Starting phenix.real_space_refine
on Tue Mar  3 12:45:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xgy_33189/03_2026/7xgy_33189.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xgy_33189/03_2026/7xgy_33189.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xgy_33189/03_2026/7xgy_33189.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xgy_33189/03_2026/7xgy_33189.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xgy_33189/03_2026/7xgy_33189.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xgy_33189/03_2026/7xgy_33189.map"
  }
  resolution = 3.5
  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=   0.001
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
     Fe      4      7.16       5
     S      12      5.16       5
     C    2954      2.51       5
     N     780      2.21       5
     O     805      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4555
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1069
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1069
          Classifications: {'peptide': 141}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 133}
    Chain: "B"
      Number of atoms: 1123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1123
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 138}
    Chain: "C"
      Number of atoms: 1068
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1068
          Classifications: {'peptide': 141}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 133}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "D"
      Number of atoms: 1123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1123
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 138}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.16, per 1000 atoms: 0.25
  Number of scatterers: 4555
  At special positions: 0
  Unit cell: (78.3841, 77.3459, 66.9639, 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)
     Fe      4     26.01
     S      12     16.00
     O     805      8.00
     N     780      7.00
     C    2954      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 363.1 milliseconds
  

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1068

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 0 sheets defined
      82.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 18
    Processing helix  chain 'A' and resid 20 through 36
    Processing helix  chain 'A' and resid 37 through 43
      removed outlier: 3.920A  pdb=" N   THR A  41 " --> pdb=" O   THR A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 72
    Processing helix  chain 'A' and resid 75 through 90
      removed outlier: 5.417A  pdb=" N   ALA A  82 " --> pdb=" O   ASN A  78 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   LEU A  83 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 113
    Processing helix  chain 'A' and resid 118 through 138
    Processing helix  chain 'B' and resid 4 through 17
    Processing helix  chain 'B' and resid 22 through 35
    Processing helix  chain 'B' and resid 37 through 41
      removed outlier: 3.563A  pdb=" N   ARG B  40 " --> pdb=" O   TRP B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 46
      removed outlier: 3.637A  pdb=" N   GLY B  46 " --> pdb=" O   GLU B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 57
    Processing helix  chain 'B' and resid 57 through 77
    Processing helix  chain 'B' and resid 80 through 85
    Processing helix  chain 'B' and resid 86 through 95
    Processing helix  chain 'B' and resid 101 through 119
    Processing helix  chain 'B' and resid 123 through 142
    Processing helix  chain 'C' and resid 3 through 18
    Processing helix  chain 'C' and resid 20 through 36
    Processing helix  chain 'C' and resid 37 through 43
      removed outlier: 3.921A  pdb=" N   THR C  41 " --> pdb=" O   THR C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 52 through 72
    Processing helix  chain 'C' and resid 75 through 90
      removed outlier: 5.417A  pdb=" N   ALA C  82 " --> pdb=" O   ASN C  78 " (cutoff:3.500A)
      removed outlier: 5.434A  pdb=" N   LEU C  83 " --> pdb=" O   ALA C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 113
    Processing helix  chain 'C' and resid 118 through 138
    Processing helix  chain 'D' and resid 4 through 17
    Processing helix  chain 'D' and resid 22 through 35
    Processing helix  chain 'D' and resid 37 through 41
      removed outlier: 3.563A  pdb=" N   ARG D  40 " --> pdb=" O   TRP D  37 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 42 through 46
      removed outlier: 3.637A  pdb=" N   GLY D  46 " --> pdb=" O   GLU D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 57
    Processing helix  chain 'D' and resid 57 through 77
    Processing helix  chain 'D' and resid 80 through 85
    Processing helix  chain 'D' and resid 86 through 95
    Processing helix  chain 'D' and resid 101 through 119
    Processing helix  chain 'D' and resid 123 through 142

    336 hydrogen bonds defined for protein.
    978 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: 0.77

  Time building geometry restraints manager: 0.50 seconds

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

  Histogram of bond lengths:
        1.22 -     1.38: 1884
        1.38 -     1.54: 2768
        1.54 -     1.71: 13
        1.71 -     1.87: 18
        1.87 -     2.03: 16
  Bond restraints: 4699
  Sorted by residual:
  bond pdb=" C   MET C  76 "
       pdb=" N   PRO C  77 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.019 1.23e-02 6.61e+03 2.36e+00
  bond pdb=" C   MET A  76 "
       pdb=" N   PRO A  77 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.019 1.23e-02 6.61e+03 2.36e+00
  bond pdb=" CA  MET C  76 "
       pdb=" C   MET C  76 "
    ideal  model  delta    sigma   weight residual
    1.524  1.542 -0.018 1.26e-02 6.30e+03 2.12e+00
  bond pdb=" C1C HEM D 201 "
       pdb=" CHC HEM D 201 "
    ideal  model  delta    sigma   weight residual
    1.378  1.349  0.029 2.00e-02 2.50e+03 2.10e+00
  bond pdb=" ND  HEM B 201 "
       pdb="FE   HEM B 201 "
    ideal  model  delta    sigma   weight residual
    2.080  1.979  0.101 7.00e-02 2.04e+02 2.09e+00
  ... (remaining 4694 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.31: 6331
        3.31 -     6.62: 102
        6.62 -     9.92: 8
        9.92 -    13.23: 2
       13.23 -    16.54: 6
  Bond angle restraints: 6449
  Sorted by residual:
  angle pdb=" CA  MET A  76 "
        pdb=" C   MET A  76 "
        pdb=" N   PRO A  77 "
      ideal   model   delta    sigma   weight residual
     118.44  124.03   -5.59 1.59e+00 3.96e-01 1.24e+01
  angle pdb=" CA  MET C  76 "
        pdb=" C   MET C  76 "
        pdb=" N   PRO C  77 "
      ideal   model   delta    sigma   weight residual
     118.44  124.01   -5.57 1.59e+00 3.96e-01 1.23e+01
  angle pdb=" N   MET A  76 "
        pdb=" CA  MET A  76 "
        pdb=" C   MET A  76 "
      ideal   model   delta    sigma   weight residual
     109.81  116.31   -6.50 2.21e+00 2.05e-01 8.64e+00
  angle pdb=" N   MET C  76 "
        pdb=" CA  MET C  76 "
        pdb=" C   MET C  76 "
      ideal   model   delta    sigma   weight residual
     109.81  116.29   -6.48 2.21e+00 2.05e-01 8.61e+00
  angle pdb=" CA  TYR D 145 "
        pdb=" CB  TYR D 145 "
        pdb=" CG  TYR D 145 "
      ideal   model   delta    sigma   weight residual
     113.90  118.98   -5.08 1.80e+00 3.09e-01 7.95e+00
  ... (remaining 6444 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.75: 2304
       16.75 -    33.51: 267
       33.51 -    50.26: 72
       50.26 -    67.01: 16
       67.01 -    83.77: 8
  Dihedral angle restraints: 2667
    sinusoidal: 1017
      harmonic: 1650
  Sorted by residual:
  dihedral pdb=" CA  TYR D 145 "
           pdb=" C   TYR D 145 "
           pdb=" N   HIS D 146 "
           pdb=" CA  HIS D 146 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.06  -25.94     0      5.00e+00 4.00e-02 2.69e+01
  dihedral pdb=" CA  TYR B 145 "
           pdb=" C   TYR B 145 "
           pdb=" N   HIS B 146 "
           pdb=" CA  HIS B 146 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.10  -25.90     0      5.00e+00 4.00e-02 2.68e+01
  dihedral pdb=" CA  ASN D  19 "
           pdb=" C   ASN D  19 "
           pdb=" N   VAL D  20 "
           pdb=" CA  VAL D  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.27  -25.73     0      5.00e+00 4.00e-02 2.65e+01
  ... (remaining 2664 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 442
       0.046 -    0.092: 183
       0.092 -    0.138: 55
       0.138 -    0.184: 14
       0.184 -    0.230: 6
  Chirality restraints: 700
  Sorted by residual:
  chirality pdb=" CA  MET A  76 "
            pdb=" N   MET A  76 "
            pdb=" C   MET A  76 "
            pdb=" CB  MET A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CA  MET C  76 "
            pdb=" N   MET C  76 "
            pdb=" C   MET C  76 "
            pdb=" CB  MET C  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CB  VAL D 109 "
            pdb=" CA  VAL D 109 "
            pdb=" CG1 VAL D 109 "
            pdb=" CG2 VAL D 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 697 not shown)

  Planarity restraints: 806
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO D 124 "   -0.065 5.00e-02 4.00e+02   9.69e-02 1.50e+01
        pdb=" N   PRO D 125 "    0.168 5.00e-02 4.00e+02
        pdb=" CA  PRO D 125 "   -0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO D 125 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 124 "    0.065 5.00e-02 4.00e+02   9.69e-02 1.50e+01
        pdb=" N   PRO B 125 "   -0.168 5.00e-02 4.00e+02
        pdb=" CA  PRO B 125 "    0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO B 125 "    0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 123 "    0.049 5.00e-02 4.00e+02   7.47e-02 8.93e+00
        pdb=" N   PRO D 124 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO D 124 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO D 124 "    0.041 5.00e-02 4.00e+02
  ... (remaining 803 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1398
        2.83 -     3.34: 4450
        3.34 -     3.86: 7905
        3.86 -     4.38: 9188
        4.38 -     4.90: 15030
  Nonbonded interactions: 37971
  Sorted by model distance:
  nonbonded pdb=" O   ALA C 130 "
            pdb=" OG1 THR C 134 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   ALA A 130 "
            pdb=" OG1 THR A 134 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   PHE C 128 "
            pdb=" OG  SER C 131 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   PHE A 128 "
            pdb=" OG  SER A 131 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   ASP C  64 "
            pdb=" OG1 THR C  67 "
     model   vdw
     2.347 3.040
  ... (remaining 37966 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 1 through 80 or (resid 81 through 82 and (name N or name C \ 
A or name C or name O or name CB )) or resid 83 through 201))
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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:             0.860
  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:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.730
  Find NCS groups from input model:        0.080
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
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      :  0.016   0.645   4701  Z= 0.351
  Angle     :  1.160  16.538   6449  Z= 0.541
  Chirality :  0.058   0.230    700
  Planarity :  0.010   0.097    806
  Dihedral  : 16.479  83.765   1599
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.53 %
    Favored  : 83.30 %
  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: -3.05 (0.30), residues: 566
  helix: -1.76 (0.20), residues: 452
  sheet:  None (None), residues: 0
  loop : -2.20 (0.59), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  31 
 TYR   0.021   0.002   TYR B 145 
 PHE   0.022   0.003   PHE D  45 
 TRP   0.006   0.002   TRP A  14 
 HIS   0.005   0.002   HIS C  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00842 ( 4699)
  covalent geometry    : angle       1.16014 ( 6449)
  hydrogen bonds       : bond        0.10036 (  336)
  hydrogen bonds       : angle       5.89433 (  978)
  Misc. bond           : bond        0.64463 (    2)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 192
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.6585 (t70) cc_final: 0.6374 (t0)
REVERT: A   85 ASP cc_start: 0.6774 (t0) cc_final: 0.6538 (t70)
REVERT: A  112 HIS cc_start: 0.7394 (m-70) cc_final: 0.6419 (m-70)
REVERT: B   40 ARG cc_start: 0.6707 (tpt170) cc_final: 0.6256 (tpt170)
REVERT: B   59 LYS cc_start: 0.7877 (mtpt) cc_final: 0.7537 (mtmt)
REVERT: B   99 ASP cc_start: 0.6595 (t0) cc_final: 0.6117 (t70)
REVERT: B  101 GLU cc_start: 0.8079 (pm20) cc_final: 0.7665 (pm20)
REVERT: B  131 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7826 (tm-30)
REVERT: C    6 ASP cc_start: 0.7273 (p0) cc_final: 0.6937 (p0)
REVERT: C   85 ASP cc_start: 0.6877 (t0) cc_final: 0.6584 (t70)
REVERT: C  112 HIS cc_start: 0.7375 (m-70) cc_final: 0.6230 (m90)
REVERT: D   40 ARG cc_start: 0.6687 (tpt170) cc_final: 0.6370 (tpt170)
REVERT: D   59 LYS cc_start: 0.7827 (mtpt) cc_final: 0.7495 (mtmt)
REVERT: D   99 ASP cc_start: 0.6574 (t0) cc_final: 0.6221 (t70)
REVERT: D  131 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7827 (tm-30)
  outliers start: 10
  outliers final: 2
  residues processed: 196
  average time/residue: 0.0918
  time to fit residues: 21.7955
Evaluate side-chains
  151 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 149
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain C residue   38 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 143 HIS
B 146 HIS
D 143 HIS
D 146 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.131787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.110364 restraints weight = 12121.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.112593 restraints weight = 9025.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.114140 restraints weight = 7379.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.114948 restraints weight = 6435.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.115905 restraints weight = 5898.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.118   4701  Z= 0.144
  Angle     :  0.699   8.881   6449  Z= 0.342
  Chirality :  0.043   0.154    700
  Planarity :  0.008   0.091    806
  Dihedral  :  9.910  75.494    632
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 23.64 %
    Favored  : 74.84 %
  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: -0.50 (0.35), residues: 566
  helix:  0.03 (0.24), residues: 446
  sheet:  None (None), residues: 0
  loop : -1.26 (0.63), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  40 
 TYR   0.011   0.001   TYR D 145 
 PHE   0.021   0.001   PHE B  85 
 TRP   0.019   0.003   TRP D  37 
 HIS   0.010   0.002   HIS B 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 4699)
  covalent geometry    : angle       0.69884 ( 6449)
  hydrogen bonds       : bond        0.03294 (  336)
  hydrogen bonds       : angle       4.85243 (  978)
  Misc. bond           : bond        0.11339 (    2)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 176
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.6607 (t70) cc_final: 0.6337 (t0)
REVERT: A  117 PHE cc_start: 0.6513 (OUTLIER) cc_final: 0.6122 (m-80)
REVERT: B   59 LYS cc_start: 0.7835 (mtpt) cc_final: 0.7579 (mtmt)
REVERT: B   99 ASP cc_start: 0.6456 (t0) cc_final: 0.6245 (t70)
REVERT: B  104 ARG cc_start: 0.7508 (ttm170) cc_final: 0.7132 (ttm-80)
REVERT: C    6 ASP cc_start: 0.7329 (p0) cc_final: 0.7018 (p0)
REVERT: C   20 HIS cc_start: 0.5890 (OUTLIER) cc_final: 0.5635 (m-70)
REVERT: D   40 ARG cc_start: 0.6966 (tpt170) cc_final: 0.6507 (tpt170)
REVERT: D   59 LYS cc_start: 0.7812 (mtpt) cc_final: 0.7568 (mtmt)
REVERT: D  101 GLU cc_start: 0.7800 (pm20) cc_final: 0.7552 (pm20)
REVERT: D  104 ARG cc_start: 0.7523 (ttm170) cc_final: 0.7242 (ttm-80)
  outliers start: 7
  outliers final: 4
  residues processed: 178
  average time/residue: 0.0857
  time to fit residues: 18.6677
Evaluate side-chains
  170 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 164
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ASN
Chi-restraints excluded: chain A residue  117 PHE
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain C residue   20 HIS
Chi-restraints excluded: chain C residue   78 ASN
Chi-restraints excluded: chain C residue  128 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0370
   chunk 19 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0050
   chunk 11 optimal weight:    0.2980
   chunk 49 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   overall best weight:    0.3272

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

Flipped N/Q/H residues before XYZ refinement:
B 108 ASN
C  58 HIS
C 112 HIS
D 108 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.135913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.114758 restraints weight = 11875.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.117022 restraints weight = 9005.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.118587 restraints weight = 7435.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.119226 restraints weight = 6492.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.120249 restraints weight = 6024.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.3320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   4701  Z= 0.123
  Angle     :  0.647   7.983   6449  Z= 0.320
  Chirality :  0.043   0.219    700
  Planarity :  0.007   0.085    806
  Dihedral  :  9.404  71.427    630
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 25.81 %
    Favored  : 71.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.37), residues: 566
  helix:  0.69 (0.24), residues: 448
  sheet:  None (None), residues: 0
  loop : -0.72 (0.68), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  40 
 TYR   0.008   0.001   TYR B 145 
 PHE   0.015   0.001   PHE B  85 
 TRP   0.023   0.002   TRP B  37 
 HIS   0.007   0.001   HIS D 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4699)
  covalent geometry    : angle       0.64676 ( 6449)
  hydrogen bonds       : bond        0.02886 (  336)
  hydrogen bonds       : angle       4.65571 (  978)
  Misc. bond           : bond        0.06568 (    2)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 186
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.6465 (t70) cc_final: 0.6205 (t0)
REVERT: A  117 PHE cc_start: 0.6317 (OUTLIER) cc_final: 0.5974 (m-80)
REVERT: B   99 ASP cc_start: 0.6608 (t0) cc_final: 0.6358 (t70)
REVERT: B  101 GLU cc_start: 0.7844 (pm20) cc_final: 0.7262 (pm20)
REVERT: C    6 ASP cc_start: 0.7204 (p0) cc_final: 0.6915 (p0)
REVERT: C   85 ASP cc_start: 0.6946 (t70) cc_final: 0.6739 (t70)
REVERT: D   30 ARG cc_start: 0.8033 (mtt-85) cc_final: 0.7778 (mtt90)
REVERT: D   40 ARG cc_start: 0.6968 (tpt170) cc_final: 0.6533 (tpt170)
REVERT: D  101 GLU cc_start: 0.7779 (pm20) cc_final: 0.7364 (pm20)
REVERT: D  131 GLN cc_start: 0.8365 (tm-30) cc_final: 0.8012 (pp30)
  outliers start: 12
  outliers final: 4
  residues processed: 191
  average time/residue: 0.0837
  time to fit residues: 19.5156
Evaluate side-chains
  178 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 173
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 HIS
Chi-restraints excluded: chain A residue  117 PHE
Chi-restraints excluded: chain A residue  140 TYR
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain D residue   45 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 36 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  58 HIS
C 112 HIS
** D  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.134598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.113807 restraints weight = 12053.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.116086 restraints weight = 8878.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.117682 restraints weight = 7189.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.118368 restraints weight = 6213.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.119387 restraints weight = 5709.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   4701  Z= 0.128
  Angle     :  0.700   9.132   6449  Z= 0.342
  Chirality :  0.045   0.198    700
  Planarity :  0.007   0.081    806
  Dihedral  :  9.329  71.645    630
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 27.55 %
    Favored  : 69.85 %
  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:  0.70 (0.37), residues: 566
  helix:  0.81 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop : -0.54 (0.68), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  30 
 TYR   0.008   0.001   TYR B 145 
 PHE   0.013   0.001   PHE B  85 
 TRP   0.022   0.002   TRP B  37 
 HIS   0.007   0.001   HIS D 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 4699)
  covalent geometry    : angle       0.70043 ( 6449)
  hydrogen bonds       : bond        0.02947 (  336)
  hydrogen bonds       : angle       4.72458 (  978)
  Misc. bond           : bond        0.07923 (    2)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 175
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 PHE cc_start: 0.6248 (OUTLIER) cc_final: 0.5971 (m-80)
REVERT: B   99 ASP cc_start: 0.6696 (t0) cc_final: 0.6427 (t70)
REVERT: B  101 GLU cc_start: 0.7794 (pm20) cc_final: 0.7332 (pm20)
REVERT: C    6 ASP cc_start: 0.7257 (p0) cc_final: 0.6956 (p0)
REVERT: C   85 ASP cc_start: 0.6968 (t70) cc_final: 0.6768 (t70)
REVERT: D   30 ARG cc_start: 0.8067 (mtt-85) cc_final: 0.7681 (mtt90)
REVERT: D   40 ARG cc_start: 0.6990 (tpt170) cc_final: 0.6545 (tpt170)
  outliers start: 12
  outliers final: 6
  residues processed: 180
  average time/residue: 0.0814
  time to fit residues: 17.9790
Evaluate side-chains
  172 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 165
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 HIS
Chi-restraints excluded: chain A residue  117 PHE
Chi-restraints excluded: chain A residue  140 TYR
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain D residue   47 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 51 optimal weight:   30.0000
   chunk 55 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   chunk 7 optimal weight:    8.9990
   chunk 4 optimal weight:    8.9990
   chunk 38 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
A 112 HIS
** B  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 102 ASN
B 108 ASN
C  58 HIS
C 112 HIS
D 102 ASN
D 108 ASN
** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.135286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.114989 restraints weight = 11780.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.117210 restraints weight = 8783.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.118914 restraints weight = 7135.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.119919 restraints weight = 6145.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.120551 restraints weight = 5560.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.3962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.084   4701  Z= 0.134
  Angle     :  0.704   8.440   6449  Z= 0.347
  Chirality :  0.045   0.178    700
  Planarity :  0.007   0.080    806
  Dihedral  :  9.298  71.068    630
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 27.98 %
    Favored  : 68.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.37), residues: 566
  helix:  0.99 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop : -0.35 (0.69), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  30 
 TYR   0.010   0.001   TYR B  35 
 PHE   0.013   0.001   PHE B  85 
 TRP   0.024   0.002   TRP B  37 
 HIS   0.007   0.002   HIS B  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 4699)
  covalent geometry    : angle       0.70377 ( 6449)
  hydrogen bonds       : bond        0.02907 (  336)
  hydrogen bonds       : angle       4.64853 (  978)
  Misc. bond           : bond        0.08180 (    2)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 171
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8095 (mm)
REVERT: B  101 GLU cc_start: 0.7634 (pm20) cc_final: 0.7159 (pm20)
REVERT: C    6 ASP cc_start: 0.7218 (p0) cc_final: 0.6944 (p0)
REVERT: D   30 ARG cc_start: 0.8055 (mtt-85) cc_final: 0.7693 (mtt90)
REVERT: D   40 ARG cc_start: 0.7030 (tpt170) cc_final: 0.6597 (tpt170)
REVERT: D   99 ASP cc_start: 0.7628 (t70) cc_final: 0.6664 (t0)
  outliers start: 14
  outliers final: 8
  residues processed: 177
  average time/residue: 0.0767
  time to fit residues: 16.7740
Evaluate side-chains
  170 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 161
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  140 TYR
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  140 TYR
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue   28 LEU
Chi-restraints excluded: chain D residue   45 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 43 optimal weight:   10.0000
   chunk 11 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 44 optimal weight:    0.3980
   chunk 47 optimal weight:    7.9990
   chunk 51 optimal weight:    0.0870
   overall best weight:    2.0962

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
A 112 HIS
** B  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  58 HIS
C 112 HIS
D  39 GLN
** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.133040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.112554 restraints weight = 12197.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.114883 restraints weight = 8986.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.116389 restraints weight = 7247.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.117542 restraints weight = 6258.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.118103 restraints weight = 5627.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.3961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.108   4701  Z= 0.165
  Angle     :  0.770   9.595   6449  Z= 0.370
  Chirality :  0.047   0.226    700
  Planarity :  0.007   0.083    806
  Dihedral  :  9.568  71.896    630
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 14.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 28.20 %
    Favored  : 68.11 %
  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:  0.85 (0.37), residues: 566
  helix:  0.97 (0.25), residues: 446
  sheet:  None (None), residues: 0
  loop : -0.68 (0.67), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  30 
 TYR   0.010   0.001   TYR B 145 
 PHE   0.015   0.001   PHE C  46 
 TRP   0.024   0.003   TRP B  37 
 HIS   0.007   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 4699)
  covalent geometry    : angle       0.77032 ( 6449)
  hydrogen bonds       : bond        0.03128 (  336)
  hydrogen bonds       : angle       4.82865 (  978)
  Misc. bond           : bond        0.10566 (    2)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8261 (mm)
REVERT: A  117 PHE cc_start: 0.6019 (OUTLIER) cc_final: 0.5308 (m-80)
REVERT: C    6 ASP cc_start: 0.7239 (p0) cc_final: 0.6950 (p0)
REVERT: D   15 TRP cc_start: 0.7487 (t-100) cc_final: 0.7255 (t-100)
REVERT: D   40 ARG cc_start: 0.7005 (tpt170) cc_final: 0.6613 (tpt170)
  outliers start: 17
  outliers final: 11
  residues processed: 173
  average time/residue: 0.0670
  time to fit residues: 14.5593
Evaluate side-chains
  170 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 157
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  117 PHE
Chi-restraints excluded: chain A residue  140 TYR
Chi-restraints excluded: chain B residue    4 THR
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  140 TYR
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue   28 LEU
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   39 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0870
   chunk 52 optimal weight:    0.6980
   chunk 19 optimal weight:   20.0000
   chunk 14 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    1.3562

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
** B  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  58 HIS
D  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.133972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.114204 restraints weight = 11904.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.116382 restraints weight = 8913.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.117878 restraints weight = 7254.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.118420 restraints weight = 6287.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.119447 restraints weight = 5805.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.4142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   4701  Z= 0.145
  Angle     :  0.763   9.357   6449  Z= 0.373
  Chirality :  0.046   0.243    700
  Planarity :  0.007   0.083    806
  Dihedral  :  9.351  70.567    630
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 30.59 %
    Favored  : 65.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.86 (0.37), residues: 566
  helix:  0.92 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop : -0.49 (0.66), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  30 
 TYR   0.010   0.001   TYR B  35 
 PHE   0.013   0.001   PHE B  85 
 TRP   0.028   0.003   TRP D  37 
 HIS   0.007   0.001   HIS B  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 4699)
  covalent geometry    : angle       0.76282 ( 6449)
  hydrogen bonds       : bond        0.03042 (  336)
  hydrogen bonds       : angle       4.79354 (  978)
  Misc. bond           : bond        0.08355 (    2)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 160
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8126 (mm)
REVERT: A  117 PHE cc_start: 0.6071 (OUTLIER) cc_final: 0.5398 (m-80)
REVERT: B   99 ASP cc_start: 0.7072 (t70) cc_final: 0.6577 (t70)
REVERT: D   40 ARG cc_start: 0.7035 (tpt170) cc_final: 0.6638 (tpt170)
  outliers start: 17
  outliers final: 14
  residues processed: 168
  average time/residue: 0.0728
  time to fit residues: 15.3081
Evaluate side-chains
  166 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 150
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  117 PHE
Chi-restraints excluded: chain A residue  140 TYR
Chi-restraints excluded: chain B residue    4 THR
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  140 TYR
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue   28 LEU
Chi-restraints excluded: chain D residue   39 GLN
Chi-restraints excluded: chain D residue   45 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 23 optimal weight:   40.0000
   chunk 55 optimal weight:    0.0980
   chunk 51 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 36 optimal weight:    8.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
** B  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  58 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.135039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.114941 restraints weight = 11942.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.117051 restraints weight = 8908.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.118574 restraints weight = 7287.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.119352 restraints weight = 6337.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.120277 restraints weight = 5809.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.4363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   4701  Z= 0.137
  Angle     :  0.755   8.460   6449  Z= 0.371
  Chirality :  0.046   0.175    700
  Planarity :  0.007   0.082    806
  Dihedral  :  9.284  69.964    630
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 29.50 %
    Favored  : 65.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.89 (0.37), residues: 566
  helix:  0.95 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop : -0.50 (0.66), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  30 
 TYR   0.008   0.001   TYR B 145 
 PHE   0.012   0.001   PHE B  85 
 TRP   0.032   0.003   TRP D  37 
 HIS   0.008   0.001   HIS D  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 4699)
  covalent geometry    : angle       0.75515 ( 6449)
  hydrogen bonds       : bond        0.03021 (  336)
  hydrogen bonds       : angle       4.77156 (  978)
  Misc. bond           : bond        0.06693 (    2)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 156
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8190 (mm)
REVERT: A  117 PHE cc_start: 0.6030 (OUTLIER) cc_final: 0.5392 (m-80)
REVERT: B   90 GLU cc_start: 0.7198 (tp30) cc_final: 0.6990 (tp30)
REVERT: D   30 ARG cc_start: 0.8129 (mtt-85) cc_final: 0.7894 (mtt90)
REVERT: D   40 ARG cc_start: 0.7037 (tpt170) cc_final: 0.6635 (tpt170)
REVERT: D   90 GLU cc_start: 0.7270 (tp30) cc_final: 0.7051 (tp30)
  outliers start: 21
  outliers final: 15
  residues processed: 168
  average time/residue: 0.0789
  time to fit residues: 16.4730
Evaluate side-chains
  169 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  117 PHE
Chi-restraints excluded: chain A residue  140 TYR
Chi-restraints excluded: chain B residue    4 THR
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  140 TYR
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue   28 LEU
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   45 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 11 optimal weight:    0.4980
   chunk 16 optimal weight:    0.0870
   chunk 1 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
** B  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  58 HIS
** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.136206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.114978 restraints weight = 12172.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.117285 restraints weight = 8877.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.118991 restraints weight = 7203.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.120169 restraints weight = 6218.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.120859 restraints weight = 5593.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.4594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   4701  Z= 0.136
  Angle     :  0.771   9.282   6449  Z= 0.379
  Chirality :  0.046   0.176    700
  Planarity :  0.007   0.081    806
  Dihedral  :  9.204  69.472    630
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 31.02 %
    Favored  : 65.08 %
  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:  0.96 (0.37), residues: 566
  helix:  1.01 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop : -0.55 (0.65), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  31 
 TYR   0.008   0.001   TYR D  35 
 PHE   0.013   0.001   PHE B  85 
 TRP   0.031   0.003   TRP B  37 
 HIS   0.008   0.001   HIS D 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 4699)
  covalent geometry    : angle       0.77067 ( 6449)
  hydrogen bonds       : bond        0.03027 (  336)
  hydrogen bonds       : angle       4.71186 (  978)
  Misc. bond           : bond        0.05845 (    2)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8015 (mm)
REVERT: A   86 LEU cc_start: 0.8032 (mt) cc_final: 0.7739 (tp)
REVERT: A  117 PHE cc_start: 0.5951 (OUTLIER) cc_final: 0.5281 (m-80)
REVERT: C   54 GLN cc_start: 0.7684 (pm20) cc_final: 0.7357 (pm20)
REVERT: D   30 ARG cc_start: 0.8076 (mtt-85) cc_final: 0.7767 (mtt90)
REVERT: D   40 ARG cc_start: 0.7124 (tpt170) cc_final: 0.6753 (tpt170)
REVERT: D   99 ASP cc_start: 0.7589 (t70) cc_final: 0.7025 (t70)
  outliers start: 18
  outliers final: 14
  residues processed: 166
  average time/residue: 0.0787
  time to fit residues: 16.1131
Evaluate side-chains
  169 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 153
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  117 PHE
Chi-restraints excluded: chain A residue  140 TYR
Chi-restraints excluded: chain B residue    4 THR
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  140 TYR
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue   28 LEU
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   45 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 44 optimal weight:    7.9990
   chunk 1 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0050
   chunk 26 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
A 112 HIS
** B  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 102 ASN
** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 112 HIS
D  39 GLN
** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.136484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.116649 restraints weight = 12278.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.119045 restraints weight = 8940.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.120685 restraints weight = 7182.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.121818 restraints weight = 6135.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.122410 restraints weight = 5485.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
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      :  0.004   0.070   4701  Z= 0.138
  Angle     :  0.793   9.393   6449  Z= 0.388
  Chirality :  0.047   0.178    700
  Planarity :  0.007   0.081    806
  Dihedral  :  9.199  68.910    630
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 32.32 %
    Favored  : 63.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    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:  0.93 (0.36), residues: 566
  helix:  1.01 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop : -0.65 (0.65), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  92 
 TYR   0.018   0.001   TYR B  35 
 PHE   0.013   0.001   PHE B  85 
 TRP   0.032   0.003   TRP B  37 
 HIS   0.009   0.001   HIS D 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 4699)
  covalent geometry    : angle       0.79319 ( 6449)
  hydrogen bonds       : bond        0.03035 (  336)
  hydrogen bonds       : angle       4.70697 (  978)
  Misc. bond           : bond        0.06274 (    2)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.5012 (mm-30) cc_final: 0.4812 (tp30)
REVERT: A   54 GLN cc_start: 0.7583 (pm20) cc_final: 0.7106 (pm20)
REVERT: A   83 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7928 (mm)
REVERT: A  117 PHE cc_start: 0.5865 (OUTLIER) cc_final: 0.5253 (m-80)
REVERT: D   30 ARG cc_start: 0.8026 (mtt-85) cc_final: 0.7716 (mtt90)
REVERT: D   40 ARG cc_start: 0.6993 (tpt170) cc_final: 0.6637 (tpt170)
  outliers start: 18
  outliers final: 14
  residues processed: 162
  average time/residue: 0.0778
  time to fit residues: 15.6451
Evaluate side-chains
  168 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 152
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  117 PHE
Chi-restraints excluded: chain A residue  140 TYR
Chi-restraints excluded: chain B residue    4 THR
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  140 TYR
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue   28 LEU
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   39 GLN
Chi-restraints excluded: chain D residue   45 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 7 optimal weight:    0.1980
   chunk 49 optimal weight:    0.9980
   chunk 35 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 23 optimal weight:   20.0000
   chunk 51 optimal weight:   30.0000
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
** B  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  58 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.137555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.116702 restraints weight = 12524.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.119308 restraints weight = 9026.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.121128 restraints weight = 7174.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.121893 restraints weight = 6105.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.122798 restraints weight = 5543.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.4851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.160   4701  Z= 0.243
  Angle     :  1.294  59.197   6449  Z= 0.726
  Chirality :  0.049   0.237    700
  Planarity :  0.007   0.081    806
  Dihedral  :  9.221  68.910    630
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 18.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 33.19 %
    Favored  : 62.69 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    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:  0.93 (0.36), residues: 566
  helix:  1.01 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop : -0.66 (0.65), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  92 
 TYR   0.018   0.001   TYR B  35 
 PHE   0.013   0.001   PHE B  85 
 TRP   0.029   0.003   TRP B  37 
 HIS   0.008   0.001   HIS D 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00568 ( 4699)
  covalent geometry    : angle       1.29411 ( 6449)
  hydrogen bonds       : bond        0.03038 (  336)
  hydrogen bonds       : angle       4.71539 (  978)
  Misc. bond           : bond        0.06275 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1085.65 seconds
wall clock time: 19 minutes 18.89 seconds (1158.89 seconds total)