Starting phenix.real_space_refine
on Mon Feb 10 20:38:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7l7h_23212/02_2025/7l7h_23212.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7l7h_23212/02_2025/7l7h_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_23212/02_2025/7l7h_23212.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7l7h_23212/02_2025/7l7h_23212.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7l7h_23212/02_2025/7l7h_23212.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7l7h_23212/02_2025/7l7h_23212.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 1.81, per 1000 atoms: 0.74
  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: 0.54
  Conformation dependent library (CDL) restraints added in 308.3 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: 0.24
  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: 0.45

  Time building geometry restraints manager: 0.64 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:             0.070
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.520
  Find NCS groups from input model:        0.140
  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:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.700
-------------------------------------------------------------------------------
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= 0.542
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 HIS   0.007   0.002   HIS D  50 
 TYR   0.037   0.006   TYR F  39 

*********************** 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  : 0.252 
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: 0.7280 (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: 0.6735 (tm-30)
REVERT: C   62 GLN cc_start: 0.8055 (mp10) cc_final: 0.7715 (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: 0.5756 (tttp)
REVERT: F   45 LYS cc_start: 0.7892 (tttt) cc_final: 0.7668 (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: 0.1542
  time to fit residues: 16.6947
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  : 0.273 
-------------------------------------------------------------------------------
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 27 optimal weight:   10.0000
   chunk 24 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 16 optimal weight:    9.9990
   chunk 12 optimal weight:    6.9990
   chunk 25 optimal weight:    8.9990
   chunk 9 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 18 optimal weight:    7.9990
   chunk 29 optimal weight:    7.9990
   overall best weight:    4.9788

-------------------------------------------------------------------------------
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 = 0.4146 r_free = 0.4146 target = 0.100984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.089009 restraints weight = 6090.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.090721 restraints weight = 3778.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.091998 restraints weight = 2655.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6406
moved from start:          0.2364

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= 0.315
  Angle     :  0.952   7.304   3309  Z= 0.527
  Chirality :  0.059   0.147    447
  Planarity :  0.004   0.013    408
  Dihedral  :  9.528  49.840    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 :  8.24 %
    Allowed  : 26.67 %
    Favored  : 65.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.70 (0.33), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.34 (0.25), residues: 336

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

*********************** 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: 21
    poor density    : 60
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 TYR cc_start: 0.5440 (t80) cc_final: 0.4925 (t80)
REVERT: A   45 LYS cc_start: 0.8338 (tttt) cc_final: 0.8032 (mptt)
REVERT: A   57 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7854 (mp0)
REVERT: C   57 GLU cc_start: 0.7663 (tt0) cc_final: 0.7414 (tm-30)
REVERT: C   65 ASN cc_start: 0.7638 (m-40) cc_final: 0.6743 (t0)
REVERT: F   58 LYS cc_start: 0.6279 (mttt) cc_final: 0.5451 (tptp)
  outliers start: 21
  outliers final: 18
  residues processed: 75
  average time/residue: 0.1341
  time to fit residues: 11.8640
Evaluate side-chains
  69 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 51
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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   71 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 23 optimal weight:    0.0470
   chunk 11 optimal weight:    7.9990
   chunk 25 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 31 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 13 optimal weight:    9.9990
   chunk 12 optimal weight:    1.9990
   chunk 1 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    3.4086

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

Flipped N/Q/H residues before XYZ refinement:
** F  62 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 = 0.4153 r_free = 0.4153 target = 0.101843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.090138 restraints weight = 6056.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.091822 restraints weight = 3757.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.093137 restraints weight = 2639.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6363
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2438  Z= 0.229
  Angle     :  0.820   6.233   3309  Z= 0.455
  Chirality :  0.056   0.141    447
  Planarity :  0.003   0.015    408
  Dihedral  :  8.463  51.749    359
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 14.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 26.79 %
    Favored  : 73.21 %
  Rotamer:
    Outliers :  9.41 %
    Allowed  : 26.67 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.36 (0.34), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.08 (0.26), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A  50 
 TYR   0.021   0.003   TYR F  39 

*********************** 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: 24
    poor density    : 54
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7192 (mt)
REVERT: A   39 TYR cc_start: 0.5353 (t80) cc_final: 0.4837 (t80)
REVERT: A   45 LYS cc_start: 0.8377 (tttt) cc_final: 0.7955 (mptt)
REVERT: C   65 ASN cc_start: 0.7639 (m-40) cc_final: 0.6799 (t0)
REVERT: D   62 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8258 (tm-30)
REVERT: E   50 HIS cc_start: 0.5516 (OUTLIER) cc_final: 0.5059 (m90)
REVERT: H   38 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7131 (tt)
  outliers start: 24
  outliers final: 17
  residues processed: 75
  average time/residue: 0.1228
  time to fit residues: 11.0332
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  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   48 VAL
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   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   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   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 21 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   chunk 11 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 31 optimal weight:    0.2980
   chunk 20 optimal weight:    9.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    3.2586

-------------------------------------------------------------------------------
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 = 0.4142 r_free = 0.4142 target = 0.101126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.089368 restraints weight = 6058.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.091092 restraints weight = 3811.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.092353 restraints weight = 2678.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6360
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2438  Z= 0.225
  Angle     :  0.799   6.263   3309  Z= 0.443
  Chirality :  0.056   0.175    447
  Planarity :  0.003   0.013    408
  Dihedral  :  7.933  36.165    359
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 26.79 %
    Favored  : 73.21 %
  Rotamer:
    Outliers : 10.98 %
    Allowed  : 26.27 %
    Favored  : 62.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.21 (0.35), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.97 (0.27), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  50 
 TYR   0.017   0.003   TYR G  39 

*********************** 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
  77 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 49
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7151 (mt)
REVERT: A   39 TYR cc_start: 0.5396 (t80) cc_final: 0.4910 (t80)
REVERT: A   45 LYS cc_start: 0.8355 (tttt) cc_final: 0.7918 (mptt)
REVERT: C   57 GLU cc_start: 0.6702 (tm-30) cc_final: 0.6347 (tm-30)
REVERT: E   50 HIS cc_start: 0.5465 (OUTLIER) cc_final: 0.4975 (m90)
REVERT: F   62 GLN cc_start: 0.7907 (mp10) cc_final: 0.7555 (tm-30)
REVERT: G   62 GLN cc_start: 0.8384 (tm-30) cc_final: 0.7990 (tm-30)
REVERT: H   38 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7138 (tt)
  outliers start: 28
  outliers final: 23
  residues processed: 73
  average time/residue: 0.1185
  time to fit residues: 10.4142
Evaluate side-chains
  71 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 45
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
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 A residue   74 VAL
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   48 VAL
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   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 18 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 15 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 20 optimal weight:    8.9990
   chunk 19 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9980
   chunk 29 optimal weight:    9.9990
   overall best weight:    6.7988

-------------------------------------------------------------------------------
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 = 0.4036 r_free = 0.4036 target = 0.095432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.084338 restraints weight = 6533.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.085862 restraints weight = 4167.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.086981 restraints weight = 2975.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6541
moved from start:          0.3531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   2438  Z= 0.400
  Angle     :  0.982   7.398   3309  Z= 0.544
  Chirality :  0.062   0.168    447
  Planarity :  0.005   0.013    408
  Dihedral  :  9.578  38.507    359
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 20.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 36.01 %
    Favored  : 63.99 %
  Rotamer:
    Outliers : 15.29 %
    Allowed  : 23.14 %
    Favored  : 61.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.75 (0.34), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.37 (0.26), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D  50 
 TYR   0.030   0.005   TYR G  39 

*********************** 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
  85 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 46
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7291 (tt)
REVERT: A   39 TYR cc_start: 0.5288 (t80) cc_final: 0.5049 (t80)
REVERT: A   45 LYS cc_start: 0.8398 (tttt) cc_final: 0.8079 (mptt)
REVERT: E   50 HIS cc_start: 0.5477 (OUTLIER) cc_final: 0.4975 (m90)
REVERT: G   62 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8414 (tm-30)
REVERT: H   38 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7550 (tp)
REVERT: H   60 LYS cc_start: 0.8219 (mttt) cc_final: 0.7670 (mptt)
  outliers start: 39
  outliers final: 36
  residues processed: 77
  average time/residue: 0.1212
  time to fit residues: 11.2057
Evaluate side-chains
  82 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 43
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   54 THR
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   49 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   52 VAL
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain C residue   72 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 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   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   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   50 HIS
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 19 optimal weight:    0.0270
   chunk 29 optimal weight:    7.9990
   chunk 28 optimal weight:    9.9990
   chunk 24 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   chunk 4 optimal weight:    8.9990
   chunk 10 optimal weight:    6.9990
   chunk 13 optimal weight:    8.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    4.6046

-------------------------------------------------------------------------------
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 = 0.4080 r_free = 0.4080 target = 0.098270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.086902 restraints weight = 6351.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.088470 restraints weight = 4070.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.089613 restraints weight = 2913.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6487
moved from start:          0.3768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   2438  Z= 0.291
  Angle     :  0.871   6.888   3309  Z= 0.482
  Chirality :  0.058   0.143    447
  Planarity :  0.003   0.011    408
  Dihedral  :  8.648  34.311    359
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 17.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 30.65 %
    Favored  : 69.35 %
  Rotamer:
    Outliers : 14.90 %
    Allowed  : 24.31 %
    Favored  : 60.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.64 (0.34), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.29 (0.26), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A  50 
 TYR   0.021   0.004   TYR G  39 

*********************** 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
  88 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 50
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7307 (tt)
REVERT: A   39 TYR cc_start: 0.5474 (t80) cc_final: 0.5090 (t80)
REVERT: A   45 LYS cc_start: 0.8402 (tttt) cc_final: 0.7945 (mptt)
REVERT: E   50 HIS cc_start: 0.5305 (OUTLIER) cc_final: 0.4813 (m90)
REVERT: G   62 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8519 (tm-30)
REVERT: H   38 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7425 (tp)
REVERT: H   60 LYS cc_start: 0.8174 (mttt) cc_final: 0.7476 (mmtm)
  outliers start: 38
  outliers final: 32
  residues processed: 79
  average time/residue: 0.1205
  time to fit residues: 11.4448
Evaluate side-chains
  82 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 47
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   54 THR
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   49 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   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 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   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   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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 12 optimal weight:   20.0000
   chunk 8 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   chunk 30 optimal weight:    4.9990
   chunk 21 optimal weight:    8.9990
   chunk 10 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0270
   chunk 22 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   overall best weight:    2.3242

-------------------------------------------------------------------------------
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 = 0.4145 r_free = 0.4145 target = 0.101269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.089250 restraints weight = 6092.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.090968 restraints weight = 3862.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.092204 restraints weight = 2735.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6335
moved from start:          0.4052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2438  Z= 0.195
  Angle     :  0.747   6.019   3309  Z= 0.412
  Chirality :  0.055   0.142    447
  Planarity :  0.002   0.013    408
  Dihedral  :  7.235  27.975    359
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 25.30 %
    Favored  : 74.70 %
  Rotamer:
    Outliers : 13.33 %
    Allowed  : 25.88 %
    Favored  : 60.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.17 (0.36), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.94 (0.27), residues: 336

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

*********************** 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
  89 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 55
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7397 (mt)
REVERT: A   45 LYS cc_start: 0.8279 (tttt) cc_final: 0.7787 (mptt)
REVERT: A   57 GLU cc_start: 0.8359 (mp0) cc_final: 0.8059 (mp0)
REVERT: E   43 LYS cc_start: 0.6932 (ttmt) cc_final: 0.6661 (tttt)
REVERT: E   50 HIS cc_start: 0.5268 (OUTLIER) cc_final: 0.4812 (m90)
REVERT: G   62 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8152 (tm-30)
REVERT: H   38 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7087 (tt)
REVERT: H   60 LYS cc_start: 0.8024 (mttt) cc_final: 0.7319 (mmtm)
REVERT: H   62 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8102 (tm-30)
  outliers start: 34
  outliers final: 27
  residues processed: 81
  average time/residue: 0.1256
  time to fit residues: 12.1385
Evaluate side-chains
  80 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 49
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
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   59 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 C residue   72 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 E residue   50 HIS
Chi-restraints excluded: chain E residue   72 THR
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   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   62 GLN
Chi-restraints excluded: chain H residue   72 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 16 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    4.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.098430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.086929 restraints weight = 6329.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.088573 restraints weight = 4009.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.089778 restraints weight = 2842.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6409
moved from start:          0.4048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   2438  Z= 0.287
  Angle     :  0.855   6.648   3309  Z= 0.471
  Chirality :  0.057   0.141    447
  Planarity :  0.003   0.012    408
  Dihedral  :  8.205  33.171    359
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 14.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 31.85 %
    Favored  : 68.15 %
  Rotamer:
    Outliers : 12.94 %
    Allowed  : 28.24 %
    Favored  : 58.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.27 (0.36), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.01 (0.27), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  50 
 TYR   0.020   0.004   TYR G  39 

*********************** 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
  82 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 49
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7261 (mt)
REVERT: A   45 LYS cc_start: 0.8319 (tttt) cc_final: 0.7897 (mptt)
REVERT: G   62 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8185 (tm-30)
REVERT: H   38 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7160 (tt)
REVERT: H   60 LYS cc_start: 0.8142 (mttt) cc_final: 0.7397 (mmtm)
REVERT: H   62 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8130 (tm-30)
  outliers start: 33
  outliers final: 31
  residues processed: 75
  average time/residue: 0.1273
  time to fit residues: 11.3677
Evaluate side-chains
  79 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 46
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   59 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   66 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain C residue   72 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 E residue   72 THR
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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 7 optimal weight:    8.9990
   chunk 28 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 13 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.4194 r_free = 0.4194 target = 0.104100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.092059 restraints weight = 5906.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.093805 restraints weight = 3696.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.095111 restraints weight = 2583.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6280
moved from start:          0.4443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2438  Z= 0.180
  Angle     :  0.736   7.491   3309  Z= 0.404
  Chirality :  0.054   0.132    447
  Planarity :  0.002   0.011    408
  Dihedral  :  6.450  25.521    359
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.54 %
    Favored  : 79.46 %
  Rotamer:
    Outliers : 11.76 %
    Allowed  : 29.02 %
    Favored  : 59.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.90 (0.37), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.73 (0.28), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  50 
 TYR   0.014   0.002   TYR B  39 

*********************** 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
  82 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 52
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7216 (mt)
REVERT: A   45 LYS cc_start: 0.8177 (tttt) cc_final: 0.7670 (mptt)
REVERT: C   61 GLU cc_start: 0.7803 (tp30) cc_final: 0.7512 (tp30)
REVERT: D   62 GLN cc_start: 0.8478 (tm-30) cc_final: 0.7984 (mp10)
REVERT: E   43 LYS cc_start: 0.7023 (ttmt) cc_final: 0.6727 (tttt)
REVERT: E   50 HIS cc_start: 0.5153 (OUTLIER) cc_final: 0.4626 (m90)
REVERT: G   62 GLN cc_start: 0.8495 (tm-30) cc_final: 0.7866 (tm-30)
REVERT: H   38 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7048 (tt)
REVERT: H   62 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8068 (tm-30)
  outliers start: 30
  outliers final: 22
  residues processed: 78
  average time/residue: 0.1222
  time to fit residues: 11.3812
Evaluate side-chains
  74 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 48
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A 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 C residue   72 THR
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   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   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
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   62 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 13 optimal weight:    0.2980
   chunk 27 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9990
   chunk 16 optimal weight:   10.0000
   chunk 15 optimal weight:   10.0000
   chunk 9 optimal weight:    8.9990
   chunk 25 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 24 optimal weight:    9.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    3.6588

-------------------------------------------------------------------------------
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 = 0.4113 r_free = 0.4113 target = 0.100472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.089128 restraints weight = 6163.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.090820 restraints weight = 3809.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.092021 restraints weight = 2665.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6359
moved from start:          0.4302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   2438  Z= 0.264
  Angle     :  0.841   7.746   3309  Z= 0.461
  Chirality :  0.056   0.142    447
  Planarity :  0.003   0.020    408
  Dihedral  :  7.474  30.750    357
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 28.27 %
    Favored  : 71.73 %
  Rotamer:
    Outliers : 10.59 %
    Allowed  : 29.80 %
    Favored  : 59.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.03 (0.37), residues: 336
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.82 (0.28), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A  50 
 TYR   0.023   0.003   TYR F  39 

********************** 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
  75 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 48
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A   45 LYS cc_start: 0.8316 (tttt) cc_final: 0.7895 (mptt)
REVERT: E   43 LYS cc_start: 0.7140 (ttmt) cc_final: 0.6879 (tttt)
REVERT: E   50 HIS cc_start: 0.5382 (OUTLIER) cc_final: 0.4806 (m90)
REVERT: G   62 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8101 (tm-30)
REVERT: H   38 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7124 (tt)
REVERT: H   62 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8073 (tm-30)
  outliers start: 27
  outliers final: 23
  residues processed: 70
  average time/residue: 0.1319
  time to fit residues: 10.9704
Evaluate side-chains
  71 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 45
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   61 GLU
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 C residue   72 THR
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   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   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
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   62 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 18 optimal weight:    0.4980
   chunk 30 optimal weight:    3.9990
   chunk 25 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 16 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    2.6986

-------------------------------------------------------------------------------
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 = 0.4139 r_free = 0.4139 target = 0.101991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.090396 restraints weight = 6145.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.092112 restraints weight = 3814.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.093360 restraints weight = 2667.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6329
moved from start:          0.4468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   2438  Z= 0.227
  Angle     :  0.803   8.148   3309  Z= 0.440
  Chirality :  0.055   0.142    447
  Planarity :  0.003   0.020    408
  Dihedral  :  7.050  30.119    357
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 23.21 %
    Favored  : 76.79 %
  Rotamer:
    Outliers : 12.16 %
    Allowed  : 27.84 %
    Favored  : 60.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.95 (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
 HIS   0.002   0.001   HIS A  50 
 TYR   0.019   0.003   TYR F  39 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1112.96 seconds
wall clock time: 20 minutes 48.32 seconds (1248.32 seconds total)