp10)
REVERT: A   58 LYS cc_start: 0.8552 (ttmm) cc_final: 0.7887 (tptt)
REVERT: A   60 LYS cc_start: 0.8603 (mmtp) cc_final: 0.8146 (mttm)
REVERT: A   61 GLU cc_start: 0.8449 (mp0) cc_final: 0.8165 (mp0)
REVERT: A   80 LYS cc_start: 0.8957 (mttp) cc_final: 0.7590 (pttp)
REVERT: A   97 LYS cc_start: 0.8641 (ptmm) cc_final: 0.7276 (tppt)
REVERT: B   46 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7315 (tm-30)
REVERT: B   57 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8151 (pm20)
REVERT: C   23 LYS cc_start: 0.9069 (mtpt) cc_final: 0.8468 (mmmt)
REVERT: C   46 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7707 (tm-30)
REVERT: C   58 LYS cc_start: 0.8482 (ttmm) cc_final: 0.7988 (pttm)
REVERT: C   60 LYS cc_start: 0.8590 (mmtp) cc_final: 0.8120 (mmtm)
REVERT: C   61 GLU cc_start: 0.8429 (mp0) cc_final: 0.7971 (mp0)
REVERT: C   80 LYS cc_start: 0.8839 (mttp) cc_final: 0.8019 (mmtt)
  outliers start: 17
  outliers final: 13
  residues processed: 65
  average time/residue: 0.1637
  time to fit residues: 11.7561
Evaluate side-chains
  67 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 53
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue   95 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 9 optimal weight:    0.6980
   chunk 11 optimal weight:    8.9990
   chunk 14 optimal weight:    5.9990
   chunk 22 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0870
   chunk 23 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 2 optimal weight:    7.9990
   overall best weight:    1.4360

-------------------------------------------------------------------------------
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 = 0.4087 r_free = 0.4087 target = 0.142852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.115056 restraints weight = 2217.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 3.28
r_work: 0.3606 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   1656  Z= 0.202
  Angle     :  0.469   3.457   2223  Z= 0.277
  Chirality :  0.049   0.128    285
  Planarity :  0.002   0.010    276
  Dihedral  :  4.710  15.448    237
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.84 %
    Favored  : 88.16 %
  Rotamer:
    Outliers :  9.09 %
    Allowed  : 20.61 %
    Favored  : 70.30 %
  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: -4.58 (0.36), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.48 (0.27), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS B  50 
 PHE   0.003   0.001   PHE B  94 
 TYR   0.013   0.002   TYR B  39 

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A   23 LYS cc_start: 0.8842 (mtpt) cc_final: 0.8356 (mtpt)
REVERT: A   24 GLN cc_start: 0.8459 (mp10) cc_final: 0.8016 (mp10)
REVERT: A   58 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8023 (tptp)
REVERT: A   60 LYS cc_start: 0.8554 (mmtp) cc_final: 0.8079 (mttm)
REVERT: A   61 GLU cc_start: 0.8429 (mp0) cc_final: 0.8143 (mp0)
REVERT: A   97 LYS cc_start: 0.8592 (ptmm) cc_final: 0.7243 (tppt)
REVERT: B   46 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7181 (tm-30)
REVERT: B   57 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8119 (pm20)
REVERT: C   23 LYS cc_start: 0.9050 (mtpt) cc_final: 0.8465 (mmmt)
REVERT: C   46 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7518 (tm-30)
REVERT: C   58 LYS cc_start: 0.8696 (ttmm) cc_final: 0.7922 (pttm)
REVERT: C   60 LYS cc_start: 0.8601 (mmtp) cc_final: 0.8072 (mmtm)
REVERT: C   61 GLU cc_start: 0.8345 (mp0) cc_final: 0.7888 (mp0)
REVERT: C   80 LYS cc_start: 0.8812 (mttp) cc_final: 0.8009 (mmtt)
  outliers start: 15
  outliers final: 13
  residues processed: 64
  average time/residue: 0.1632
  time to fit residues: 11.5991
Evaluate side-chains
  69 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue   95 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 17 optimal weight:   10.0000
   chunk 2 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 15 optimal weight:    7.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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 = 0.4070 r_free = 0.4070 target = 0.141332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.113393 restraints weight = 2207.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 3.27
r_work: 0.3588 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   1656  Z= 0.240
  Angle     :  0.487   3.078   2223  Z= 0.287
  Chirality :  0.049   0.129    285
  Planarity :  0.002   0.011    276
  Dihedral  :  4.816  15.342    237
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.72 %
    Favored  : 87.28 %
  Rotamer:
    Outliers :  9.09 %
    Allowed  : 18.79 %
    Favored  : 72.12 %
  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: -4.47 (0.36), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.40 (0.27), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B  50 
 PHE   0.003   0.001   PHE B  94 
 TYR   0.012   0.002   TYR B  39 

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A   23 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8389 (mtpt)
REVERT: A   24 GLN cc_start: 0.8465 (mp10) cc_final: 0.8037 (mp10)
REVERT: A   58 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8053 (tptp)
REVERT: A   60 LYS cc_start: 0.8578 (mmtp) cc_final: 0.8092 (mttm)
REVERT: A   61 GLU cc_start: 0.8413 (mp0) cc_final: 0.8135 (mp0)
REVERT: A   80 LYS cc_start: 0.8938 (mttp) cc_final: 0.7580 (pttp)
REVERT: A   97 LYS cc_start: 0.8607 (ptmm) cc_final: 0.7250 (tppt)
REVERT: B   46 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7272 (tm-30)
REVERT: B   57 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8066 (pm20)
REVERT: C   23 LYS cc_start: 0.9041 (mtpt) cc_final: 0.8482 (mmmt)
REVERT: C   46 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7607 (tm-30)
REVERT: C   58 LYS cc_start: 0.8591 (ttmm) cc_final: 0.8089 (pttm)
REVERT: C   60 LYS cc_start: 0.8600 (mmtp) cc_final: 0.8121 (mmtm)
REVERT: C   61 GLU cc_start: 0.8375 (mp0) cc_final: 0.7938 (mp0)
REVERT: C   80 LYS cc_start: 0.8826 (mttp) cc_final: 0.8050 (mmtt)
  outliers start: 15
  outliers final: 13
  residues processed: 66
  average time/residue: 0.1776
  time to fit residues: 12.9645
Evaluate side-chains
  69 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue   95 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 2 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 0 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.4129 r_free = 0.4129 target = 0.145820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.117253 restraints weight = 2215.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 3.39
r_work: 0.3644 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   1656  Z= 0.138
  Angle     :  0.432   3.115   2223  Z= 0.255
  Chirality :  0.049   0.129    285
  Planarity :  0.002   0.012    276
  Dihedral  :  4.367  14.957    237
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.53 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 22.42 %
    Favored  : 71.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.28 (0.39), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.26 (0.29), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS B  50 
 PHE   0.002   0.001   PHE B  94 
 TYR   0.012   0.002   TYR B  39 

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8445 (mp10) cc_final: 0.8001 (mp10)
REVERT: A   61 GLU cc_start: 0.8432 (mp0) cc_final: 0.8154 (mp0)
REVERT: B   46 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7198 (tm-30)
REVERT: C   23 LYS cc_start: 0.9046 (mtpt) cc_final: 0.8437 (mmmt)
REVERT: C   46 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7473 (tm-30)
REVERT: C   58 LYS cc_start: 0.8693 (ttmm) cc_final: 0.7835 (pttm)
REVERT: C   60 LYS cc_start: 0.8552 (mmtp) cc_final: 0.7986 (mmtm)
REVERT: C   61 GLU cc_start: 0.8359 (mp0) cc_final: 0.7896 (mp0)
REVERT: C   80 LYS cc_start: 0.8758 (mttp) cc_final: 0.7934 (mmtt)
  outliers start: 10
  outliers final: 10
  residues processed: 58
  average time/residue: 0.1390
  time to fit residues: 9.1859
Evaluate side-chains
  59 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   95 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   chunk 14 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0060
   chunk 6 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0270
   chunk 7 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.5456

-------------------------------------------------------------------------------
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 = 0.4172 r_free = 0.4172 target = 0.148073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.119728 restraints weight = 2258.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3826 rms_B_bonded: 3.38
r_work: 0.3723 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.2820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   1656  Z= 0.116
  Angle     :  0.442   5.788   2223  Z= 0.258
  Chirality :  0.049   0.125    285
  Planarity :  0.002   0.014    276
  Dihedral  :  3.977  14.227    237
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.96 %
    Favored  : 89.04 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 27.27 %
    Favored  : 69.09 %
  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: -4.03 (0.41), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.06 (0.31), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  50 
 PHE   0.001   0.000   PHE C  94 
 TYR   0.013   0.002   TYR B  39 

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8488 (mp10) cc_final: 0.8070 (mp10)
REVERT: A   61 GLU cc_start: 0.8398 (mp0) cc_final: 0.8118 (mp0)
REVERT: B   46 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7183 (tm-30)
REVERT: B   58 LYS cc_start: 0.8729 (ttmm) cc_final: 0.8075 (tptt)
REVERT: C   23 LYS cc_start: 0.9043 (mtpt) cc_final: 0.8461 (mmmt)
REVERT: C   46 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7485 (tm-30)
REVERT: C   58 LYS cc_start: 0.8663 (ttmm) cc_final: 0.7899 (pttm)
REVERT: C   60 LYS cc_start: 0.8579 (mmtp) cc_final: 0.7910 (tptt)
REVERT: C   61 GLU cc_start: 0.8213 (mp0) cc_final: 0.7805 (mp0)
REVERT: C   80 LYS cc_start: 0.8728 (mttp) cc_final: 0.7909 (mmtt)
  outliers start: 6
  outliers final: 6
  residues processed: 62
  average time/residue: 0.1806
  time to fit residues: 12.3352
Evaluate side-chains
  57 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   95 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 20 optimal weight:    0.0970
   chunk 8 optimal weight:    7.9990
   chunk 3 optimal weight:    0.0050
   chunk 18 optimal weight:    7.9990
   chunk 5 optimal weight:    0.0670
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.6332

-------------------------------------------------------------------------------
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 = 0.4179 r_free = 0.4179 target = 0.148726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.120413 restraints weight = 2261.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3833 rms_B_bonded: 3.45
r_work: 0.3730 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   1656  Z= 0.126
  Angle     :  0.472   7.319   2223  Z= 0.275
  Chirality :  0.049   0.124    285
  Planarity :  0.002   0.017    276
  Dihedral  :  3.962  13.908    237
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.53 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 27.27 %
    Favored  : 69.09 %
  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: -3.88 (0.42), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.95 (0.32), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B  50 
 PHE   0.001   0.000   PHE C  94 
 TYR   0.012   0.002   TYR B  39 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1285.00 seconds
wall clock time: 23 minutes 33.48 seconds (1413.48 seconds total)