Starting phenix.real_space_refine
on Wed Sep 17 20:08:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n8n_24238/09_2025/7n8n_24238.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n8n_24238/09_2025/7n8n_24238.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n8n_24238/09_2025/7n8n_24238.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n8n_24238/09_2025/7n8n_24238.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n8n_24238/09_2025/7n8n_24238.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n8n_24238/09_2025/7n8n_24238.map"
  }
  resolution = 3.89
  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=   0.002 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     248      5.49       5
     S      30      5.16       5
     C    6180      2.51       5
     N    2053      2.21       5
     O    2610      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11121
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1501
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1501
          Classifications: {'peptide': 197}
          Link IDs: {'PTRANS': 5, 'TRANS': 191}
    Chain: "B"
      Number of atoms: 1500
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1500
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 4, 'TRANS': 197}
    Chain: "C"
      Number of atoms: 1501
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1501
          Classifications: {'peptide': 197}
          Link IDs: {'PTRANS': 5, 'TRANS': 191}
    Chain: "D"
      Number of atoms: 1500
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1500
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 4, 'TRANS': 197}
    Chain: "I"
      Number of atoms: 2543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 2543
          Classifications: {'DNA': 125}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 124}
    Chain: "J"
      Number of atoms: 2576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 2576
          Classifications: {'DNA': 125}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 124}
  Time building chain proxies: 2.79, per 1000 atoms: 0.25
  Number of scatterers: 11121
  At special positions: 0
  Unit cell: (86.265, 111.825, 116.085, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P     248     15.00
     O    2610      8.00
     N    2053      7.00
     C    6180      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.14
  Conformation dependent library (CDL) restraints added in 277.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1468

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 2 sheets defined
      67.4% alpha, 0.5% beta
      124 base pairs and 197 stacking pairs defined.
    Time for finding SS restraints: 1.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 46
    Processing helix  chain 'A' and resid 54 through 80
      removed outlier: 3.701A  pdb=" N   ILE A  58 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 97
      removed outlier: 3.561A  pdb=" N   VAL A  90 " --> pdb=" O   MET A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 121
      removed outlier: 3.975A  pdb=" N   GLN A 121 " --> pdb=" O   SER A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 143
    Processing helix  chain 'A' and resid 150 through 165
    Processing helix  chain 'A' and resid 172 through 201
    Processing helix  chain 'A' and resid 207 through 219
    Processing helix  chain 'B' and resid 38 through 44
    Processing helix  chain 'B' and resid 45 through 50
    Processing helix  chain 'B' and resid 56 through 81
    Processing helix  chain 'B' and resid 90 through 102
    Processing helix  chain 'B' and resid 103 through 127
    Processing helix  chain 'B' and resid 129 through 133
      removed outlier: 4.171A  pdb=" N   SER B 133 " --> pdb=" O   GLY B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 151
      removed outlier: 4.885A  pdb=" N   GLU B 146 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   ARG B 147 " --> pdb=" O   ALA B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 188
    Processing helix  chain 'B' and resid 194 through 205
    Processing helix  chain 'B' and resid 205 through 213
    Processing helix  chain 'C' and resid 34 through 46
    Processing helix  chain 'C' and resid 54 through 80
      removed outlier: 3.701A  pdb=" N   ILE C  58 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 97
      removed outlier: 3.562A  pdb=" N   VAL C  90 " --> pdb=" O   MET C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 121
      removed outlier: 3.976A  pdb=" N   GLN C 121 " --> pdb=" O   SER C 118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 136 through 143
    Processing helix  chain 'C' and resid 150 through 165
    Processing helix  chain 'C' and resid 172 through 201
    Processing helix  chain 'C' and resid 207 through 219
    Processing helix  chain 'D' and resid 38 through 44
    Processing helix  chain 'D' and resid 45 through 50
    Processing helix  chain 'D' and resid 56 through 81
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 127
    Processing helix  chain 'D' and resid 129 through 133
      removed outlier: 4.171A  pdb=" N   SER D 133 " --> pdb=" O   GLY D 130 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 140 through 151
      removed outlier: 4.884A  pdb=" N   GLU D 146 " --> pdb=" O   VAL D 142 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   ARG D 147 " --> pdb=" O   ALA D 143 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 188
    Processing helix  chain 'D' and resid 194 through 205
    Processing helix  chain 'D' and resid 205 through 213
    Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85
    Processing sheet with id=AA2, first strand: chain 'C' and resid 84 through 85

    388 hydrogen bonds defined for protein.
    1152 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      321 hydrogen bonds
      638 hydrogen bond angles
      0 basepair planarities
      124 basepair parallelities
      197 stacking parallelities
  Total time for adding SS restraints: 2.32

  Time building geometry restraints manager: 1.52 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2475
        1.33 -     1.45: 3579
        1.45 -     1.57: 5210
        1.57 -     1.69: 496
        1.69 -     1.81: 52
  Bond restraints: 11812
  Sorted by residual:
  bond pdb=" CZ  ARG B 157 "
       pdb=" NH2 ARG B 157 "
    ideal  model  delta    sigma   weight residual
    1.330  1.307  0.023 1.30e-02 5.92e+03 3.01e+00
  bond pdb=" CZ  ARG D 157 "
       pdb=" NH2 ARG D 157 "
    ideal  model  delta    sigma   weight residual
    1.330  1.308  0.022 1.30e-02 5.92e+03 2.98e+00
  bond pdb=" CA  VAL A  56 "
       pdb=" CB  VAL A  56 "
    ideal  model  delta    sigma   weight residual
    1.539  1.548 -0.009 5.40e-03 3.43e+04 2.77e+00
  bond pdb=" CA  VAL C  56 "
       pdb=" CB  VAL C  56 "
    ideal  model  delta    sigma   weight residual
    1.539  1.547 -0.008 5.40e-03 3.43e+04 2.30e+00
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.467 -0.045 3.00e-02 1.11e+03 2.28e+00
  ... (remaining 11807 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 16515
        2.25 -     4.51: 440
        4.51 -     6.76: 38
        6.76 -     9.02: 0
        9.02 -    11.27: 4
  Bond angle restraints: 16997
  Sorted by residual:
  angle pdb=" CB  MET C 157 "
        pdb=" CG  MET C 157 "
        pdb=" SD  MET C 157 "
      ideal   model   delta    sigma   weight residual
     112.70  102.55   10.15 3.00e+00 1.11e-01 1.15e+01
  angle pdb=" CB  MET A 157 "
        pdb=" CG  MET A 157 "
        pdb=" SD  MET A 157 "
      ideal   model   delta    sigma   weight residual
     112.70  102.57   10.13 3.00e+00 1.11e-01 1.14e+01
  angle pdb=" CA  LEU B 166 "
        pdb=" CB  LEU B 166 "
        pdb=" CG  LEU B 166 "
      ideal   model   delta    sigma   weight residual
     116.30  105.03   11.27 3.50e+00 8.16e-02 1.04e+01
  angle pdb=" CA  LEU D 166 "
        pdb=" CB  LEU D 166 "
        pdb=" CG  LEU D 166 "
      ideal   model   delta    sigma   weight residual
     116.30  105.03   11.27 3.50e+00 8.16e-02 1.04e+01
  angle pdb=" C4   DT I -64 "
        pdb=" C5   DT I -64 "
        pdb=" C7   DT I -64 "
      ideal   model   delta    sigma   weight residual
     122.40  117.59    4.81 1.50e+00 4.44e-01 1.03e+01
  ... (remaining 16992 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.91: 5236
       34.91 -    69.81: 1210
       69.81 -   104.72: 17
      104.72 -   139.63: 2
      139.63 -   174.54: 3
  Dihedral angle restraints: 6468
    sinusoidal: 4198
      harmonic: 2270
  Sorted by residual:
  dihedral pdb=" CA  SER C 131 "
           pdb=" C   SER C 131 "
           pdb=" N   GLU C 132 "
           pdb=" CA  GLU C 132 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -63.39 -116.61     0      5.00e+00 4.00e-02 5.44e+02
  dihedral pdb=" CA  SER A 131 "
           pdb=" C   SER A 131 "
           pdb=" N   GLU A 132 "
           pdb=" CA  GLU A 132 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -63.45 -116.55     0      5.00e+00 4.00e-02 5.43e+02
  dihedral pdb=" CA  LYS C 112 "
           pdb=" C   LYS C 112 "
           pdb=" N   GLY C 113 "
           pdb=" CA  GLY C 113 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -99.23  -80.77     0      5.00e+00 4.00e-02 2.61e+02
  ... (remaining 6465 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1311
       0.036 -    0.072: 474
       0.072 -    0.108: 133
       0.108 -    0.143: 39
       0.143 -    0.179: 7
  Chirality restraints: 1964
  Sorted by residual:
  chirality pdb=" CG  LEU C  41 "
            pdb=" CB  LEU C  41 "
            pdb=" CD1 LEU C  41 "
            pdb=" CD2 LEU C  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 8.04e-01
  chirality pdb=" CG  LEU A  41 "
            pdb=" CB  LEU A  41 "
            pdb=" CD1 LEU A  41 "
            pdb=" CD2 LEU A  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 7.71e-01
  chirality pdb=" CG  LEU D 166 "
            pdb=" CB  LEU D 166 "
            pdb=" CD1 LEU D 166 "
            pdb=" CD2 LEU D 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.74e-01
  ... (remaining 1961 not shown)

  Planarity restraints: 1276
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 135 "    0.014 2.00e-02 2.50e+03   2.77e-02 7.65e+00
        pdb=" C   LYS B 135 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   LYS B 135 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ALA B 136 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS D 135 "   -0.014 2.00e-02 2.50e+03   2.76e-02 7.60e+00
        pdb=" C   LYS D 135 "    0.048 2.00e-02 2.50e+03
        pdb=" O   LYS D 135 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ALA D 136 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D  65 "   -0.013 2.00e-02 2.50e+03   2.68e-02 7.20e+00
        pdb=" CG  ASN D  65 "    0.046 2.00e-02 2.50e+03
        pdb=" OD1 ASN D  65 "   -0.017 2.00e-02 2.50e+03
        pdb=" ND2 ASN D  65 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1273 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 246
        2.61 -     3.18: 10949
        3.18 -     3.75: 22515
        3.75 -     4.33: 27845
        4.33 -     4.90: 37785
  Nonbonded interactions: 99340
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 132 "
            pdb=" OG  SER A 135 "
     model   vdw
     2.035 3.040
  nonbonded pdb=" O   GLU C 132 "
            pdb=" OG  SER C 135 "
     model   vdw
     2.036 3.040
  nonbonded pdb=" OG  SER A 185 "
            pdb=" O   GLY D 219 "
     model   vdw
     2.101 3.040
  nonbonded pdb=" O   LYS A  35 "
            pdb=" OG1 THR A  38 "
     model   vdw
     2.103 3.040
  nonbonded pdb=" O   LYS C  35 "
            pdb=" OG1 THR C  38 "
     model   vdw
     2.104 3.040
  ... (remaining 99335 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'
  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:             1.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.220
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  11812  Z= 0.307
  Angle     :  0.849  11.271  16997  Z= 0.504
  Chirality :  0.042   0.179   1964
  Planarity :  0.006   0.054   1276
  Dihedral  : 27.929 174.537   5000
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 27.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.62 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.77 %

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 aren not related in a simple way.
  whole: -1.71 (0.28), residues: 790
  helix: -0.13 (0.22), residues: 484
  sheet:  None (None), residues: 0
  loop : -2.82 (0.31), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  59 
 TYR   0.020   0.002   TYR D 121 
 PHE   0.024   0.004   PHE C 154 
 HIS   0.011   0.002   HIS C 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00639 (11812)
  covalent geometry    : angle       0.84898 (16997)
  hydrogen bonds       : bond        0.13569 (  709)
  hydrogen bonds       : angle       5.49303 ( 1790)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8660 (m-80) cc_final: 0.8387 (m-80)
REVERT: A   71 GLN cc_start: 0.9698 (mt0) cc_final: 0.9420 (mt0)
REVERT: A  216 MET cc_start: 0.9220 (tpt) cc_final: 0.9011 (tpt)
REVERT: B   45 MET cc_start: 0.8391 (mmm) cc_final: 0.8031 (mmm)
REVERT: B  121 TYR cc_start: 0.9022 (t80) cc_final: 0.8629 (t80)
REVERT: B  166 LEU cc_start: 0.9596 (tp) cc_final: 0.9356 (tp)
REVERT: B  187 ASP cc_start: 0.9258 (m-30) cc_final: 0.9057 (m-30)
REVERT: C   69 LEU cc_start: 0.9641 (mm) cc_final: 0.9422 (mm)
REVERT: C   71 GLN cc_start: 0.9440 (mt0) cc_final: 0.9211 (mm-40)
REVERT: C   77 MET cc_start: 0.9414 (ppp) cc_final: 0.9130 (ppp)
REVERT: C   83 LYS cc_start: 0.9484 (mtmt) cc_final: 0.9191 (ptmt)
REVERT: C  157 MET cc_start: 0.9086 (mtt) cc_final: 0.8543 (mmm)
REVERT: C  177 ASP cc_start: 0.9514 (m-30) cc_final: 0.9240 (p0)
REVERT: C  199 TYR cc_start: 0.9337 (m-10) cc_final: 0.9093 (m-80)
REVERT: C  216 MET cc_start: 0.8803 (tpt) cc_final: 0.8269 (tpp)
REVERT: D  108 ARG cc_start: 0.8586 (mtm110) cc_final: 0.8270 (ttp80)
REVERT: D  174 MET cc_start: 0.9714 (mmp) cc_final: 0.9334 (mmp)
REVERT: D  176 GLU cc_start: 0.9412 (tt0) cc_final: 0.9143 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.0969
  time to fit residues: 25.3311
Evaluate side-chains
  115 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    5.9990
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A  40 HIS
B  56 GLN
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 GLN
C 167 HIS
C 170 HIS
D  44 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.063301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.047356 restraints weight = 66741.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.049132 restraints weight = 39570.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.050347 restraints weight = 27637.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.051147 restraints weight = 21472.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.051741 restraints weight = 18048.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  11812  Z= 0.227
  Angle     :  0.746  11.406  16997  Z= 0.426
  Chirality :  0.042   0.232   1964
  Planarity :  0.006   0.069   1276
  Dihedral  : 31.116 174.047   3544
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 18.67
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.10 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 11.61 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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 aren not related in a simple way.
  whole: -1.37 (0.28), residues: 790
  helix:  0.04 (0.22), residues: 512
  sheet:  None (None), residues: 0
  loop : -2.72 (0.32), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 153 
 TYR   0.021   0.002   TYR B 172 
 PHE   0.013   0.002   PHE A  61 
 HIS   0.007   0.001   HIS D 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 (11812)
  covalent geometry    : angle       0.74551 (16997)
  hydrogen bonds       : bond        0.06349 (  709)
  hydrogen bonds       : angle       4.73651 ( 1790)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8561 (m-80) cc_final: 0.8245 (m-80)
REVERT: A  142 MET cc_start: 0.8985 (ptm) cc_final: 0.8656 (ptp)
REVERT: B   45 MET cc_start: 0.8529 (mmm) cc_final: 0.8206 (mmm)
REVERT: B  121 TYR cc_start: 0.8924 (t80) cc_final: 0.8317 (t80)
REVERT: B  187 ASP cc_start: 0.9184 (m-30) cc_final: 0.8955 (m-30)
REVERT: C   71 GLN cc_start: 0.9401 (mt0) cc_final: 0.9063 (mt0)
REVERT: C   77 MET cc_start: 0.9355 (ppp) cc_final: 0.8947 (ppp)
REVERT: C  199 TYR cc_start: 0.9291 (m-10) cc_final: 0.9065 (m-80)
REVERT: C  216 MET cc_start: 0.8869 (tpt) cc_final: 0.8290 (tpp)
REVERT: D  108 ARG cc_start: 0.8642 (mtm110) cc_final: 0.8291 (ttp80)
REVERT: D  174 MET cc_start: 0.9649 (mmp) cc_final: 0.9408 (mmp)
  outliers start: 22
  outliers final: 15
  residues processed: 147
  average time/residue: 0.0955
  time to fit residues: 20.3032
Evaluate side-chains
  138 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  207 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  217 PHE
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain D residue   44 ASN
Chi-restraints excluded: chain D residue   45 MET
Chi-restraints excluded: chain D residue   70 LEU
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   96 LEU
Chi-restraints excluded: chain D residue  109 HIS
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain D residue  148 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 67 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 88 optimal weight:   10.0000
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
A  32 GLN
B  44 ASN
B  65 ASN
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 203 GLN
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  71 GLN
** D 204 ASN ** 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 = 0.3669 r_free = 0.3669 target = 0.064628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.048163 restraints weight = 65808.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.050010 restraints weight = 38965.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.051335 restraints weight = 27111.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.052237 restraints weight = 20959.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.052875 restraints weight = 17388.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  11812  Z= 0.189
  Angle     :  0.708  12.337  16997  Z= 0.403
  Chirality :  0.040   0.273   1964
  Planarity :  0.005   0.070   1276
  Dihedral  : 30.827 174.019   3544
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 16.50
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.96 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 15.94 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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 aren not related in a simple way.
  whole: -1.15 (0.28), residues: 790
  helix:  0.21 (0.22), residues: 506
  sheet:  None (None), residues: 0
  loop : -2.56 (0.32), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  59 
 TYR   0.010   0.001   TYR B 121 
 PHE   0.014   0.002   PHE D 173 
 HIS   0.005   0.001   HIS D 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (11812)
  covalent geometry    : angle       0.70844 (16997)
  hydrogen bonds       : bond        0.05179 (  709)
  hydrogen bonds       : angle       4.58142 ( 1790)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8389 (m-80) cc_final: 0.8049 (m-80)
REVERT: B  121 TYR cc_start: 0.8934 (t80) cc_final: 0.8353 (t80)
REVERT: B  187 ASP cc_start: 0.9135 (m-30) cc_final: 0.8920 (m-30)
REVERT: C   64 MET cc_start: 0.8582 (mmt) cc_final: 0.8211 (mmt)
REVERT: C   71 GLN cc_start: 0.9447 (mt0) cc_final: 0.9085 (mt0)
REVERT: C   77 MET cc_start: 0.9424 (ppp) cc_final: 0.9023 (ppp)
REVERT: C   83 LYS cc_start: 0.9194 (mtmt) cc_final: 0.8938 (ptmt)
REVERT: C  199 TYR cc_start: 0.9286 (m-10) cc_final: 0.8930 (m-80)
REVERT: C  216 MET cc_start: 0.8823 (tpt) cc_final: 0.8256 (tpp)
REVERT: D  174 MET cc_start: 0.9669 (mmp) cc_final: 0.9380 (mmp)
  outliers start: 20
  outliers final: 12
  residues processed: 136
  average time/residue: 0.0895
  time to fit residues: 17.8993
Evaluate side-chains
  130 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  217 PHE
Chi-restraints excluded: chain C residue   33 ILE
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain D residue   45 MET
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue  115 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 94 optimal weight:    8.9990
   chunk 97 optimal weight:    7.9990
   chunk 79 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9990
   chunk 75 optimal weight:    8.9990
   chunk 24 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 74 optimal weight:    4.9990
   chunk 76 optimal weight:    7.9990
   chunk 100 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  65 ASN
** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.058541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.042994 restraints weight = 71375.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.044591 restraints weight = 42099.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.045720 restraints weight = 29441.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.046421 restraints weight = 22924.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.046966 restraints weight = 19405.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.3025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.067  11812  Z= 0.349
  Angle     :  0.794  12.500  16997  Z= 0.460
  Chirality :  0.044   0.263   1964
  Planarity :  0.007   0.078   1276
  Dihedral  : 31.097 176.816   3544
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 24.35
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  9.24 %
    Favored  : 90.51 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 17.80 %
    Favored  : 78.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

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 aren not related in a simple way.
  whole: -1.48 (0.28), residues: 790
  helix: -0.04 (0.22), residues: 506
  sheet:  None (None), residues: 0
  loop : -2.71 (0.33), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 203 
 TYR   0.017   0.002   TYR B 121 
 PHE   0.032   0.003   PHE C 154 
 HIS   0.007   0.002   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00740 (11812)
  covalent geometry    : angle       0.79409 (16997)
  hydrogen bonds       : bond        0.09550 (  709)
  hydrogen bonds       : angle       4.92357 ( 1790)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8446 (m-80) cc_final: 0.8077 (m-80)
REVERT: A   71 GLN cc_start: 0.9606 (mt0) cc_final: 0.9368 (mt0)
REVERT: A   95 GLU cc_start: 0.9323 (pp20) cc_final: 0.8913 (tp30)
REVERT: A  177 ASP cc_start: 0.9221 (m-30) cc_final: 0.8974 (m-30)
REVERT: A  212 GLU cc_start: 0.9469 (mp0) cc_final: 0.9188 (mp0)
REVERT: B  109 HIS cc_start: 0.9096 (t70) cc_final: 0.8411 (t-90)
REVERT: B  187 ASP cc_start: 0.9225 (m-30) cc_final: 0.9008 (m-30)
REVERT: C   64 MET cc_start: 0.8752 (mmt) cc_final: 0.8036 (mmt)
REVERT: C   77 MET cc_start: 0.9395 (ppp) cc_final: 0.9121 (ppp)
REVERT: C  139 ARG cc_start: 0.8761 (mmm160) cc_final: 0.8034 (mpt-90)
REVERT: C  216 MET cc_start: 0.8838 (tpt) cc_final: 0.8267 (tpp)
REVERT: D   82 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8507 (mm)
  outliers start: 24
  outliers final: 18
  residues processed: 130
  average time/residue: 0.0856
  time to fit residues: 16.1781
Evaluate side-chains
  126 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  207 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  217 PHE
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  167 HIS
Chi-restraints excluded: chain C residue  178 MET
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain D residue   45 MET
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   69 PHE
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  217 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 91 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 99 optimal weight:    6.9990
   chunk 33 optimal weight:    0.5980
   chunk 52 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 88 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 57 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    3.5188

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

Flipped N/Q/H residues before XYZ refinement:
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 170 HIS
** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.059671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.043916 restraints weight = 68708.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.045604 restraints weight = 40312.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.046749 restraints weight = 28005.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.047537 restraints weight = 21746.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.048026 restraints weight = 18236.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  11812  Z= 0.252
  Angle     :  0.743  10.513  16997  Z= 0.427
  Chirality :  0.041   0.242   1964
  Planarity :  0.006   0.072   1276
  Dihedral  : 31.250 179.158   3544
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 19.41
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.34 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 21.36 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

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 aren not related in a simple way.
  whole: -1.27 (0.28), residues: 790
  helix:  0.09 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -2.57 (0.33), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  59 
 TYR   0.017   0.002   TYR B 172 
 PHE   0.035   0.003   PHE A 154 
 HIS   0.006   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 (11812)
  covalent geometry    : angle       0.74263 (16997)
  hydrogen bonds       : bond        0.06187 (  709)
  hydrogen bonds       : angle       4.73438 ( 1790)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 114
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8460 (m-80) cc_final: 0.8061 (m-80)
REVERT: A   71 GLN cc_start: 0.9623 (mt0) cc_final: 0.9401 (mt0)
REVERT: A   95 GLU cc_start: 0.9280 (pp20) cc_final: 0.8973 (tp30)
REVERT: A  177 ASP cc_start: 0.9164 (m-30) cc_final: 0.8964 (m-30)
REVERT: B  109 HIS cc_start: 0.9160 (t70) cc_final: 0.8375 (t-90)
REVERT: B  121 TYR cc_start: 0.9001 (t80) cc_final: 0.8423 (t80)
REVERT: B  187 ASP cc_start: 0.9175 (m-30) cc_final: 0.8964 (m-30)
REVERT: C   64 MET cc_start: 0.8674 (mmt) cc_final: 0.7822 (mmt)
REVERT: C   77 MET cc_start: 0.9433 (ppp) cc_final: 0.9109 (ppp)
REVERT: C   95 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7282 (tp30)
REVERT: C  216 MET cc_start: 0.8811 (tpt) cc_final: 0.8259 (tpp)
REVERT: D  174 MET cc_start: 0.9628 (mmm) cc_final: 0.9413 (mmp)
  outliers start: 25
  outliers final: 13
  residues processed: 126
  average time/residue: 0.0885
  time to fit residues: 16.6049
Evaluate side-chains
  120 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  217 PHE
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue   95 GLU
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  178 MET
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain D residue   45 MET
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  217 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 94 optimal weight:    7.9990
   chunk 88 optimal weight:   10.0000
   chunk 77 optimal weight:   30.0000
   chunk 90 optimal weight:   10.0000
   chunk 99 optimal weight:    8.9990
   chunk 61 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.059035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.043270 restraints weight = 69586.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.044924 restraints weight = 41119.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.046060 restraints weight = 28713.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.046808 restraints weight = 22343.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.047368 restraints weight = 18845.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.4122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  11812  Z= 0.250
  Angle     :  0.728  10.616  16997  Z= 0.419
  Chirality :  0.041   0.232   1964
  Planarity :  0.006   0.071   1276
  Dihedral  : 31.252 179.228   3544
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 19.36
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.85 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 23.84 %
    Favored  : 72.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

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 aren not related in a simple way.
  whole: -1.23 (0.28), residues: 790
  helix:  0.15 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -2.63 (0.33), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 203 
 TYR   0.020   0.002   TYR B 172 
 PHE   0.030   0.003   PHE C 154 
 HIS   0.006   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 (11812)
  covalent geometry    : angle       0.72792 (16997)
  hydrogen bonds       : bond        0.06990 (  709)
  hydrogen bonds       : angle       4.68331 ( 1790)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8391 (m-80) cc_final: 0.7970 (m-80)
REVERT: A   71 GLN cc_start: 0.9620 (mt0) cc_final: 0.9389 (mt0)
REVERT: A   95 GLU cc_start: 0.9268 (pp20) cc_final: 0.8976 (tp30)
REVERT: A  177 ASP cc_start: 0.9194 (m-30) cc_final: 0.8966 (m-30)
REVERT: B  109 HIS cc_start: 0.9179 (t70) cc_final: 0.8422 (t-90)
REVERT: B  187 ASP cc_start: 0.9174 (m-30) cc_final: 0.8944 (m-30)
REVERT: C   64 MET cc_start: 0.8662 (mmt) cc_final: 0.7936 (mmt)
REVERT: C   77 MET cc_start: 0.9449 (ppp) cc_final: 0.9055 (ppp)
REVERT: C   95 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7465 (tp30)
REVERT: C  199 TYR cc_start: 0.9424 (m-80) cc_final: 0.8919 (m-80)
REVERT: C  210 ASP cc_start: 0.8780 (m-30) cc_final: 0.8149 (t0)
REVERT: C  216 MET cc_start: 0.8797 (tpt) cc_final: 0.8219 (tpp)
  outliers start: 22
  outliers final: 14
  residues processed: 126
  average time/residue: 0.0918
  time to fit residues: 17.1814
Evaluate side-chains
  115 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  207 THR
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  217 PHE
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue   95 GLU
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  161 ILE
Chi-restraints excluded: chain C residue  178 MET
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain D residue   45 MET
Chi-restraints excluded: chain D residue   48 GLN
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue  217 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 83 optimal weight:    7.9990
   chunk 57 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 2 optimal weight:    9.9990
   chunk 34 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 88 optimal weight:   10.0000
   chunk 50 optimal weight:    8.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  78 GLN
** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 167 HIS
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** 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 = 0.3566 r_free = 0.3566 target = 0.059453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.043658 restraints weight = 68971.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.045335 restraints weight = 40673.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.046437 restraints weight = 28319.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.047271 restraints weight = 22144.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.047871 restraints weight = 18482.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.4392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  11812  Z= 0.228
  Angle     :  0.738  14.497  16997  Z= 0.418
  Chirality :  0.040   0.245   1964
  Planarity :  0.006   0.070   1276
  Dihedral  : 31.319 178.560   3544
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 19.26
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.58 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 25.70 %
    Favored  : 71.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

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 aren not related in a simple way.
  whole: -1.15 (0.29), residues: 790
  helix:  0.20 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -2.57 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  59 
 TYR   0.018   0.002   TYR B 172 
 PHE   0.028   0.002   PHE C 154 
 HIS   0.005   0.001   HIS C  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 (11812)
  covalent geometry    : angle       0.73807 (16997)
  hydrogen bonds       : bond        0.06031 (  709)
  hydrogen bonds       : angle       4.64673 ( 1790)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8323 (m-80) cc_final: 0.7879 (m-80)
REVERT: A   71 GLN cc_start: 0.9630 (mt0) cc_final: 0.9397 (mt0)
REVERT: A   95 GLU cc_start: 0.9259 (pp20) cc_final: 0.8935 (tp30)
REVERT: A  177 ASP cc_start: 0.9153 (m-30) cc_final: 0.8932 (m-30)
REVERT: B   40 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8722 (mm)
REVERT: B  109 HIS cc_start: 0.9235 (t70) cc_final: 0.8462 (t-90)
REVERT: B  121 TYR cc_start: 0.8920 (t80) cc_final: 0.8390 (t80)
REVERT: B  187 ASP cc_start: 0.9148 (m-30) cc_final: 0.8930 (m-30)
REVERT: C   64 MET cc_start: 0.8631 (mmt) cc_final: 0.7860 (mmt)
REVERT: C   71 GLN cc_start: 0.9477 (mt0) cc_final: 0.9114 (mt0)
REVERT: C   77 MET cc_start: 0.9449 (ppp) cc_final: 0.9066 (ppp)
REVERT: C   95 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7590 (tp30)
REVERT: C  199 TYR cc_start: 0.9383 (m-80) cc_final: 0.8900 (m-80)
REVERT: C  210 ASP cc_start: 0.8752 (m-30) cc_final: 0.8133 (t0)
REVERT: C  216 MET cc_start: 0.8788 (tpt) cc_final: 0.8212 (tpp)
  outliers start: 21
  outliers final: 13
  residues processed: 121
  average time/residue: 0.0905
  time to fit residues: 16.3481
Evaluate side-chains
  116 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  207 THR
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue  217 PHE
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue   95 GLU
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  161 ILE
Chi-restraints excluded: chain C residue  167 HIS
Chi-restraints excluded: chain C residue  178 MET
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain D residue  217 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 69 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9990
   chunk 74 optimal weight:    6.9990
   chunk 76 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   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  40 HIS
** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 GLN
** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 139 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.062443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.046474 restraints weight = 66458.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.048194 restraints weight = 38954.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.049387 restraints weight = 27110.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.050191 restraints weight = 20977.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.050794 restraints weight = 17568.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.4753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11812  Z= 0.172
  Angle     :  0.717  11.279  16997  Z= 0.401
  Chirality :  0.039   0.236   1964
  Planarity :  0.005   0.067   1276
  Dihedral  : 31.164 179.200   3544
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 17.09
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.70 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 27.55 %
    Favored  : 70.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.52 %

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 aren not related in a simple way.
  whole: -0.92 (0.29), residues: 790
  helix:  0.36 (0.23), residues: 508
  sheet:  None (None), residues: 0
  loop : -2.43 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  59 
 TYR   0.012   0.002   TYR B 172 
 PHE   0.022   0.002   PHE C 154 
 HIS   0.004   0.001   HIS C 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (11812)
  covalent geometry    : angle       0.71750 (16997)
  hydrogen bonds       : bond        0.04666 (  709)
  hydrogen bonds       : angle       4.46321 ( 1790)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8165 (m-10) cc_final: 0.7725 (m-80)
REVERT: A   64 MET cc_start: 0.7857 (ttm) cc_final: 0.7414 (tpp)
REVERT: A   71 GLN cc_start: 0.9619 (mt0) cc_final: 0.9401 (mt0)
REVERT: A   95 GLU cc_start: 0.9223 (pp20) cc_final: 0.8896 (tp30)
REVERT: A  177 ASP cc_start: 0.9076 (m-30) cc_final: 0.8847 (m-30)
REVERT: B   45 MET cc_start: 0.8087 (mmm) cc_final: 0.7754 (mmm)
REVERT: B  121 TYR cc_start: 0.8973 (t80) cc_final: 0.8517 (t80)
REVERT: B  126 GLU cc_start: 0.9394 (pt0) cc_final: 0.9151 (pp20)
REVERT: B  174 MET cc_start: 0.9419 (mmm) cc_final: 0.9026 (mmm)
REVERT: B  187 ASP cc_start: 0.9119 (m-30) cc_final: 0.8918 (m-30)
REVERT: C   64 MET cc_start: 0.8620 (mmt) cc_final: 0.7895 (mmt)
REVERT: C   77 MET cc_start: 0.9464 (ppp) cc_final: 0.9016 (ppp)
REVERT: C   82 ARG cc_start: 0.8949 (tpm170) cc_final: 0.8612 (mmm160)
REVERT: C   95 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7372 (tp30)
REVERT: C  154 PHE cc_start: 0.8949 (t80) cc_final: 0.8504 (t80)
REVERT: C  199 TYR cc_start: 0.9373 (m-80) cc_final: 0.8969 (m-80)
REVERT: C  210 ASP cc_start: 0.8687 (m-30) cc_final: 0.7932 (t0)
REVERT: C  216 MET cc_start: 0.8702 (tpt) cc_final: 0.8137 (tpp)
  outliers start: 13
  outliers final: 8
  residues processed: 122
  average time/residue: 0.0907
  time to fit residues: 16.5158
Evaluate side-chains
  113 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  217 PHE
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue   95 GLU
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  161 ILE
Chi-restraints excluded: chain C residue  178 MET
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain D residue  217 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 100 optimal weight:    6.9990
   chunk 15 optimal weight:    0.4980
   chunk 82 optimal weight:    8.9990
   chunk 77 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 21 optimal weight:   10.0000
   chunk 84 optimal weight:    7.9990
   chunk 47 optimal weight:    0.4980
   chunk 44 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  40 HIS
** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 204 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.063912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.047962 restraints weight = 65156.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.049668 restraints weight = 38604.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.050896 restraints weight = 26915.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.051692 restraints weight = 20819.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.052301 restraints weight = 17444.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.5064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11812  Z= 0.165
  Angle     :  0.712  11.423  16997  Z= 0.398
  Chirality :  0.040   0.335   1964
  Planarity :  0.005   0.065   1276
  Dihedral  : 30.995 179.972   3544
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 16.30
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.56 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 29.26 %
    Favored  : 68.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.52 %

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 aren not related in a simple way.
  whole: -0.90 (0.29), residues: 790
  helix:  0.30 (0.23), residues: 508
  sheet:  None (None), residues: 0
  loop : -2.25 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 108 
 TYR   0.013   0.002   TYR B 172 
 PHE   0.034   0.003   PHE B 209 
 HIS   0.014   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (11812)
  covalent geometry    : angle       0.71198 (16997)
  hydrogen bonds       : bond        0.04530 (  709)
  hydrogen bonds       : angle       4.36613 ( 1790)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 MET cc_start: 0.7697 (ttm) cc_final: 0.7141 (tpp)
REVERT: A   71 GLN cc_start: 0.9619 (mt0) cc_final: 0.9408 (mt0)
REVERT: A   95 GLU cc_start: 0.9244 (pp20) cc_final: 0.8977 (tp30)
REVERT: A  177 ASP cc_start: 0.9067 (m-30) cc_final: 0.8846 (m-30)
REVERT: B   45 MET cc_start: 0.8083 (mmm) cc_final: 0.7792 (mmm)
REVERT: B  121 TYR cc_start: 0.8865 (t80) cc_final: 0.8606 (t80)
REVERT: B  126 GLU cc_start: 0.9400 (pt0) cc_final: 0.9153 (pp20)
REVERT: B  174 MET cc_start: 0.9430 (mmm) cc_final: 0.9172 (mmm)
REVERT: B  187 ASP cc_start: 0.9096 (m-30) cc_final: 0.8881 (m-30)
REVERT: C   64 MET cc_start: 0.8407 (mmt) cc_final: 0.7743 (mmt)
REVERT: C   77 MET cc_start: 0.9427 (ppp) cc_final: 0.8950 (ppp)
REVERT: C  178 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.9214 (ptp)
REVERT: C  210 ASP cc_start: 0.8622 (m-30) cc_final: 0.7920 (t0)
REVERT: C  216 MET cc_start: 0.8641 (tpt) cc_final: 0.8103 (tpp)
REVERT: D  139 GLN cc_start: 0.9117 (tt0) cc_final: 0.8876 (tt0)
REVERT: D  204 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8912 (p0)
  outliers start: 13
  outliers final: 7
  residues processed: 125
  average time/residue: 0.0894
  time to fit residues: 16.7570
Evaluate side-chains
  120 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  217 PHE
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  161 ILE
Chi-restraints excluded: chain C residue  167 HIS
Chi-restraints excluded: chain C residue  178 MET
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain D residue   45 MET
Chi-restraints excluded: chain D residue  204 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 59 optimal weight:    9.9990
   chunk 87 optimal weight:    7.9990
   chunk 38 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 77 optimal weight:    7.9990
   chunk 79 optimal weight:    8.9990
   chunk 26 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 101 optimal weight:    8.9990
   overall best weight:    2.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.060717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.044948 restraints weight = 69025.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.046577 restraints weight = 41183.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.047708 restraints weight = 28930.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.048432 restraints weight = 22587.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.049021 restraints weight = 19128.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.5107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  11812  Z= 0.225
  Angle     :  0.713  11.225  16997  Z= 0.406
  Chirality :  0.039   0.230   1964
  Planarity :  0.006   0.069   1276
  Dihedral  : 31.073 178.063   3544
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 20.45
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.09 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 29.10 %
    Favored  : 68.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.52 %

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 aren not related in a simple way.
  whole: -0.86 (0.29), residues: 790
  helix:  0.37 (0.23), residues: 508
  sheet:  None (None), residues: 0
  loop : -2.31 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 203 
 TYR   0.017   0.002   TYR B 172 
 PHE   0.027   0.003   PHE C 154 
 HIS   0.004   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 (11812)
  covalent geometry    : angle       0.71333 (16997)
  hydrogen bonds       : bond        0.06265 (  709)
  hydrogen bonds       : angle       4.44354 ( 1790)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 MET cc_start: 0.7836 (ttm) cc_final: 0.7359 (tpp)
REVERT: A   71 GLN cc_start: 0.9616 (mt0) cc_final: 0.9405 (mt0)
REVERT: A   95 GLU cc_start: 0.9289 (OUTLIER) cc_final: 0.8974 (tp30)
REVERT: A  177 ASP cc_start: 0.9129 (m-30) cc_final: 0.8912 (m-30)
REVERT: B   40 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8679 (mm)
REVERT: B   45 MET cc_start: 0.8149 (mmm) cc_final: 0.7915 (mmm)
REVERT: B  105 ASP cc_start: 0.9418 (p0) cc_final: 0.8633 (p0)
REVERT: B  121 TYR cc_start: 0.8942 (t80) cc_final: 0.8640 (t80)
REVERT: B  174 MET cc_start: 0.9462 (mmm) cc_final: 0.9177 (mmm)
REVERT: C   64 MET cc_start: 0.8513 (mmt) cc_final: 0.7837 (mmt)
REVERT: C   77 MET cc_start: 0.9439 (ppp) cc_final: 0.8976 (ppp)
REVERT: C   95 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7512 (tp30)
REVERT: C  178 MET cc_start: 0.9449 (OUTLIER) cc_final: 0.9231 (ptp)
REVERT: C  210 ASP cc_start: 0.8652 (m-30) cc_final: 0.8092 (t0)
REVERT: C  216 MET cc_start: 0.8649 (tpt) cc_final: 0.8117 (tpp)
REVERT: D  204 ASN cc_start: 0.9240 (OUTLIER) cc_final: 0.8999 (p0)
REVERT: D  217 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8378 (p90)
  outliers start: 15
  outliers final: 8
  residues processed: 115
  average time/residue: 0.0964
  time to fit residues: 16.2091
Evaluate side-chains
  115 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  217 PHE
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue   95 GLU
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  161 ILE
Chi-restraints excluded: chain C residue  167 HIS
Chi-restraints excluded: chain C residue  178 MET
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain D residue   45 MET
Chi-restraints excluded: chain D residue  204 ASN
Chi-restraints excluded: chain D residue  217 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    9.9990
   chunk 4 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 67 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 89 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.060810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.045016 restraints weight = 69074.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.046663 restraints weight = 41190.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.047806 restraints weight = 28887.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.048593 restraints weight = 22510.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.049073 restraints weight = 18910.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.5126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.203  11812  Z= 0.265
  Angle     :  0.917  59.199  16997  Z= 0.548
  Chirality :  0.041   0.461   1964
  Planarity :  0.006   0.069   1276
  Dihedral  : 31.075 178.059   3544
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 21.58
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.96 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 28.79 %
    Favored  : 68.42 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.52 %

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 aren not related in a simple way.
  whole: -0.84 (0.29), residues: 790
  helix:  0.37 (0.23), residues: 506
  sheet:  None (None), residues: 0
  loop : -2.27 (0.34), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.058   0.001   ARG B 108 
 TYR   0.014   0.002   TYR B 172 
 PHE   0.026   0.003   PHE C 154 
 HIS   0.006   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 (11812)
  covalent geometry    : angle       0.91701 (16997)
  hydrogen bonds       : bond        0.06223 (  709)
  hydrogen bonds       : angle       4.46055 ( 1790)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1954.43 seconds
wall clock time: 34 minutes 35.53 seconds (2075.53 seconds total)