Starting phenix.real_space_refine
on Tue Feb  3 12:55:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ka4_62204/02_2026/9ka4_62204.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ka4_62204/02_2026/9ka4_62204.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ka4_62204/02_2026/9ka4_62204.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ka4_62204/02_2026/9ka4_62204.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ka4_62204/02_2026/9ka4_62204.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ka4_62204/02_2026/9ka4_62204.map"
  }
  resolution = 3.42
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    1602      2.51       5
     N     438      2.21       5
     O     522      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2562
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "D"
      Number of atoms: 427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 427
          Classifications: {'peptide': 62}
          Link IDs: {'TRANS': 61}
  Restraints were copied for chains:
    C, E, A, F, B
  Time building chain proxies: 0.44, per 1000 atoms: 0.17
  Number of scatterers: 2562
  At special positions: 0
  Unit cell: (97.94, 92.13, 31.54, 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     522      8.00
     N     438      7.00
     C    1602      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: 0.19
  Conformation dependent library (CDL) restraints added in 111.8 milliseconds
  

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  648

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 25.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'E' and resid 39 through 40
      removed outlier: 6.492A  pdb=" N   TYR D  39 " --> pdb=" O   VAL E  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 46 through 50
      removed outlier: 8.163A  pdb=" N   GLU D  46 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 8.247A  pdb=" N   VAL E  49 " --> pdb=" O   GLU D  46 " (cutoff:3.500A)
      removed outlier: 8.877A  pdb=" N   VAL D  48 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   VAL F  48 " --> pdb=" O   GLY D  47 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   VAL D  49 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   HIS F  50 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 62 through 66
      removed outlier: 6.906A  pdb=" N   GLN D  62 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   ASN F  65 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   THR D  64 " --> pdb=" O   ASN F  65 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 70 through 71
      removed outlier: 6.557A  pdb=" N   VAL D  70 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 77 through 79
      removed outlier: 6.431A  pdb=" N   ALA D  78 " --> pdb=" O   GLN E  79 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   THR D  81 " --> pdb=" O   LYS F  80 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   VAL F  82 " --> pdb=" O   THR D  81 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 95 through 96
      removed outlier: 7.066A  pdb=" N   VAL D  95 " --> pdb=" O   LYS F  96 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 39 through 40
      removed outlier: 6.721A  pdb=" N   TYR C  39 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 46 through 50
      removed outlier: 8.224A  pdb=" N   GLU C  46 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 8.425A  pdb=" N   VAL A  49 " --> pdb=" O   GLU C  46 " (cutoff:3.500A)
      removed outlier: 9.021A  pdb=" N   VAL C  48 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   VAL B  48 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   VAL C  49 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   HIS B  50 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 62 through 66
      removed outlier: 6.760A  pdb=" N   GLN C  62 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   ASN B  65 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   THR C  64 " --> pdb=" O   ASN B  65 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 70 through 71
      removed outlier: 6.667A  pdb=" N   VAL C  70 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 77 through 82
      removed outlier: 6.295A  pdb=" N   ALA C  78 " --> pdb=" O   GLN A  79 " (cutoff:3.500A)
      removed outlier: 7.384A  pdb=" N   THR A  81 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   LYS C  80 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   THR C  81 " --> pdb=" O   LYS B  80 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   VAL B  82 " --> pdb=" O   THR C  81 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 95 through 96
      removed outlier: 6.899A  pdb=" N   VAL C  95 " --> pdb=" O   LYS B  96 " (cutoff:3.500A)

    22 hydrogen bonds defined for protein.
    66 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: 0.34

  Time building geometry restraints manager: 0.26 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 450
        1.29 -     1.35: 396
        1.35 -     1.41: 108
        1.41 -     1.48: 426
        1.48 -     1.54: 1194
  Bond restraints: 2574
  Sorted by residual:
  bond pdb=" CB  GLN F  79 "
       pdb=" CG  GLN F  79 "
    ideal  model  delta    sigma   weight residual
    1.520  1.493  0.027 3.00e-02 1.11e+03 7.81e-01
  bond pdb=" CA  ALA B  57 "
       pdb=" CB  ALA B  57 "
    ideal  model  delta    sigma   weight residual
    1.535  1.521  0.014 1.58e-02 4.01e+03 7.60e-01
  bond pdb=" CA  ALA F  57 "
       pdb=" CB  ALA F  57 "
    ideal  model  delta    sigma   weight residual
    1.535  1.521  0.014 1.58e-02 4.01e+03 7.58e-01
  bond pdb=" CA  ALA C  57 "
       pdb=" CB  ALA C  57 "
    ideal  model  delta    sigma   weight residual
    1.535  1.521  0.014 1.58e-02 4.01e+03 7.47e-01
  bond pdb=" CA  ALA E  57 "
       pdb=" CB  ALA E  57 "
    ideal  model  delta    sigma   weight residual
    1.535  1.521  0.014 1.58e-02 4.01e+03 7.44e-01
  ... (remaining 2569 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 3307
        1.43 -     2.86: 164
        2.86 -     4.29: 9
        4.29 -     5.72: 12
        5.72 -     7.16: 6
  Bond angle restraints: 3498
  Sorted by residual:
  angle pdb=" C   VAL C  49 "
        pdb=" N   HIS C  50 "
        pdb=" CA  HIS C  50 "
      ideal   model   delta    sigma   weight residual
     121.62  116.37    5.25 1.83e+00 2.99e-01 8.22e+00
  angle pdb=" C   VAL B  49 "
        pdb=" N   HIS B  50 "
        pdb=" CA  HIS B  50 "
      ideal   model   delta    sigma   weight residual
     121.62  116.39    5.23 1.83e+00 2.99e-01 8.18e+00
  angle pdb=" C   VAL A  49 "
        pdb=" N   HIS A  50 "
        pdb=" CA  HIS A  50 "
      ideal   model   delta    sigma   weight residual
     121.62  116.39    5.23 1.83e+00 2.99e-01 8.17e+00
  angle pdb=" C   VAL D  49 "
        pdb=" N   HIS D  50 "
        pdb=" CA  HIS D  50 "
      ideal   model   delta    sigma   weight residual
     121.62  116.40    5.22 1.83e+00 2.99e-01 8.13e+00
  angle pdb=" C   VAL E  49 "
        pdb=" N   HIS E  50 "
        pdb=" CA  HIS E  50 "
      ideal   model   delta    sigma   weight residual
     121.62  116.43    5.19 1.83e+00 2.99e-01 8.04e+00
  ... (remaining 3493 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     7.04: 1110
        7.04 -    14.07: 252
       14.07 -    21.11: 78
       21.11 -    28.14: 42
       28.14 -    35.18: 18
  Dihedral angle restraints: 1500
    sinusoidal: 480
      harmonic: 1020
  Sorted by residual:
  dihedral pdb=" CA  THR E  59 "
           pdb=" C   THR E  59 "
           pdb=" N   LYS E  60 "
           pdb=" CA  LYS E  60 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  166.03   13.97     0      5.00e+00 4.00e-02 7.81e+00
  dihedral pdb=" CA  THR A  59 "
           pdb=" C   THR A  59 "
           pdb=" N   LYS A  60 "
           pdb=" CA  LYS A  60 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  166.03   13.97     0      5.00e+00 4.00e-02 7.80e+00
  dihedral pdb=" CA  THR B  59 "
           pdb=" C   THR B  59 "
           pdb=" N   LYS B  60 "
           pdb=" CA  LYS B  60 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  166.05   13.95     0      5.00e+00 4.00e-02 7.78e+00
  ... (remaining 1497 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 224
       0.034 -    0.068: 135
       0.068 -    0.102: 49
       0.102 -    0.136: 54
       0.136 -    0.170: 12
  Chirality restraints: 474
  Sorted by residual:
  chirality pdb=" CA  VAL E  49 "
            pdb=" N   VAL E  49 "
            pdb=" C   VAL E  49 "
            pdb=" CB  VAL E  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.20e-01
  chirality pdb=" CA  VAL A  49 "
            pdb=" N   VAL A  49 "
            pdb=" C   VAL A  49 "
            pdb=" CB  VAL A  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.07e-01
  chirality pdb=" CA  VAL B  49 "
            pdb=" N   VAL B  49 "
            pdb=" C   VAL B  49 "
            pdb=" CB  VAL B  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.07e-01
  ... (remaining 471 not shown)

  Planarity restraints: 432
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  39 "   -0.004 2.00e-02 2.50e+03   6.12e-03 7.49e-01
        pdb=" CG  TYR B  39 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  39 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  39 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  39 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  39 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  39 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B  39 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS E  50 "    0.007 2.00e-02 2.50e+03   7.01e-03 7.38e-01
        pdb=" CG  HIS E  50 "   -0.015 2.00e-02 2.50e+03
        pdb=" ND1 HIS E  50 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS E  50 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 HIS E  50 "    0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS E  50 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS F  50 "    0.007 2.00e-02 2.50e+03   6.98e-03 7.30e-01
        pdb=" CG  HIS F  50 "   -0.015 2.00e-02 2.50e+03
        pdb=" ND1 HIS F  50 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 HIS F  50 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 HIS F  50 "    0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS F  50 "    0.002 2.00e-02 2.50e+03
  ... (remaining 429 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 449
        2.77 -     3.30: 2331
        3.30 -     3.83: 3962
        3.83 -     4.37: 4022
        4.37 -     4.90: 8554
  Nonbonded interactions: 19318
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS D  80 "
            pdb=" OE1 GLU E  46 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" OE1 GLU C  46 "
            pdb=" NZ  LYS B  80 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" O   GLY E  84 "
            pdb=" OG  SER E  87 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   GLY F  84 "
            pdb=" OG  SER F  87 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   GLY A  84 "
            pdb=" OG  SER A  87 "
     model   vdw
     2.247 3.040
  ... (remaining 19313 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 'D'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'A'
  selection = chain 'F'
  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:             3.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.290
  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:             0.000
  Load rotamer database and sin/cos tables:1.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7116
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      :  0.006   0.027   2574  Z= 0.291
  Angle     :  0.801   7.155   3498  Z= 0.463
  Chirality :  0.060   0.170    474
  Planarity :  0.003   0.007    432
  Dihedral  : 10.828  35.177    852
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 18.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.33 (0.34), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.29 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.012   0.005   TYR B  39 
 PHE   0.009   0.003   PHE B  94 
 HIS   0.007   0.004   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00625 ( 2574)
  covalent geometry    : angle       0.80074 ( 3498)
  hydrogen bonds       : bond        0.16534 (   22)
  hydrogen bonds       : angle       8.13619 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.092 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.0907
  time to fit residues: 2.8687
Evaluate side-chains
  24 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 26 optimal weight:    8.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 30 optimal weight:    7.9990
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    4.1588

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

Flipped N/Q/H residues before XYZ refinement:
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 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 = 0.4585 r_free = 0.4585 target = 0.148868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.129284 restraints weight = 3395.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.4396 rms_B_bonded: 2.42
r_work: 0.4313 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.4197 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.4197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.1133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   2574  Z= 0.245
  Angle     :  0.729   7.213   3498  Z= 0.400
  Chirality :  0.060   0.173    474
  Planarity :  0.003   0.009    432
  Dihedral  :  5.483  14.040    372
  Min Nonbonded Distance : 2.653

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.44 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.50 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.75 (0.36), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.85 (0.27), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.019   0.006   TYR D  39 
 PHE   0.012   0.003   PHE D  94 
 HIS   0.008   0.004   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 ( 2574)
  covalent geometry    : angle       0.72862 ( 3498)
  hydrogen bonds       : bond        0.02587 (   22)
  hydrogen bonds       : angle       5.93133 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.093 
Fit side-chains
REVERT: C   72 THR cc_start: 0.8247 (m) cc_final: 0.7951 (m)
REVERT: A   72 THR cc_start: 0.8068 (m) cc_final: 0.7791 (m)
  outliers start: 4
  outliers final: 4
  residues processed: 36
  average time/residue: 0.0861
  time to fit residues: 3.6035
Evaluate side-chains
  34 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 30
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   79 GLN
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain B residue   48 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0370
   chunk 24 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0870
   chunk 21 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.6236

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

Flipped N/Q/H residues before XYZ refinement:
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4710 r_free = 0.4710 target = 0.159790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.140732 restraints weight = 3245.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.4529 rms_B_bonded: 2.41
r_work: 0.4454 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.4347 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.4347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   2574  Z= 0.076
  Angle     :  0.495   4.559   3498  Z= 0.270
  Chirality :  0.053   0.139    474
  Planarity :  0.002   0.009    432
  Dihedral  :  4.135  12.146    372
  Min Nonbonded Distance : 2.657

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 12.50 %
    Favored  : 86.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.62 (0.33), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.75 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR B  39 
 PHE   0.005   0.001   PHE E  94 
 HIS   0.002   0.001   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00161 ( 2574)
  covalent geometry    : angle       0.49455 ( 3498)
  hydrogen bonds       : bond        0.01378 (   22)
  hydrogen bonds       : angle       4.97631 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.065 
Fit side-chains
REVERT: D   72 THR cc_start: 0.7614 (m) cc_final: 0.7032 (m)
REVERT: C   72 THR cc_start: 0.7976 (m) cc_final: 0.7324 (m)
REVERT: A   72 THR cc_start: 0.7848 (m) cc_final: 0.7525 (m)
  outliers start: 2
  outliers final: 1
  residues processed: 29
  average time/residue: 0.0599
  time to fit residues: 2.0151
Evaluate side-chains
  28 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 18 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 2 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   overall best weight:    3.7186

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

Flipped N/Q/H residues before XYZ refinement:
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 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 = 0.4609 r_free = 0.4609 target = 0.150620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.131220 restraints weight = 3370.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.4437 rms_B_bonded: 2.38
r_work: 0.4353 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.4240 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.4240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.022   2574  Z= 0.217
  Angle     :  0.647   6.519   3498  Z= 0.355
  Chirality :  0.058   0.167    474
  Planarity :  0.002   0.010    432
  Dihedral  :  4.836  12.852    372
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.61 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 13.64 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.24 (0.36), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.46 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.016   0.005   TYR C  39 
 PHE   0.009   0.002   PHE D  94 
 HIS   0.007   0.004   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 2574)
  covalent geometry    : angle       0.64748 ( 3498)
  hydrogen bonds       : bond        0.01739 (   22)
  hydrogen bonds       : angle       5.62451 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 30
  time to evaluate  : 0.084 
Fit side-chains
REVERT: C   83 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7774 (mp0)
REVERT: E   83 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8107 (mp0)
REVERT: A   72 THR cc_start: 0.8161 (m) cc_final: 0.7867 (m)
REVERT: B   39 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.6696 (m-10)
REVERT: B   83 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7757 (mp0)
  outliers start: 10
  outliers final: 8
  residues processed: 39
  average time/residue: 0.0771
  time to fit residues: 3.4905
Evaluate side-chains
  38 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 29
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain C residue   39 TYR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain E residue   39 TYR
Chi-restraints excluded: chain E residue   79 GLN
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain B residue   39 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 19 optimal weight:    0.7980
   chunk 18 optimal weight:    0.4980
   chunk 14 optimal weight:    0.5980
   chunk 20 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 31 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:    8.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 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 = 0.4662 r_free = 0.4662 target = 0.155438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.135658 restraints weight = 3267.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.4490 rms_B_bonded: 2.44
r_work: 0.4409 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.4294 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.4294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   2574  Z= 0.120
  Angle     :  0.535   5.340   3498  Z= 0.292
  Chirality :  0.055   0.154    474
  Planarity :  0.002   0.007    432
  Dihedral  :  4.281  11.953    372
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 16.67 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.14 (0.36), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.38 (0.27), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.002   TYR E  39 
 PHE   0.006   0.002   PHE D  94 
 HIS   0.004   0.002   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 2574)
  covalent geometry    : angle       0.53491 ( 3498)
  hydrogen bonds       : bond        0.01394 (   22)
  hydrogen bonds       : angle       5.20413 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 29
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A   72 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7705 (m)
REVERT: F   39 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.6809 (m-10)
REVERT: B   83 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7706 (mp0)
  outliers start: 7
  outliers final: 4
  residues processed: 34
  average time/residue: 0.0783
  time to fit residues: 3.1659
Evaluate side-chains
  33 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 27
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain F residue   39 TYR
Chi-restraints excluded: chain F residue   79 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 26 optimal weight:    7.9990
   chunk 10 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0000
   chunk 1 optimal weight:    0.6980
   chunk 17 optimal weight:    7.9990
   chunk 16 optimal weight:    0.3980
   chunk 5 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 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 = 0.4713 r_free = 0.4713 target = 0.161101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.141710 restraints weight = 3190.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.4539 rms_B_bonded: 2.32
r_work: 0.4460 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.4351 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.4351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2574  Z= 0.094
  Angle     :  0.496   4.742   3498  Z= 0.271
  Chirality :  0.053   0.144    474
  Planarity :  0.002   0.013    432
  Dihedral  :  3.861  10.859    372
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.05 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.97 (0.37), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.002   TYR D  39 
 PHE   0.005   0.001   PHE A  94 
 HIS   0.003   0.002   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00199 ( 2574)
  covalent geometry    : angle       0.49612 ( 3498)
  hydrogen bonds       : bond        0.01182 (   22)
  hydrogen bonds       : angle       4.89865 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 25
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A   72 THR cc_start: 0.7922 (OUTLIER) cc_final: 0.7623 (m)
  outliers start: 5
  outliers final: 4
  residues processed: 27
  average time/residue: 0.1079
  time to fit residues: 3.3617
Evaluate side-chains
  29 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   79 GLN
Chi-restraints excluded: chain F residue   79 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 34 optimal weight:    9.9990
   chunk 18 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0870
   chunk 26 optimal weight:    8.9990
   chunk 22 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    4.0166

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

Flipped N/Q/H residues before XYZ refinement:
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 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 = 0.4607 r_free = 0.4607 target = 0.150146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.130811 restraints weight = 3350.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.4422 rms_B_bonded: 2.37
r_work: 0.4333 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.4219 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.4219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.024   2574  Z= 0.238
  Angle     :  0.676   6.614   3498  Z= 0.372
  Chirality :  0.060   0.166    474
  Planarity :  0.002   0.008    432
  Dihedral  :  4.799  12.318    372
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.17 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 13.26 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.72 (0.39), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.018   0.006   TYR C  39 
 PHE   0.009   0.002   PHE D  94 
 HIS   0.008   0.004   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 ( 2574)
  covalent geometry    : angle       0.67605 ( 3498)
  hydrogen bonds       : bond        0.01664 (   22)
  hydrogen bonds       : angle       5.72611 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 30
  time to evaluate  : 0.101 
Fit side-chains
REVERT: C   83 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7664 (mp0)
REVERT: E   83 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8152 (mp0)
REVERT: A   72 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7920 (m)
REVERT: A   83 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8039 (mp0)
REVERT: B   83 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7785 (mp0)
  outliers start: 13
  outliers final: 11
  residues processed: 39
  average time/residue: 0.0870
  time to fit residues: 3.9883
Evaluate side-chains
  42 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 30
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain C residue   39 TYR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain E residue   39 TYR
Chi-restraints excluded: chain E residue   79 GLN
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   79 GLN
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   79 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 13 optimal weight:   10.0000
   chunk 17 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   chunk 18 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    0.2980
   chunk 34 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 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 = 0.4714 r_free = 0.4714 target = 0.160252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.140465 restraints weight = 3213.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.4520 rms_B_bonded: 2.46
r_work: 0.4435 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.4323 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.4323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   2574  Z= 0.081
  Angle     :  0.492   4.370   3498  Z= 0.267
  Chirality :  0.053   0.140    474
  Planarity :  0.002   0.017    432
  Dihedral  :  3.782  10.898    372
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 17.42 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.82 (0.38), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.29), residues: 360

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00171 ( 2574)
  covalent geometry    : angle       0.49227 ( 3498)
  hydrogen bonds       : bond        0.01136 (   22)
  hydrogen bonds       : angle       4.99437 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.056 
Fit side-chains
REVERT: D   43 LYS cc_start: 0.8144 (mttt) cc_final: 0.7642 (mtpt)
REVERT: A   72 THR cc_start: 0.7869 (OUTLIER) cc_final: 0.7532 (m)
  outliers start: 3
  outliers final: 1
  residues processed: 24
  average time/residue: 0.0761
  time to fit residues: 2.0711
Evaluate side-chains
  26 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain F residue   79 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 9 optimal weight:    0.0030
   chunk 6 optimal weight:   10.0000
   chunk 2 optimal weight:    7.9990
   chunk 15 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:    7.9990
   chunk 34 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    2.7998

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

Flipped N/Q/H residues before XYZ refinement:
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 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 = 0.4648 r_free = 0.4648 target = 0.155538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.136089 restraints weight = 3332.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.4465 rms_B_bonded: 2.35
r_work: 0.4380 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.4268 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.4268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2574  Z= 0.175
  Angle     :  0.613   5.891   3498  Z= 0.334
  Chirality :  0.057   0.157    474
  Planarity :  0.002   0.008    432
  Dihedral  :  4.320  11.419    372
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 18.18 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.60 (0.40), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.004   TYR D  39 
 PHE   0.007   0.002   PHE D  94 
 HIS   0.006   0.003   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 2574)
  covalent geometry    : angle       0.61332 ( 3498)
  hydrogen bonds       : bond        0.01463 (   22)
  hydrogen bonds       : angle       5.37520 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.059 
Fit side-chains
REVERT: D   43 LYS cc_start: 0.8330 (mttt) cc_final: 0.7794 (mtpt)
REVERT: D   83 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7713 (mp0)
REVERT: E   83 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8099 (mp0)
REVERT: A   72 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7827 (m)
REVERT: B   83 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7696 (mp0)
  outliers start: 2
  outliers final: 1
  residues processed: 31
  average time/residue: 0.0743
  time to fit residues: 2.6618
Evaluate side-chains
  32 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 30
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain F residue   79 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 29 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   chunk 35 optimal weight:    0.6980
   chunk 16 optimal weight:    6.9990
   chunk 11 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   chunk 8 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 22 optimal weight:   10.0000
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 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 = 0.4688 r_free = 0.4688 target = 0.159461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.139848 restraints weight = 3257.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.4510 rms_B_bonded: 2.34
r_work: 0.4429 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.4318 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.4318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   2574  Z= 0.114
  Angle     :  0.548   5.466   3498  Z= 0.299
  Chirality :  0.054   0.150    474
  Planarity :  0.002   0.018    432
  Dihedral  :  3.911  10.926    372
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 18.94 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.60 (0.40), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.002   TYR B  39 
 PHE   0.006   0.001   PHE C  94 
 HIS   0.004   0.002   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 2574)
  covalent geometry    : angle       0.54838 ( 3498)
  hydrogen bonds       : bond        0.01218 (   22)
  hydrogen bonds       : angle       5.15455 (   66)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.091 
Fit side-chains
REVERT: D   43 LYS cc_start: 0.8344 (mttt) cc_final: 0.7791 (mtpt)
REVERT: A   72 THR cc_start: 0.7935 (OUTLIER) cc_final: 0.7654 (m)
REVERT: B   83 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7694 (mp0)
  outliers start: 1
  outliers final: 0
  residues processed: 27
  average time/residue: 0.0971
  time to fit residues: 2.9833
Evaluate side-chains
  28 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   chunk 32 optimal weight:    8.9990
   chunk 30 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 12 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
D  79 GLN
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 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 = 0.4619 r_free = 0.4619 target = 0.153013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.133726 restraints weight = 3360.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.4419 rms_B_bonded: 2.35
r_work: 0.4329 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.4213 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.4213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.2165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   2574  Z= 0.240
  Angle     :  0.702   6.525   3498  Z= 0.384
  Chirality :  0.060   0.165    474
  Planarity :  0.002   0.009    432
  Dihedral  :  4.711  12.164    372
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.17 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 18.18 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.50 (0.40), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.90 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.015   0.005   TYR A  39 
 PHE   0.009   0.002   PHE D  94 
 HIS   0.008   0.004   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 ( 2574)
  covalent geometry    : angle       0.70168 ( 3498)
  hydrogen bonds       : bond        0.01694 (   22)
  hydrogen bonds       : angle       5.71905 (   66)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 921.11 seconds
wall clock time: 16 minutes 27.70 seconds (987.70 seconds total)