Starting phenix.real_space_refine
on Tue Feb  3 14:01:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8eqt_28545/02_2026/8eqt_28545_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8eqt_28545/02_2026/8eqt_28545.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8eqt_28545/02_2026/8eqt_28545.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8eqt_28545/02_2026/8eqt_28545.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8eqt_28545/02_2026/8eqt_28545_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8eqt_28545/02_2026/8eqt_28545_neut.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      16      5.16       5
     C    2122      2.51       5
     N     490      2.21       5
     O     574      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3206
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1562
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 191, 1562
          Classifications: {'peptide': 191}
          Link IDs: {'PTRANS': 4, 'TRANS': 186}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1562
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 191, 1562
          Classifications: {'peptide': 191}
          Link IDs: {'PTRANS': 4, 'TRANS': 186}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 41
          Unusual residues: {'PEE': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 61
    Chain: "B"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 41
          Unusual residues: {'PEE': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 61
  Time building chain proxies: 0.78, per 1000 atoms: 0.24
  Number of scatterers: 3206
  At special positions: 0
  Unit cell: (63.3, 59.924, 91.152, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      16     16.00
     P       4     15.00
     O     574      8.00
     N     490      7.00
     C    2122      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: 0.33
  Conformation dependent library (CDL) restraints added in 118.5 milliseconds
  

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  728

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 2 sheets defined
      49.7% alpha, 20.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 61
    Processing helix  chain 'A' and resid 67 through 100
      removed outlier: 4.095A  pdb=" N   SER A  92 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 134
    Processing helix  chain 'A' and resid 136 through 141
      removed outlier: 3.567A  pdb=" N   LEU A 140 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 224
    Processing helix  chain 'B' and resid 43 through 61
    Processing helix  chain 'B' and resid 67 through 100
      removed outlier: 4.095A  pdb=" N   SER B  92 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 134
    Processing helix  chain 'B' and resid 136 through 141
      removed outlier: 3.567A  pdb=" N   LEU B 140 " --> pdb=" O   LYS B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 224
    Processing sheet with id=AA1, first strand: chain 'A' and resid 155 through 160
      removed outlier: 6.214A  pdb=" N   HIS A 150 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 8.438A  pdb=" N   CYS A 200 " --> pdb=" O   HIS A 150 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   ILE A 232 " --> pdb=" O   TYR A 215 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   THR A 217 " --> pdb=" O   PHE A 230 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   PHE A 230 " --> pdb=" O   THR A 217 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 155 through 160
      removed outlier: 6.214A  pdb=" N   HIS B 150 " --> pdb=" O   CYS B 200 " (cutoff:3.500A)
      removed outlier: 8.438A  pdb=" N   CYS B 200 " --> pdb=" O   HIS B 150 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   ILE B 232 " --> pdb=" O   TYR B 215 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   THR B 217 " --> pdb=" O   PHE B 230 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   PHE B 230 " --> pdb=" O   THR B 217 " (cutoff:3.500A)

    204 hydrogen bonds defined for protein.
    594 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: 0.49

  Time building geometry restraints manager: 0.40 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 464
        1.31 -     1.44: 1042
        1.44 -     1.57: 1764
        1.57 -     1.69: 8
        1.69 -     1.82: 18
  Bond restraints: 3296
  Sorted by residual:
  bond pdb=" C10 PEE B 402 "
       pdb=" O2  PEE B 402 "
    ideal  model  delta    sigma   weight residual
    1.332  1.423 -0.091 2.00e-02 2.50e+03 2.05e+01
  bond pdb=" C10 PEE A 401 "
       pdb=" O2  PEE A 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.423 -0.091 2.00e-02 2.50e+03 2.05e+01
  bond pdb=" C10 PEE B 401 "
       pdb=" O2  PEE B 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.421 -0.089 2.00e-02 2.50e+03 2.00e+01
  bond pdb=" C10 PEE A 402 "
       pdb=" O2  PEE A 402 "
    ideal  model  delta    sigma   weight residual
    1.332  1.421 -0.089 2.00e-02 2.50e+03 2.00e+01
  bond pdb=" C30 PEE B 402 "
       pdb=" O3  PEE B 402 "
    ideal  model  delta    sigma   weight residual
    1.327  1.410 -0.083 2.00e-02 2.50e+03 1.74e+01
  ... (remaining 3291 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.47: 4442
        3.47 -     6.94: 30
        6.94 -    10.42: 10
       10.42 -    13.89: 2
       13.89 -    17.36: 4
  Bond angle restraints: 4488
  Sorted by residual:
  angle pdb=" O3P PEE A 401 "
        pdb=" P   PEE A 401 "
        pdb=" O4P PEE A 401 "
      ideal   model   delta    sigma   weight residual
      92.91  110.27  -17.36 3.00e+00 1.11e-01 3.35e+01
  angle pdb=" O3P PEE B 402 "
        pdb=" P   PEE B 402 "
        pdb=" O4P PEE B 402 "
      ideal   model   delta    sigma   weight residual
      92.91  110.27  -17.36 3.00e+00 1.11e-01 3.35e+01
  angle pdb=" O3P PEE B 401 "
        pdb=" P   PEE B 401 "
        pdb=" O4P PEE B 401 "
      ideal   model   delta    sigma   weight residual
      92.91  109.90  -16.99 3.00e+00 1.11e-01 3.21e+01
  angle pdb=" O3P PEE A 402 "
        pdb=" P   PEE A 402 "
        pdb=" O4P PEE A 402 "
      ideal   model   delta    sigma   weight residual
      92.91  109.90  -16.99 3.00e+00 1.11e-01 3.21e+01
  angle pdb=" O1P PEE A 401 "
        pdb=" P   PEE A 401 "
        pdb=" O2P PEE A 401 "
      ideal   model   delta    sigma   weight residual
     119.43  108.94   10.49 3.00e+00 1.11e-01 1.22e+01
  ... (remaining 4483 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.38: 1822
       29.38 -    58.76: 34
       58.76 -    88.14: 10
       88.14 -   117.52: 6
      117.52 -   146.90: 6
  Dihedral angle restraints: 1878
    sinusoidal: 740
      harmonic: 1138
  Sorted by residual:
  dihedral pdb=" C4  PEE A 401 "
           pdb=" O4P PEE A 401 "
           pdb=" P   PEE A 401 "
           pdb=" O2P PEE A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -75.78   71.12 -146.90     1      3.00e+01 1.11e-03 1.96e+01
  dihedral pdb=" C4  PEE B 402 "
           pdb=" O4P PEE B 402 "
           pdb=" P   PEE B 402 "
           pdb=" O2P PEE B 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -75.78   71.12 -146.90     1      3.00e+01 1.11e-03 1.96e+01
  dihedral pdb=" C3  PEE B 401 "
           pdb=" C1  PEE B 401 "
           pdb=" C2  PEE B 401 "
           pdb=" O3P PEE B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.73  -79.00  141.73     1      3.00e+01 1.11e-03 1.90e+01
  ... (remaining 1875 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 446
       0.065 -    0.129: 54
       0.129 -    0.193: 0
       0.193 -    0.258: 0
       0.258 -    0.322: 4
  Chirality restraints: 504
  Sorted by residual:
  chirality pdb=" C2  PEE B 402 "
            pdb=" C1  PEE B 402 "
            pdb=" C3  PEE B 402 "
            pdb=" O2  PEE B 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.65    0.32 2.00e-01 2.50e+01 2.60e+00
  chirality pdb=" C2  PEE A 401 "
            pdb=" C1  PEE A 401 "
            pdb=" C3  PEE A 401 "
            pdb=" O2  PEE A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.65    0.32 2.00e-01 2.50e+01 2.60e+00
  chirality pdb=" C2  PEE B 401 "
            pdb=" C1  PEE B 401 "
            pdb=" C3  PEE B 401 "
            pdb=" O2  PEE B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.64    0.31 2.00e-01 2.50e+01 2.37e+00
  ... (remaining 501 not shown)

  Planarity restraints: 530
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B  79 "   -0.007 2.00e-02 2.50e+03   1.34e-02 1.78e+00
        pdb=" C   PHE B  79 "    0.023 2.00e-02 2.50e+03
        pdb=" O   PHE B  79 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   VAL B  80 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A  79 "    0.007 2.00e-02 2.50e+03   1.34e-02 1.78e+00
        pdb=" C   PHE A  79 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   PHE A  79 "    0.009 2.00e-02 2.50e+03
        pdb=" N   VAL A  80 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A  87 "    0.006 2.00e-02 2.50e+03   1.22e-02 1.49e+00
        pdb=" C   PHE A  87 "   -0.021 2.00e-02 2.50e+03
        pdb=" O   PHE A  87 "    0.008 2.00e-02 2.50e+03
        pdb=" N   VAL A  88 "    0.007 2.00e-02 2.50e+03
  ... (remaining 527 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 339
        2.75 -     3.29: 3168
        3.29 -     3.83: 5423
        3.83 -     4.36: 6176
        4.36 -     4.90: 10490
  Nonbonded interactions: 25596
  Sorted by model distance:
  nonbonded pdb=" O   THR B  89 "
            pdb=" OG  SER B  92 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   THR A  89 "
            pdb=" OG  SER A  92 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   PRO B  42 "
            pdb=" OH  TYR B  91 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   PRO A  42 "
            pdb=" OH  TYR A  91 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OG1 THR A 151 "
            pdb=" O   TYR A 154 "
     model   vdw
     2.248 3.040
  ... (remaining 25591 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 40 through 238 or (resid 401 through 402 and (name N or na \ 
me C1 or name C10 or name C11 or name C2 or name C3 or name C30 or name C31 or n \ 
ame C4 or name C5 or name O1P or name O2 or name O2P or name O3 or name O3P or n \ 
ame O4 or name O4P or name O5 or name P ))))
  selection = (chain 'B' and (resid 40 through 401 or (resid 402 and (name N or name C1 or nam \ 
e C10 or name C11 or name C2 or name C3 or name C30 or name C31 or name C4 or na \ 
me C5 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or na \ 
me O4P or name O5 or name P ))))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.250
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     5.000
  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:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.091   3296  Z= 0.318
  Angle     :  0.888  17.361   4488  Z= 0.355
  Chirality :  0.046   0.322    504
  Planarity :  0.004   0.026    530
  Dihedral  : 17.012 146.900   1150
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  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:  0.61 (0.40), residues: 374
  helix:  1.18 (0.37), residues: 164
  sheet:  0.65 (0.56), residues: 90
  loop : -0.77 (0.48), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 126 
 TYR   0.006   0.001   TYR B 156 
 PHE   0.005   0.001   PHE B 114 
 TRP   0.011   0.001   TRP A 149 
 HIS   0.003   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00634 ( 3296)
  covalent geometry    : angle       0.88755 ( 4488)
  hydrogen bonds       : bond        0.12924 (  204)
  hydrogen bonds       : angle       6.59782 (  594)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A   89 THR cc_start: 0.9351 (m) cc_final: 0.9042 (p)
REVERT: A  105 PHE cc_start: 0.9339 (m-80) cc_final: 0.9061 (m-80)
REVERT: A  106 LEU cc_start: 0.8382 (pp) cc_final: 0.8127 (tp)
REVERT: A  134 ARG cc_start: 0.8323 (tpt170) cc_final: 0.6923 (ttt180)
REVERT: A  136 LYS cc_start: 0.8499 (pttt) cc_final: 0.8201 (pttt)
REVERT: A  154 TYR cc_start: 0.8408 (t80) cc_final: 0.7536 (t80)
REVERT: A  183 ASP cc_start: 0.9086 (p0) cc_final: 0.8709 (p0)
REVERT: B   89 THR cc_start: 0.9350 (m) cc_final: 0.9042 (p)
REVERT: B  105 PHE cc_start: 0.9337 (m-80) cc_final: 0.9058 (m-80)
REVERT: B  106 LEU cc_start: 0.8384 (pp) cc_final: 0.8127 (tp)
REVERT: B  134 ARG cc_start: 0.8321 (tpt170) cc_final: 0.6922 (ttt180)
REVERT: B  136 LYS cc_start: 0.8499 (pttt) cc_final: 0.8199 (pttt)
REVERT: B  154 TYR cc_start: 0.8403 (t80) cc_final: 0.7532 (t80)
REVERT: B  183 ASP cc_start: 0.9088 (p0) cc_final: 0.8717 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.0584
  time to fit residues: 12.5251
Evaluate side-chains
  82 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0670
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A 116 GLN
B 116 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.102795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.078114 restraints weight = 6306.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 4.02
r_work: 0.2826 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.3452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3296  Z= 0.132
  Angle     :  0.501   4.252   4488  Z= 0.261
  Chirality :  0.041   0.135    504
  Planarity :  0.003   0.022    530
  Dihedral  : 17.470 146.435    480
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 17.34 %
    Favored  : 79.19 %
  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:  1.74 (0.41), residues: 374
  helix:  2.72 (0.37), residues: 168
  sheet:  0.77 (0.57), residues: 86
  loop : -0.89 (0.46), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 134 
 TYR   0.008   0.001   TYR B 113 
 PHE   0.025   0.002   PHE A 230 
 TRP   0.011   0.001   TRP A 193 
 HIS   0.005   0.001   HIS A  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 3296)
  covalent geometry    : angle       0.50125 ( 4488)
  hydrogen bonds       : bond        0.02728 (  204)
  hydrogen bonds       : angle       4.48477 (  594)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A  102 GLU cc_start: 0.8538 (mp0) cc_final: 0.8128 (mp0)
REVERT: A  106 LEU cc_start: 0.8443 (pp) cc_final: 0.8228 (tp)
REVERT: A  134 ARG cc_start: 0.8018 (tpt170) cc_final: 0.7572 (ttt180)
REVERT: A  154 TYR cc_start: 0.8437 (t80) cc_final: 0.7729 (t80)
REVERT: A  194 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8492 (mt-10)
REVERT: A  198 LYS cc_start: 0.8584 (mtmt) cc_final: 0.8163 (mtmt)
REVERT: A  216 SER cc_start: 0.9056 (t) cc_final: 0.8707 (p)
REVERT: A  233 TYR cc_start: 0.9604 (m-80) cc_final: 0.9026 (m-80)
REVERT: B  102 GLU cc_start: 0.8556 (mp0) cc_final: 0.8142 (mp0)
REVERT: B  106 LEU cc_start: 0.8442 (pp) cc_final: 0.8226 (tp)
REVERT: B  134 ARG cc_start: 0.8034 (tpt170) cc_final: 0.7579 (ttt180)
REVERT: B  154 TYR cc_start: 0.8440 (t80) cc_final: 0.7734 (t80)
REVERT: B  194 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8476 (mt-10)
REVERT: B  198 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8162 (mtmt)
REVERT: B  216 SER cc_start: 0.9047 (t) cc_final: 0.8698 (p)
REVERT: B  233 TYR cc_start: 0.9602 (m-80) cc_final: 0.9006 (m-80)
  outliers start: 12
  outliers final: 10
  residues processed: 122
  average time/residue: 0.0466
  time to fit residues: 6.8091
Evaluate side-chains
  102 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain B residue   81 CYS
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  229 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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 = 0.3395 r_free = 0.3395 target = 0.100209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.075313 restraints weight = 6360.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 4.03
r_work: 0.2789 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.4072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3296  Z= 0.143
  Angle     :  0.499   8.070   4488  Z= 0.251
  Chirality :  0.040   0.128    504
  Planarity :  0.003   0.022    530
  Dihedral  : 16.741 146.640    480
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 19.65 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.75 (0.41), residues: 374
  helix:  2.80 (0.37), residues: 168
  sheet:  0.73 (0.58), residues: 86
  loop : -0.98 (0.44), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B  68 
 TYR   0.006   0.001   TYR A 109 
 PHE   0.016   0.002   PHE A  43 
 TRP   0.010   0.001   TRP B 128 
 HIS   0.003   0.002   HIS A 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3296)
  covalent geometry    : angle       0.49863 ( 4488)
  hydrogen bonds       : bond        0.02784 (  204)
  hydrogen bonds       : angle       4.31522 (  594)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 GLU cc_start: 0.8384 (mp0) cc_final: 0.8152 (mp0)
REVERT: A  105 PHE cc_start: 0.9312 (m-80) cc_final: 0.9068 (m-80)
REVERT: A  134 ARG cc_start: 0.8161 (tpt170) cc_final: 0.7634 (ttt180)
REVERT: A  136 LYS cc_start: 0.8749 (pttt) cc_final: 0.8456 (pttt)
REVERT: A  155 ASP cc_start: 0.7966 (p0) cc_final: 0.7486 (p0)
REVERT: A  194 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8508 (mt-10)
REVERT: A  211 TYR cc_start: 0.8129 (m-80) cc_final: 0.7876 (m-80)
REVERT: A  216 SER cc_start: 0.9121 (t) cc_final: 0.8887 (p)
REVERT: A  232 ILE cc_start: 0.9401 (mm) cc_final: 0.9109 (mm)
REVERT: B  102 GLU cc_start: 0.8368 (mp0) cc_final: 0.8122 (mp0)
REVERT: B  134 ARG cc_start: 0.8177 (tpt170) cc_final: 0.7637 (ttt180)
REVERT: B  136 LYS cc_start: 0.8747 (pttt) cc_final: 0.8457 (pttt)
REVERT: B  155 ASP cc_start: 0.7953 (p0) cc_final: 0.7478 (p0)
REVERT: B  194 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8493 (mt-10)
REVERT: B  211 TYR cc_start: 0.8132 (m-80) cc_final: 0.7879 (m-80)
REVERT: B  216 SER cc_start: 0.9117 (t) cc_final: 0.8886 (p)
REVERT: B  232 ILE cc_start: 0.9392 (mm) cc_final: 0.9090 (mm)
  outliers start: 14
  outliers final: 14
  residues processed: 124
  average time/residue: 0.0728
  time to fit residues: 10.8756
Evaluate side-chains
  122 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  227 HIS
Chi-restraints excluded: chain B residue   81 CYS
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  227 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 182 HIS
A 227 HIS
B 182 HIS
B 227 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.099280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.074838 restraints weight = 6376.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.2951 rms_B_bonded: 3.95
r_work: 0.2772 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.4623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3296  Z= 0.139
  Angle     :  0.463   5.692   4488  Z= 0.248
  Chirality :  0.039   0.137    504
  Planarity :  0.003   0.021    530
  Dihedral  : 16.224 145.006    480
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 21.39 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.77 (0.41), residues: 374
  helix:  2.73 (0.36), residues: 180
  sheet:  0.79 (0.56), residues: 84
  loop : -1.26 (0.47), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 134 
 TYR   0.005   0.001   TYR B 160 
 PHE   0.017   0.002   PHE A 114 
 TRP   0.009   0.001   TRP A 128 
 HIS   0.003   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3296)
  covalent geometry    : angle       0.46252 ( 4488)
  hydrogen bonds       : bond        0.02573 (  204)
  hydrogen bonds       : angle       4.17871 (  594)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A  102 GLU cc_start: 0.8313 (mp0) cc_final: 0.8061 (mp0)
REVERT: A  134 ARG cc_start: 0.8137 (tpt170) cc_final: 0.7597 (ttt180)
REVERT: A  154 TYR cc_start: 0.8416 (t80) cc_final: 0.7981 (t80)
REVERT: A  155 ASP cc_start: 0.7897 (p0) cc_final: 0.7380 (p0)
REVERT: A  194 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8533 (mt-10)
REVERT: A  211 TYR cc_start: 0.8210 (m-80) cc_final: 0.7916 (m-80)
REVERT: A  226 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8105 (tm-30)
REVERT: A  227 HIS cc_start: 0.8582 (OUTLIER) cc_final: 0.7763 (m90)
REVERT: B  102 GLU cc_start: 0.8321 (mp0) cc_final: 0.8049 (mp0)
REVERT: B  134 ARG cc_start: 0.8157 (tpt170) cc_final: 0.7596 (ttt180)
REVERT: B  154 TYR cc_start: 0.8422 (t80) cc_final: 0.7996 (t80)
REVERT: B  155 ASP cc_start: 0.7914 (p0) cc_final: 0.7395 (p0)
REVERT: B  194 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8537 (mt-10)
REVERT: B  211 TYR cc_start: 0.8222 (m-80) cc_final: 0.7929 (m-80)
REVERT: B  226 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8095 (tm-30)
REVERT: B  227 HIS cc_start: 0.8592 (OUTLIER) cc_final: 0.7777 (m90)
  outliers start: 14
  outliers final: 12
  residues processed: 102
  average time/residue: 0.0471
  time to fit residues: 5.8032
Evaluate side-chains
  94 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  227 HIS
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue   81 CYS
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  227 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0170
   chunk 20 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.7018

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

Flipped N/Q/H residues before XYZ refinement:
A  70 GLN
A 227 HIS
B  70 GLN
B 227 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.101499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.076529 restraints weight = 6206.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.2990 rms_B_bonded: 3.89
r_work: 0.2821 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.4755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3296  Z= 0.129
  Angle     :  0.481   8.778   4488  Z= 0.245
  Chirality :  0.039   0.137    504
  Planarity :  0.003   0.020    530
  Dihedral  : 15.935 141.310    480
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 25.14 %
    Favored  : 70.81 %
  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:  1.89 (0.42), residues: 374
  helix:  2.69 (0.35), residues: 192
  sheet:  0.75 (0.55), residues: 84
  loop : -1.35 (0.49), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 122 
 TYR   0.006   0.001   TYR A 109 
 PHE   0.016   0.002   PHE A 114 
 TRP   0.009   0.001   TRP A 128 
 HIS   0.007   0.002   HIS B 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 3296)
  covalent geometry    : angle       0.48113 ( 4488)
  hydrogen bonds       : bond        0.02527 (  204)
  hydrogen bonds       : angle       4.09217 (  594)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 GLU cc_start: 0.8312 (mp0) cc_final: 0.8029 (mp0)
REVERT: A  134 ARG cc_start: 0.8225 (tpt170) cc_final: 0.7718 (ttt180)
REVERT: A  154 TYR cc_start: 0.8392 (t80) cc_final: 0.8053 (t80)
REVERT: A  155 ASP cc_start: 0.8010 (p0) cc_final: 0.7475 (p0)
REVERT: A  194 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8480 (mt-10)
REVERT: A  198 LYS cc_start: 0.8526 (mtmt) cc_final: 0.7896 (mmtm)
REVERT: A  211 TYR cc_start: 0.8228 (m-80) cc_final: 0.7973 (m-80)
REVERT: B  102 GLU cc_start: 0.8307 (mp0) cc_final: 0.8026 (mp0)
REVERT: B  134 ARG cc_start: 0.8233 (tpt170) cc_final: 0.7715 (ttt180)
REVERT: B  154 TYR cc_start: 0.8407 (t80) cc_final: 0.8079 (t80)
REVERT: B  155 ASP cc_start: 0.8015 (p0) cc_final: 0.7483 (p0)
REVERT: B  194 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8494 (mt-10)
REVERT: B  211 TYR cc_start: 0.8240 (m-80) cc_final: 0.7987 (m-80)
REVERT: B  234 ASN cc_start: 0.9228 (t0) cc_final: 0.8985 (t0)
  outliers start: 14
  outliers final: 12
  residues processed: 101
  average time/residue: 0.0652
  time to fit residues: 7.9476
Evaluate side-chains
  95 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  227 HIS
Chi-restraints excluded: chain B residue   81 CYS
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  227 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 14 optimal weight:    0.4980
   chunk 32 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 204 HIS
A 227 HIS
B 150 HIS
B 204 HIS
B 227 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.101755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.077361 restraints weight = 6132.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 3.81
r_work: 0.2821 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.4840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3296  Z= 0.125
  Angle     :  0.429   4.592   4488  Z= 0.233
  Chirality :  0.039   0.137    504
  Planarity :  0.003   0.020    530
  Dihedral  : 15.742 136.083    480
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 25.14 %
    Favored  : 70.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.98 (0.42), residues: 374
  helix:  2.86 (0.36), residues: 192
  sheet:  0.67 (0.53), residues: 84
  loop : -1.38 (0.50), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 122 
 TYR   0.005   0.001   TYR B 109 
 PHE   0.023   0.002   PHE A 114 
 TRP   0.009   0.001   TRP B 128 
 HIS   0.005   0.001   HIS A 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3296)
  covalent geometry    : angle       0.42948 ( 4488)
  hydrogen bonds       : bond        0.02461 (  204)
  hydrogen bonds       : angle       4.04612 (  594)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A  134 ARG cc_start: 0.8194 (tpt170) cc_final: 0.7746 (ttt180)
REVERT: A  154 TYR cc_start: 0.8373 (t80) cc_final: 0.8049 (t80)
REVERT: A  155 ASP cc_start: 0.7991 (p0) cc_final: 0.7437 (p0)
REVERT: A  194 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8475 (mt-10)
REVERT: A  198 LYS cc_start: 0.8517 (mtmt) cc_final: 0.7898 (mmtm)
REVERT: A  211 TYR cc_start: 0.8247 (m-80) cc_final: 0.8013 (m-80)
REVERT: A  227 HIS cc_start: 0.8607 (OUTLIER) cc_final: 0.7730 (m90)
REVERT: B  102 GLU cc_start: 0.8284 (mp0) cc_final: 0.7976 (mp0)
REVERT: B  134 ARG cc_start: 0.8213 (tpt170) cc_final: 0.7754 (ttt180)
REVERT: B  154 TYR cc_start: 0.8386 (t80) cc_final: 0.8071 (t80)
REVERT: B  155 ASP cc_start: 0.7946 (p0) cc_final: 0.7374 (p0)
REVERT: B  194 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8481 (mt-10)
REVERT: B  198 LYS cc_start: 0.8530 (mtmt) cc_final: 0.7877 (mmtm)
REVERT: B  211 TYR cc_start: 0.8251 (m-80) cc_final: 0.8016 (m-80)
REVERT: B  226 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8004 (tm-30)
REVERT: B  227 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.7765 (m90)
  outliers start: 15
  outliers final: 13
  residues processed: 97
  average time/residue: 0.0763
  time to fit residues: 8.8313
Evaluate side-chains
  95 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  227 HIS
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue   81 CYS
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  227 HIS
Chi-restraints excluded: chain B residue  237 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 9 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 227 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.101097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.076744 restraints weight = 6281.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 3.83
r_work: 0.2811 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.4977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3296  Z= 0.141
  Angle     :  0.495   9.190   4488  Z= 0.252
  Chirality :  0.039   0.134    504
  Planarity :  0.003   0.020    530
  Dihedral  : 15.629 134.787    480
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 23.99 %
    Favored  : 70.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.99 (0.42), residues: 374
  helix:  2.93 (0.36), residues: 192
  sheet:  0.54 (0.54), residues: 84
  loop : -1.38 (0.51), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 126 
 TYR   0.005   0.001   TYR B 160 
 PHE   0.021   0.002   PHE A 114 
 TRP   0.010   0.001   TRP B 128 
 HIS   0.008   0.001   HIS A 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 3296)
  covalent geometry    : angle       0.49495 ( 4488)
  hydrogen bonds       : bond        0.02518 (  204)
  hydrogen bonds       : angle       4.05485 (  594)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A  134 ARG cc_start: 0.8223 (tpt170) cc_final: 0.7777 (ttt180)
REVERT: A  154 TYR cc_start: 0.8373 (t80) cc_final: 0.8026 (t80)
REVERT: A  155 ASP cc_start: 0.7988 (p0) cc_final: 0.7422 (p0)
REVERT: A  194 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8481 (mt-10)
REVERT: A  198 LYS cc_start: 0.8541 (mtmt) cc_final: 0.7936 (mmtm)
REVERT: A  211 TYR cc_start: 0.8244 (m-80) cc_final: 0.8009 (m-80)
REVERT: A  227 HIS cc_start: 0.8565 (OUTLIER) cc_final: 0.7852 (m-70)
REVERT: B  134 ARG cc_start: 0.8244 (tpt170) cc_final: 0.7760 (ttt180)
REVERT: B  154 TYR cc_start: 0.8383 (t80) cc_final: 0.8054 (t80)
REVERT: B  155 ASP cc_start: 0.7942 (p0) cc_final: 0.7351 (p0)
REVERT: B  194 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8495 (mt-10)
REVERT: B  198 LYS cc_start: 0.8552 (mtmt) cc_final: 0.7900 (mmtm)
REVERT: B  211 TYR cc_start: 0.8251 (m-80) cc_final: 0.8016 (m-80)
REVERT: B  226 GLU cc_start: 0.8633 (tm-30) cc_final: 0.7997 (tm-30)
REVERT: B  227 HIS cc_start: 0.8669 (OUTLIER) cc_final: 0.7798 (m90)
REVERT: B  234 ASN cc_start: 0.9262 (t0) cc_final: 0.9029 (t0)
  outliers start: 19
  outliers final: 15
  residues processed: 102
  average time/residue: 0.0735
  time to fit residues: 8.9836
Evaluate side-chains
  101 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  227 HIS
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue   81 CYS
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  227 HIS
Chi-restraints excluded: chain B residue  237 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 16 optimal weight:    0.4980
   chunk 11 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 227 HIS
B 227 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.100763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.076001 restraints weight = 6305.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 3.87
r_work: 0.2798 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.5006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3296  Z= 0.140
  Angle     :  0.493   9.342   4488  Z= 0.258
  Chirality :  0.039   0.135    504
  Planarity :  0.003   0.020    530
  Dihedral  : 15.534 132.612    480
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 23.70 %
    Favored  : 70.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.43), residues: 374
  helix:  2.97 (0.36), residues: 192
  sheet:  0.46 (0.54), residues: 84
  loop : -1.37 (0.50), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 126 
 TYR   0.006   0.001   TYR B 109 
 PHE   0.020   0.002   PHE A 114 
 TRP   0.010   0.001   TRP B 128 
 HIS   0.005   0.001   HIS B 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 3296)
  covalent geometry    : angle       0.49284 ( 4488)
  hydrogen bonds       : bond        0.02480 (  204)
  hydrogen bonds       : angle       4.03331 (  594)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A  134 ARG cc_start: 0.8231 (tpt170) cc_final: 0.7784 (ttt180)
REVERT: A  154 TYR cc_start: 0.8312 (t80) cc_final: 0.7968 (t80)
REVERT: A  155 ASP cc_start: 0.7983 (p0) cc_final: 0.7400 (p0)
REVERT: A  194 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8480 (mt-10)
REVERT: A  198 LYS cc_start: 0.8576 (mtmt) cc_final: 0.7927 (mmtm)
REVERT: A  211 TYR cc_start: 0.8285 (m-80) cc_final: 0.8070 (m-80)
REVERT: A  226 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8024 (tm-30)
REVERT: A  227 HIS cc_start: 0.8645 (OUTLIER) cc_final: 0.7828 (m90)
REVERT: A  234 ASN cc_start: 0.9195 (t0) cc_final: 0.8963 (t0)
REVERT: B  134 ARG cc_start: 0.8273 (tpt170) cc_final: 0.7804 (ttt180)
REVERT: B  154 TYR cc_start: 0.8340 (t80) cc_final: 0.8009 (t80)
REVERT: B  155 ASP cc_start: 0.7938 (p0) cc_final: 0.7339 (p0)
REVERT: B  194 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8492 (mt-10)
REVERT: B  198 LYS cc_start: 0.8563 (mtmt) cc_final: 0.7895 (mmtm)
REVERT: B  211 TYR cc_start: 0.8256 (m-80) cc_final: 0.8044 (m-80)
REVERT: B  226 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8015 (tm-30)
REVERT: B  227 HIS cc_start: 0.8700 (OUTLIER) cc_final: 0.7709 (m90)
  outliers start: 19
  outliers final: 15
  residues processed: 99
  average time/residue: 0.0542
  time to fit residues: 6.4689
Evaluate side-chains
  101 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  227 HIS
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue   81 CYS
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  227 HIS
Chi-restraints excluded: chain B residue  237 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 227 HIS
B 227 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.100818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.076270 restraints weight = 6283.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 3.84
r_work: 0.2808 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.5094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3296  Z= 0.133
  Angle     :  0.489   9.624   4488  Z= 0.256
  Chirality :  0.039   0.134    504
  Planarity :  0.003   0.020    530
  Dihedral  : 15.466 132.565    480
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 23.12 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.43), residues: 374
  helix:  2.99 (0.36), residues: 192
  sheet:  0.43 (0.54), residues: 84
  loop : -1.37 (0.50), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 122 
 TYR   0.005   0.001   TYR A 109 
 PHE   0.019   0.002   PHE A 114 
 TRP   0.010   0.001   TRP A 128 
 HIS   0.007   0.001   HIS A 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3296)
  covalent geometry    : angle       0.48867 ( 4488)
  hydrogen bonds       : bond        0.02451 (  204)
  hydrogen bonds       : angle       4.00552 (  594)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A  134 ARG cc_start: 0.8273 (tpt170) cc_final: 0.7849 (ttt180)
REVERT: A  154 TYR cc_start: 0.8299 (t80) cc_final: 0.7974 (t80)
REVERT: A  155 ASP cc_start: 0.7979 (p0) cc_final: 0.7398 (p0)
REVERT: A  194 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8454 (mt-10)
REVERT: A  198 LYS cc_start: 0.8542 (mtmt) cc_final: 0.7889 (mmtm)
REVERT: A  211 TYR cc_start: 0.8313 (m-80) cc_final: 0.8085 (m-80)
REVERT: A  226 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8006 (tm-30)
REVERT: A  227 HIS cc_start: 0.8642 (OUTLIER) cc_final: 0.7798 (m90)
REVERT: A  234 ASN cc_start: 0.9207 (t0) cc_final: 0.8967 (t0)
REVERT: B  134 ARG cc_start: 0.8283 (tpt170) cc_final: 0.7822 (ttt180)
REVERT: B  154 TYR cc_start: 0.8297 (t80) cc_final: 0.7980 (t80)
REVERT: B  155 ASP cc_start: 0.7939 (p0) cc_final: 0.7340 (p0)
REVERT: B  194 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8484 (mt-10)
REVERT: B  198 LYS cc_start: 0.8548 (mtmt) cc_final: 0.7819 (mmtm)
REVERT: B  211 TYR cc_start: 0.8281 (m-80) cc_final: 0.8067 (m-80)
REVERT: B  226 GLU cc_start: 0.8612 (tm-30) cc_final: 0.7961 (tm-30)
REVERT: B  227 HIS cc_start: 0.8660 (OUTLIER) cc_final: 0.7669 (m90)
REVERT: B  234 ASN cc_start: 0.9276 (t0) cc_final: 0.9074 (t0)
  outliers start: 18
  outliers final: 14
  residues processed: 98
  average time/residue: 0.0747
  time to fit residues: 8.7274
Evaluate side-chains
  99 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  227 HIS
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue   81 CYS
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  227 HIS
Chi-restraints excluded: chain B residue  237 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0050
   chunk 26 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.7798

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

Flipped N/Q/H residues before XYZ refinement:
A  70 GLN
A 227 HIS
B  70 GLN
B 227 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.100814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.076323 restraints weight = 6321.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 3.85
r_work: 0.2804 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.5106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3296  Z= 0.141
  Angle     :  0.500   9.795   4488  Z= 0.262
  Chirality :  0.040   0.135    504
  Planarity :  0.003   0.020    530
  Dihedral  : 15.437 132.872    480
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 22.83 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.99 (0.43), residues: 374
  helix:  2.99 (0.36), residues: 192
  sheet:  0.44 (0.54), residues: 84
  loop : -1.41 (0.51), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 126 
 TYR   0.005   0.001   TYR A 206 
 PHE   0.026   0.002   PHE A 114 
 TRP   0.010   0.001   TRP B 128 
 HIS   0.006   0.001   HIS A 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3296)
  covalent geometry    : angle       0.50045 ( 4488)
  hydrogen bonds       : bond        0.02456 (  204)
  hydrogen bonds       : angle       4.01445 (  594)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A  134 ARG cc_start: 0.8257 (tpt170) cc_final: 0.7806 (ttt180)
REVERT: A  154 TYR cc_start: 0.8298 (t80) cc_final: 0.7977 (t80)
REVERT: A  155 ASP cc_start: 0.7997 (p0) cc_final: 0.7415 (p0)
REVERT: A  194 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8453 (mt-10)
REVERT: A  198 LYS cc_start: 0.8524 (mtmt) cc_final: 0.7868 (mmtm)
REVERT: A  211 TYR cc_start: 0.8317 (m-80) cc_final: 0.8100 (m-80)
REVERT: A  226 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8186 (tp30)
REVERT: A  227 HIS cc_start: 0.8663 (OUTLIER) cc_final: 0.7761 (m90)
REVERT: A  234 ASN cc_start: 0.9228 (t0) cc_final: 0.8979 (t0)
REVERT: B  134 ARG cc_start: 0.8269 (tpt170) cc_final: 0.7796 (ttt180)
REVERT: B  154 TYR cc_start: 0.8259 (t80) cc_final: 0.7950 (t80)
REVERT: B  155 ASP cc_start: 0.7917 (p0) cc_final: 0.7278 (p0)
REVERT: B  194 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8461 (mt-10)
REVERT: B  198 LYS cc_start: 0.8562 (mtmt) cc_final: 0.7835 (mmtm)
REVERT: B  211 TYR cc_start: 0.8314 (m-80) cc_final: 0.8097 (m-80)
REVERT: B  226 GLU cc_start: 0.8621 (tm-30) cc_final: 0.7981 (tm-30)
REVERT: B  227 HIS cc_start: 0.8683 (OUTLIER) cc_final: 0.7648 (m90)
REVERT: B  234 ASN cc_start: 0.9279 (t0) cc_final: 0.9076 (t0)
  outliers start: 19
  outliers final: 15
  residues processed: 99
  average time/residue: 0.0748
  time to fit residues: 8.8590
Evaluate side-chains
  102 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  227 HIS
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue   81 CYS
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  227 HIS
Chi-restraints excluded: chain B residue  229 THR
Chi-restraints excluded: chain B residue  237 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 14 optimal weight:    0.0870
   chunk 17 optimal weight:    0.0870
   chunk 20 optimal weight:    0.2980
   chunk 10 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 25 optimal weight:    0.4980
   chunk 32 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.3336

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

Flipped N/Q/H residues before XYZ refinement:
A  70 GLN
A 227 HIS
B  70 GLN
B 227 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.103134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.078506 restraints weight = 6253.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 3.84
r_work: 0.2839 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.5198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   3296  Z= 0.103
  Angle     :  0.513  10.152   4488  Z= 0.261
  Chirality :  0.039   0.135    504
  Planarity :  0.002   0.020    530
  Dihedral  : 15.280 133.289    480
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 25.14 %
    Favored  : 71.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.43), residues: 374
  helix:  2.98 (0.36), residues: 192
  sheet:  0.52 (0.54), residues: 84
  loop : -1.45 (0.51), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 126 
 TYR   0.005   0.001   TYR A 206 
 PHE   0.026   0.002   PHE A 114 
 TRP   0.010   0.001   TRP A 128 
 HIS   0.006   0.001   HIS A 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 3296)
  covalent geometry    : angle       0.51277 ( 4488)
  hydrogen bonds       : bond        0.02329 (  204)
  hydrogen bonds       : angle       3.92510 (  594)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 899.66 seconds
wall clock time: 16 minutes 12.02 seconds (972.02 seconds total)