Starting phenix.real_space_refine
on Tue Mar  3 10:58:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7l7h_23212/03_2026/7l7h_23212.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7l7h_23212/03_2026/7l7h_23212.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7l7h_23212/03_2026/7l7h_23212.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7l7h_23212/03_2026/7l7h_23212.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7l7h_23212/03_2026/7l7h_23212.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7l7h_23212/03_2026/7l7h_23212.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.005
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    1518      2.51       5
     N     424      2.21       5
     O     488      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2430
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 304
          Classifications: {'peptide': 44}
          Link IDs: {'TRANS': 43}
    Chain: "B"
      Number of atoms: 304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 304
          Classifications: {'peptide': 44}
          Link IDs: {'TRANS': 43}
    Chain: "C"
      Number of atoms: 304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 304
          Classifications: {'peptide': 44}
          Link IDs: {'TRANS': 43}
    Chain: "D"
      Number of atoms: 304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 304
          Classifications: {'peptide': 44}
          Link IDs: {'TRANS': 43}
    Chain: "E"
      Number of atoms: 304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 304
          Classifications: {'peptide': 44}
          Link IDs: {'TRANS': 43}
    Chain: "F"
      Number of atoms: 304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 304
          Classifications: {'peptide': 44}
          Link IDs: {'TRANS': 43}
    Chain: "G"
      Number of atoms: 302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 302
          Classifications: {'peptide': 44}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 43}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "H"
      Number of atoms: 304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 304
          Classifications: {'peptide': 44}
          Link IDs: {'TRANS': 43}
  Time building chain proxies: 0.72, per 1000 atoms: 0.30
  Number of scatterers: 2430
  At special positions: 0
  Unit cell: (101.65, 82.39, 40.66, 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     488      8.00
     N     424      7.00
     C    1518      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: 0.20
  Conformation dependent library (CDL) restraints added in 107.2 milliseconds
  

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  592

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 64
      removed outlier: 7.461A  pdb=" N   VAL A  63 " --> pdb=" O   THR B  64 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   VAL B  63 " --> pdb=" O   THR C  64 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   VAL C  63 " --> pdb=" O   THR D  64 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 74
    Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 40
      removed outlier: 6.443A  pdb=" N   TYR B  39 " --> pdb=" O   VAL C  40 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 49
      removed outlier: 6.830A  pdb=" N   VAL B  48 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   VAL C  48 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 38 through 39
      removed outlier: 3.513A  pdb=" N   TYR F  39 " --> pdb=" O   LEU G  38 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 48 through 49
      removed outlier: 6.402A  pdb=" N   VAL E  48 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   VAL F  48 " --> pdb=" O   VAL G  49 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 57
      removed outlier: 3.639A  pdb=" N   THR H  54 " --> pdb=" O   ALA G  53 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 63 through 64
      removed outlier: 6.755A  pdb=" N   VAL G  63 " --> pdb=" O   THR H  64 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    7 hydrogen bonds defined for protein.
    21 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: 0.20

  Time building geometry restraints manager: 0.27 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: 424
        1.29 -     1.36: 392
        1.36 -     1.43: 117
        1.43 -     1.50: 507
        1.50 -     1.58: 998
  Bond restraints: 2438
  Sorted by residual:
  bond pdb=" CA  THR D  54 "
       pdb=" CB  THR D  54 "
    ideal  model  delta    sigma   weight residual
    1.526  1.469  0.057 1.53e-02 4.27e+03 1.40e+01
  bond pdb=" CB  THR D  44 "
       pdb=" CG2 THR D  44 "
    ideal  model  delta    sigma   weight residual
    1.521  1.448  0.073 3.30e-02 9.18e+02 4.89e+00
  bond pdb=" CB  GLU A  61 "
       pdb=" CG  GLU A  61 "
    ideal  model  delta    sigma   weight residual
    1.520  1.576 -0.056 3.00e-02 1.11e+03 3.55e+00
  bond pdb=" CA  THR F  44 "
       pdb=" CB  THR F  44 "
    ideal  model  delta    sigma   weight residual
    1.534  1.508  0.025 1.45e-02 4.76e+03 3.07e+00
  bond pdb=" CG  LEU C  38 "
       pdb=" CD1 LEU C  38 "
    ideal  model  delta    sigma   weight residual
    1.521  1.464  0.057 3.30e-02 9.18e+02 2.97e+00
  ... (remaining 2433 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 2821
        1.86 -     3.72: 390
        3.72 -     5.58: 71
        5.58 -     7.43: 21
        7.43 -     9.29: 6
  Bond angle restraints: 3309
  Sorted by residual:
  angle pdb=" N   LYS B  60 "
        pdb=" CA  LYS B  60 "
        pdb=" C   LYS B  60 "
      ideal   model   delta    sigma   weight residual
     114.04  107.66    6.38 1.24e+00 6.50e-01 2.65e+01
  angle pdb=" N   ALA A  78 "
        pdb=" CA  ALA A  78 "
        pdb=" C   ALA A  78 "
      ideal   model   delta    sigma   weight residual
     110.42  117.53   -7.11 1.46e+00 4.69e-01 2.37e+01
  angle pdb=" C   VAL B  37 "
        pdb=" N   LEU B  38 "
        pdb=" CA  LEU B  38 "
      ideal   model   delta    sigma   weight residual
     121.31  128.32   -7.01 1.49e+00 4.50e-01 2.21e+01
  angle pdb=" N   ALA E  78 "
        pdb=" CA  ALA E  78 "
        pdb=" C   ALA E  78 "
      ideal   model   delta    sigma   weight residual
     110.42  116.94   -6.52 1.46e+00 4.69e-01 2.00e+01
  angle pdb=" N   VAL H  77 "
        pdb=" CA  VAL H  77 "
        pdb=" C   VAL H  77 "
      ideal   model   delta    sigma   weight residual
     112.17  107.93    4.24 9.50e-01 1.11e+00 1.99e+01
  ... (remaining 3304 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.23: 1220
       17.23 -    34.46: 156
       34.46 -    51.69: 29
       51.69 -    68.92: 1
       68.92 -    86.14: 1
  Dihedral angle restraints: 1407
    sinusoidal: 463
      harmonic: 944
  Sorted by residual:
  dihedral pdb=" CA  VAL A  37 "
           pdb=" C   VAL A  37 "
           pdb=" N   LEU A  38 "
           pdb=" CA  LEU A  38 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.04   27.96     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  GLY G  68 "
           pdb=" C   GLY G  68 "
           pdb=" N   ALA G  69 "
           pdb=" CA  ALA G  69 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.44   26.56     0      5.00e+00 4.00e-02 2.82e+01
  dihedral pdb=" CA  VAL F  66 "
           pdb=" C   VAL F  66 "
           pdb=" N   GLY F  67 "
           pdb=" CA  GLY F  67 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.80   25.20     0      5.00e+00 4.00e-02 2.54e+01
  ... (remaining 1404 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 200
       0.051 -    0.102: 158
       0.102 -    0.153: 69
       0.153 -    0.204: 17
       0.204 -    0.255: 3
  Chirality restraints: 447
  Sorted by residual:
  chirality pdb=" CB  VAL E  71 "
            pdb=" CA  VAL E  71 "
            pdb=" CG1 VAL E  71 "
            pdb=" CG2 VAL E  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" CB  VAL H  40 "
            pdb=" CA  VAL H  40 "
            pdb=" CG1 VAL H  40 "
            pdb=" CG2 VAL H  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" CB  THR C  44 "
            pdb=" CA  THR C  44 "
            pdb=" OG1 THR C  44 "
            pdb=" CG2 THR C  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 444 not shown)

  Planarity restraints: 408
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F  39 "    0.025 2.00e-02 2.50e+03   1.60e-02 5.14e+00
        pdb=" CG  TYR F  39 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TYR F  39 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR F  39 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR F  39 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR F  39 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR F  39 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR F  39 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B  44 "    0.011 2.00e-02 2.50e+03   2.15e-02 4.61e+00
        pdb=" C   THR B  44 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   THR B  44 "    0.014 2.00e-02 2.50e+03
        pdb=" N   LYS B  45 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F  52 "    0.010 2.00e-02 2.50e+03   2.02e-02 4.09e+00
        pdb=" C   VAL F  52 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   VAL F  52 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ALA F  53 "    0.012 2.00e-02 2.50e+03
  ... (remaining 405 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 319
        2.74 -     3.28: 2220
        3.28 -     3.82: 3663
        3.82 -     4.36: 3947
        4.36 -     4.90: 7666
  Nonbonded interactions: 17815
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A  44 "
            pdb=" O   GLU A  46 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OG1 THR B  44 "
            pdb=" O   GLU B  46 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OG1 THR H  44 "
            pdb=" O   GLU H  46 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OG1 THR G  44 "
            pdb=" O   GLU G  46 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OG1 THR D  44 "
            pdb=" O   GLU D  46 "
     model   vdw
     2.286 3.040
  ... (remaining 17810 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ 
 or name CB )) or resid 38 through 79))
  selection = (chain 'B' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ 
 or name CB )) or resid 38 through 79))
  selection = (chain 'C' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ 
 or name CB )) or resid 38 through 79))
  selection = (chain 'D' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ 
 or name CB )) or resid 38 through 79))
  selection = (chain 'E' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ 
 or name CB )) or resid 38 through 79))
  selection = (chain 'F' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ 
 or name CB )) or resid 38 through 79))
  selection = chain 'G'
  selection = (chain 'H' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ 
 or name CB )) or resid 38 through 79))
}

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 group one per residue
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:             0.060
  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:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.280
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5872
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      :  0.008   0.073   2438  Z= 0.422
  Angle     :  1.471   9.292   3309  Z= 0.882
  Chirality :  0.079   0.255    447
  Planarity :  0.006   0.021    408
  Dihedral  : 15.099  86.144    815
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 36.31 %
    Favored  : 63.69 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 17.25 %
    Favored  : 79.22 %
  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: -6.00 (0.32), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.56 (0.24), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.037   0.006   TYR F  39 
 HIS   0.007   0.002   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00847 ( 2438)
  covalent geometry    : angle       1.47133 ( 3309)
  hydrogen bonds       : bond        0.29324 (    7)
  hydrogen bonds       : angle       9.18814 (   21)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A   39 TYR cc_start: 0.5199 (t80) cc_final: 0.4885 (t80)
REVERT: A   45 LYS cc_start: 0.8316 (tttt) cc_final: 0.7992 (mptt)
REVERT: A   57 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7576 (mp0)
REVERT: B   39 TYR cc_start: 0.6141 (m-80) cc_final: 0.5798 (m-80)
REVERT: B   57 GLU cc_start: 0.7606 (tt0) cc_final: 0.7279 (tt0)
REVERT: B   62 GLN cc_start: 0.7537 (mt0) cc_final: 0.7328 (mp10)
REVERT: C   45 LYS cc_start: 0.7943 (tttt) cc_final: 0.7654 (mttp)
REVERT: C   57 GLU cc_start: 0.7546 (tt0) cc_final: 0.6736 (tm-30)
REVERT: C   62 GLN cc_start: 0.8054 (mp10) cc_final: 0.7714 (mp10)
REVERT: C   65 ASN cc_start: 0.6956 (m-40) cc_final: 0.6148 (t0)
REVERT: D   57 GLU cc_start: 0.7576 (tt0) cc_final: 0.7180 (tm-30)
REVERT: E   43 LYS cc_start: 0.6426 (ttmt) cc_final: 0.5757 (tttp)
REVERT: F   45 LYS cc_start: 0.7892 (tttt) cc_final: 0.7669 (mttt)
REVERT: F   58 LYS cc_start: 0.5783 (mttt) cc_final: 0.5209 (tptp)
  outliers start: 9
  outliers final: 8
  residues processed: 94
  average time/residue: 0.0640
  time to fit residues: 7.0267
Evaluate side-chains
  70 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain H residue   52 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 31 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.101258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.089231 restraints weight = 6071.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.090961 restraints weight = 3780.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.092244 restraints weight = 2652.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.093081 restraints weight = 2021.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.093790 restraints weight = 1660.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.4019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6382
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   2438  Z= 0.234
  Angle     :  0.946   7.413   3309  Z= 0.523
  Chirality :  0.059   0.146    447
  Planarity :  0.004   0.013    408
  Dihedral  :  9.410  48.784    360
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 16.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 26.49 %
    Favored  : 73.51 %
  Rotamer:
    Outliers :  7.84 %
    Allowed  : 26.67 %
    Favored  : 65.49 %
  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: -5.66 (0.33), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.30 (0.25), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.030   0.005   TYR G  39 
 HIS   0.004   0.002   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 2438)
  covalent geometry    : angle       0.94576 ( 3309)
  hydrogen bonds       : bond        0.03059 (    7)
  hydrogen bonds       : angle       6.69723 (   21)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 61
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A   39 TYR cc_start: 0.5438 (t80) cc_final: 0.4931 (t80)
REVERT: A   45 LYS cc_start: 0.8328 (tttt) cc_final: 0.8020 (mptt)
REVERT: C   57 GLU cc_start: 0.7636 (tt0) cc_final: 0.7406 (tm-30)
REVERT: C   65 ASN cc_start: 0.7630 (m-40) cc_final: 0.6732 (t0)
REVERT: F   58 LYS cc_start: 0.6352 (mttt) cc_final: 0.5515 (tptp)
REVERT: F   62 GLN cc_start: 0.7786 (mp10) cc_final: 0.7475 (mp10)
REVERT: G   62 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8188 (tm-30)
  outliers start: 20
  outliers final: 17
  residues processed: 75
  average time/residue: 0.0606
  time to fit residues: 5.3989
Evaluate side-chains
  67 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 50
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   50 HIS
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue   72 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0470
   chunk 26 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 3 optimal weight:    0.2980
   chunk 21 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   chunk 11 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   overall best weight:    1.8684

-------------------------------------------------------------------------------
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 = 0.4198 r_free = 0.4198 target = 0.104869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.092885 restraints weight = 5946.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.094718 restraints weight = 3646.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.096022 restraints weight = 2522.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.096979 restraints weight = 1897.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.097687 restraints weight = 1523.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.4077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6289
moved from start:          0.3192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2438  Z= 0.131
  Angle     :  0.767   5.565   3309  Z= 0.424
  Chirality :  0.054   0.149    447
  Planarity :  0.002   0.014    408
  Dihedral  :  7.741  57.048    359
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.24 %
    Favored  : 79.76 %
  Rotamer:
    Outliers :  7.84 %
    Allowed  : 26.27 %
    Favored  : 65.88 %
  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: -5.17 (0.35), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.93 (0.26), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.015   0.002   TYR F  39 
 HIS   0.002   0.001   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 2438)
  covalent geometry    : angle       0.76678 ( 3309)
  hydrogen bonds       : bond        0.02302 (    7)
  hydrogen bonds       : angle       5.85547 (   21)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 58
  time to evaluate  : 0.094 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7327 (mt)
REVERT: A   39 TYR cc_start: 0.5268 (t80) cc_final: 0.4759 (t80)
REVERT: A   45 LYS cc_start: 0.8369 (tttt) cc_final: 0.7909 (mptt)
REVERT: B   57 GLU cc_start: 0.7561 (tt0) cc_final: 0.7312 (tt0)
REVERT: C   65 ASN cc_start: 0.7707 (m-40) cc_final: 0.6843 (t0)
REVERT: E   45 LYS cc_start: 0.8420 (mttt) cc_final: 0.8176 (mttm)
REVERT: E   50 HIS cc_start: 0.5339 (OUTLIER) cc_final: 0.4823 (m90)
REVERT: G   62 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8060 (tm-30)
REVERT: H   38 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7023 (tt)
  outliers start: 20
  outliers final: 14
  residues processed: 75
  average time/residue: 0.0497
  time to fit residues: 4.4354
Evaluate side-chains
  65 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 48
  time to evaluate  : 0.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain D residue   50 HIS
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   50 HIS
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   71 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain H residue   38 LEU
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue   72 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 24 optimal weight:    9.9990
   chunk 31 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 13 optimal weight:    8.9990
   chunk 14 optimal weight:    7.9990
   chunk 28 optimal weight:    6.9990
   chunk 18 optimal weight:    0.0980
   chunk 26 optimal weight:    9.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    4.9986

-------------------------------------------------------------------------------
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 = 0.4084 r_free = 0.4084 target = 0.098063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.086403 restraints weight = 6366.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.088104 restraints weight = 3970.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.089314 restraints weight = 2794.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.090187 restraints weight = 2133.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.090816 restraints weight = 1733.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6385
moved from start:          0.3235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   2438  Z= 0.232
  Angle     :  0.885   6.681   3309  Z= 0.491
  Chirality :  0.058   0.144    447
  Planarity :  0.004   0.012    408
  Dihedral  :  8.770  40.246    358
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 15.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 30.95 %
    Favored  : 69.05 %
  Rotamer:
    Outliers : 10.98 %
    Allowed  : 25.10 %
    Favored  : 63.92 %
  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: -5.40 (0.35), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.11 (0.26), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.024   0.004   TYR G  39 
 HIS   0.004   0.001   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 2438)
  covalent geometry    : angle       0.88450 ( 3309)
  hydrogen bonds       : bond        0.02839 (    7)
  hydrogen bonds       : angle       6.03435 (   21)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 50
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A   39 TYR cc_start: 0.5496 (t80) cc_final: 0.5025 (t80)
REVERT: A   45 LYS cc_start: 0.8402 (tttt) cc_final: 0.7999 (mptt)
REVERT: C   61 GLU cc_start: 0.8016 (tp30) cc_final: 0.7753 (tp30)
REVERT: C   65 ASN cc_start: 0.7605 (m-40) cc_final: 0.6735 (t0)
REVERT: D   61 GLU cc_start: 0.7672 (tp30) cc_final: 0.7459 (tp30)
REVERT: E   50 HIS cc_start: 0.5400 (OUTLIER) cc_final: 0.4877 (m90)
REVERT: H   38 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7212 (tt)
  outliers start: 28
  outliers final: 22
  residues processed: 73
  average time/residue: 0.0476
  time to fit residues: 4.2412
Evaluate side-chains
  69 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 45
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain D residue   50 HIS
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   50 HIS
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   71 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain H residue   38 LEU
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   72 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 12 optimal weight:   20.0000
   chunk 8 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 19 optimal weight:    0.1980
   chunk 11 optimal weight:   10.0000
   chunk 20 optimal weight:    0.0770
   chunk 25 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 28 optimal weight:   20.0000
   overall best weight:    1.2142

-------------------------------------------------------------------------------
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 = 0.4218 r_free = 0.4218 target = 0.104973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.092909 restraints weight = 5818.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.094722 restraints weight = 3639.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.096076 restraints weight = 2537.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.097072 restraints weight = 1905.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.097845 restraints weight = 1521.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.4105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6240
moved from start:          0.3882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2438  Z= 0.110
  Angle     :  0.684   5.361   3309  Z= 0.380
  Chirality :  0.054   0.149    447
  Planarity :  0.002   0.012    408
  Dihedral  :  6.406  25.171    358
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.05 %
    Favored  : 80.95 %
  Rotamer:
    Outliers :  7.84 %
    Allowed  : 28.24 %
    Favored  : 63.92 %
  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: -4.89 (0.36), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.72 (0.28), residues: 336

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 2438)
  covalent geometry    : angle       0.68412 ( 3309)
  hydrogen bonds       : bond        0.01764 (    7)
  hydrogen bonds       : angle       5.55216 (   21)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A   45 LYS cc_start: 0.8178 (tttt) cc_final: 0.7725 (mptt)
REVERT: C   61 GLU cc_start: 0.7764 (tp30) cc_final: 0.7528 (tp30)
REVERT: C   65 ASN cc_start: 0.7541 (m-40) cc_final: 0.6894 (t0)
  outliers start: 20
  outliers final: 15
  residues processed: 69
  average time/residue: 0.0411
  time to fit residues: 3.5041
Evaluate side-chains
  61 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 46
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain D residue   50 HIS
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain H residue   52 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 30 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0770
   chunk 12 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 24 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   overall best weight:    2.6146

-------------------------------------------------------------------------------
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 = 0.4152 r_free = 0.4152 target = 0.101279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.089429 restraints weight = 5999.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.091150 restraints weight = 3789.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.092411 restraints weight = 2662.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.093324 restraints weight = 2026.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.094036 restraints weight = 1631.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.4032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6295
moved from start:          0.3904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2438  Z= 0.143
  Angle     :  0.735   5.462   3309  Z= 0.406
  Chirality :  0.055   0.143    447
  Planarity :  0.003   0.019    408
  Dihedral  :  6.831  29.025    357
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 22.62 %
    Favored  : 77.38 %
  Rotamer:
    Outliers : 10.98 %
    Allowed  : 24.71 %
    Favored  : 64.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -4.81 (0.37), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.66 (0.28), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.019   0.003   TYR F  39 
 HIS   0.002   0.001   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 2438)
  covalent geometry    : angle       0.73514 ( 3309)
  hydrogen bonds       : bond        0.01804 (    7)
  hydrogen bonds       : angle       5.24908 (   21)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 47
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A   39 TYR cc_start: 0.5284 (t80) cc_final: 0.4815 (t80)
REVERT: A   45 LYS cc_start: 0.8274 (tttt) cc_final: 0.7875 (mptt)
REVERT: C   65 ASN cc_start: 0.7588 (m-40) cc_final: 0.6770 (t0)
REVERT: E   50 HIS cc_start: 0.5382 (OUTLIER) cc_final: 0.4821 (m90)
REVERT: G   62 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8097 (tm-30)
REVERT: H   38 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7233 (tt)
  outliers start: 28
  outliers final: 24
  residues processed: 71
  average time/residue: 0.0404
  time to fit residues: 3.4415
Evaluate side-chains
  72 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 46
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain D residue   50 HIS
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   50 HIS
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   50 HIS
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain H residue   38 LEU
Chi-restraints excluded: chain H residue   52 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 8 optimal weight:    0.0070
   chunk 1 optimal weight:    9.9990
   chunk 25 optimal weight:    0.0000
   chunk 7 optimal weight:    9.9990
   chunk 14 optimal weight:    0.0470
   chunk 15 optimal weight:    0.9990
   chunk 5 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 20 optimal weight:    9.9990
   chunk 12 optimal weight:    6.9990
   chunk 23 optimal weight:    9.9990
   overall best weight:    1.0104

-------------------------------------------------------------------------------
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 = 0.4227 r_free = 0.4227 target = 0.106251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.094245 restraints weight = 5694.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.096043 restraints weight = 3527.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.097313 restraints weight = 2460.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.098259 restraints weight = 1867.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.098993 restraints weight = 1503.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.4115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6206
moved from start:          0.4344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2438  Z= 0.114
  Angle     :  0.691   6.631   3309  Z= 0.381
  Chirality :  0.054   0.154    447
  Planarity :  0.002   0.014    408
  Dihedral  :  5.835  24.305    357
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.37 %
    Favored  : 83.63 %
  Rotamer:
    Outliers :  9.02 %
    Allowed  : 26.27 %
    Favored  : 64.71 %
  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: -4.54 (0.38), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.45 (0.29), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.012   0.001   TYR B  39 
 HIS   0.001   0.000   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 2438)
  covalent geometry    : angle       0.69126 ( 3309)
  hydrogen bonds       : bond        0.01658 (    7)
  hydrogen bonds       : angle       4.87947 (   21)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 51
  time to evaluate  : 0.082 
Fit side-chains
REVERT: A   45 LYS cc_start: 0.8191 (tttt) cc_final: 0.7745 (mptt)
REVERT: A   57 GLU cc_start: 0.7960 (mp0) cc_final: 0.7486 (mp0)
REVERT: C   65 ASN cc_start: 0.7508 (m-40) cc_final: 0.6868 (t0)
REVERT: E   50 HIS cc_start: 0.5157 (OUTLIER) cc_final: 0.4532 (m90)
REVERT: G   62 GLN cc_start: 0.8388 (tm-30) cc_final: 0.7813 (tm-30)
REVERT: H   38 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7077 (tt)
  outliers start: 23
  outliers final: 18
  residues processed: 69
  average time/residue: 0.0413
  time to fit residues: 3.3946
Evaluate side-chains
  63 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 43
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain D residue   50 HIS
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   50 HIS
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   50 HIS
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain H residue   38 LEU
Chi-restraints excluded: chain H residue   52 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   chunk 8 optimal weight:   20.0000
   chunk 25 optimal weight:   10.0000
   chunk 2 optimal weight:    0.6980
   chunk 3 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 29 optimal weight:    8.9990
   chunk 15 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    4.9388

-------------------------------------------------------------------------------
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 = 0.4091 r_free = 0.4091 target = 0.098464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.087244 restraints weight = 6437.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.088835 restraints weight = 4124.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.090004 restraints weight = 2937.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.090786 restraints weight = 2249.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.091436 restraints weight = 1841.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6437
moved from start:          0.4007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   2438  Z= 0.231
  Angle     :  0.904   6.594   3309  Z= 0.498
  Chirality :  0.059   0.145    447
  Planarity :  0.004   0.017    408
  Dihedral  :  7.839  32.313    356
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 14.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 27.98 %
    Favored  : 72.02 %
  Rotamer:
    Outliers : 12.16 %
    Allowed  : 23.14 %
    Favored  : 64.71 %
  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: -4.94 (0.37), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.76 (0.28), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.029   0.004   TYR F  39 
 HIS   0.003   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 2438)
  covalent geometry    : angle       0.90446 ( 3309)
  hydrogen bonds       : bond        0.02436 (    7)
  hydrogen bonds       : angle       5.48179 (   21)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 53
  time to evaluate  : 0.094 
Fit side-chains
REVERT: A   45 LYS cc_start: 0.8333 (tttt) cc_final: 0.7962 (mptt)
REVERT: C   65 ASN cc_start: 0.7645 (m-40) cc_final: 0.6836 (t0)
REVERT: E   50 HIS cc_start: 0.5561 (OUTLIER) cc_final: 0.4972 (m90)
REVERT: G   62 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8410 (tm-30)
REVERT: H   38 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7296 (tt)
REVERT: H   60 LYS cc_start: 0.8081 (mttt) cc_final: 0.7412 (mmtm)
  outliers start: 31
  outliers final: 28
  residues processed: 79
  average time/residue: 0.0505
  time to fit residues: 4.7823
Evaluate side-chains
  78 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 48
  time to evaluate  : 0.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain D residue   50 HIS
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   50 HIS
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   50 HIS
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   71 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain H residue   38 LEU
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue   72 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 17 optimal weight:    0.0070
   chunk 15 optimal weight:    8.9990
   chunk 30 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 20 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9980
   chunk 21 optimal weight:    6.9990
   overall best weight:    4.6004

-------------------------------------------------------------------------------
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 = 0.4103 r_free = 0.4103 target = 0.098934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.087563 restraints weight = 6433.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.089144 restraints weight = 4129.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.090332 restraints weight = 2953.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.091188 restraints weight = 2274.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.091675 restraints weight = 1850.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6441
moved from start:          0.4158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   2438  Z= 0.220
  Angle     :  0.926   8.186   3309  Z= 0.509
  Chirality :  0.059   0.141    447
  Planarity :  0.003   0.019    408
  Dihedral  :  8.003  34.510    356
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 15.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 26.79 %
    Favored  : 73.21 %
  Rotamer:
    Outliers : 13.33 %
    Allowed  : 23.14 %
    Favored  : 63.53 %
  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: -5.12 (0.36), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.90 (0.28), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.028   0.004   TYR F  39 
 HIS   0.002   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 2438)
  covalent geometry    : angle       0.92560 ( 3309)
  hydrogen bonds       : bond        0.02091 (    7)
  hydrogen bonds       : angle       5.73055 (   21)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 50
  time to evaluate  : 0.089 
Fit side-chains
REVERT: A   45 LYS cc_start: 0.8298 (tttt) cc_final: 0.7918 (mptt)
REVERT: E   43 LYS cc_start: 0.7232 (ttmt) cc_final: 0.6934 (tttt)
REVERT: E   50 HIS cc_start: 0.5389 (OUTLIER) cc_final: 0.4799 (m90)
REVERT: F   62 GLN cc_start: 0.7875 (mp10) cc_final: 0.7565 (mp10)
REVERT: G   62 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8400 (tm-30)
REVERT: H   38 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7302 (tt)
REVERT: H   60 LYS cc_start: 0.8152 (mttt) cc_final: 0.7514 (mmtm)
  outliers start: 34
  outliers final: 32
  residues processed: 77
  average time/residue: 0.0608
  time to fit residues: 5.5260
Evaluate side-chains
  82 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 48
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain D residue   50 HIS
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   50 HIS
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   50 HIS
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   71 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain H residue   38 LEU
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   72 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 1 optimal weight:    6.9990
   chunk 11 optimal weight:    9.9990
   chunk 4 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 29 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 17 optimal weight:    6.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.4222 r_free = 0.4222 target = 0.105951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.093754 restraints weight = 5964.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.095533 restraints weight = 3703.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.096808 restraints weight = 2589.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.097659 restraints weight = 1972.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.098391 restraints weight = 1611.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.4109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6225
moved from start:          0.4634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   2438  Z= 0.130
  Angle     :  0.782   7.607   3309  Z= 0.429
  Chirality :  0.055   0.158    447
  Planarity :  0.003   0.020    408
  Dihedral  :  5.912  24.159    356
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.15 %
    Favored  : 81.85 %
  Rotamer:
    Outliers :  7.06 %
    Allowed  : 29.41 %
    Favored  : 63.53 %
  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: -4.74 (0.38), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.61 (0.29), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.001   TYR B  39 
 HIS   0.001   0.000   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 2438)
  covalent geometry    : angle       0.78176 ( 3309)
  hydrogen bonds       : bond        0.01669 (    7)
  hydrogen bonds       : angle       4.91477 (   21)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.071 
Fit side-chains
REVERT: A   45 LYS cc_start: 0.8152 (tttt) cc_final: 0.7688 (mptt)
REVERT: E   43 LYS cc_start: 0.7192 (ttmt) cc_final: 0.6886 (tttt)
REVERT: E   50 HIS cc_start: 0.5270 (OUTLIER) cc_final: 0.4668 (m90)
REVERT: F   62 GLN cc_start: 0.7811 (mp10) cc_final: 0.7506 (tm-30)
REVERT: G   62 GLN cc_start: 0.8347 (tm-30) cc_final: 0.7845 (tm-30)
REVERT: H   38 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.6968 (tt)
  outliers start: 18
  outliers final: 15
  residues processed: 62
  average time/residue: 0.0591
  time to fit residues: 4.3246
Evaluate side-chains
  61 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 44
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain D residue   50 HIS
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   50 HIS
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   50 HIS
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain H residue   38 LEU
Chi-restraints excluded: chain H residue   52 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 8 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 20 optimal weight:    0.0040
   chunk 4 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    4.4000

-------------------------------------------------------------------------------
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 = 0.4110 r_free = 0.4110 target = 0.099358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.087995 restraints weight = 6373.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.089592 restraints weight = 4090.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.090792 restraints weight = 2921.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.091666 restraints weight = 2241.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.092308 restraints weight = 1816.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6415
moved from start:          0.4384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   2438  Z= 0.213
  Angle     :  0.903   6.763   3309  Z= 0.496
  Chirality :  0.058   0.141    447
  Planarity :  0.004   0.016    408
  Dihedral  :  7.532  31.558    356
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 27.08 %
    Favored  : 72.92 %
  Rotamer:
    Outliers :  9.41 %
    Allowed  : 27.06 %
    Favored  : 63.53 %
  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: -4.97 (0.37), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.78 (0.29), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.027   0.004   TYR F  39 
 HIS   0.003   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 2438)
  covalent geometry    : angle       0.90279 ( 3309)
  hydrogen bonds       : bond        0.01920 (    7)
  hydrogen bonds       : angle       5.53157 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 599.50 seconds
wall clock time: 11 minutes 9.11 seconds (669.11 seconds total)