Starting phenix.real_space_refine
on Mon Jun  9 22:15:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n8n_24238/06_2025/7n8n_24238.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n8n_24238/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n8n_24238/06_2025/7n8n_24238.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n8n_24238/06_2025/7n8n_24238.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n8n_24238/06_2025/7n8n_24238.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n8n_24238/06_2025/7n8n_24238.cif"
  }
  resolution = 3.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.10, per 1000 atoms: 0.64
  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: 3.15
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 5.64
  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: 4.40

  Time building geometry restraints manager: 3.61 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:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     33.170
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.880
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 HIS   0.011   0.002   HIS C 219 
 PHE   0.024   0.004   PHE C 154 
 TYR   0.020   0.002   TYR D 121 
 ARG   0.007   0.001   ARG C  59 

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

*********************** 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  : 0.818 
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: 0.2182
  time to fit residues: 56.2105
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  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 77 optimal weight:    0.0870
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 41 optimal weight:    7.9990
   chunk 79 optimal weight:    8.9990
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:   20.0000
   chunk 59 optimal weight:    9.9990
   chunk 92 optimal weight:    7.9990
   overall best weight:    1.1362

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

Flipped N/Q/H residues before XYZ refinement:
A  40 HIS
B  44 ASN
B  56 GLN
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 GLN
C 167 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 = 0.3687 r_free = 0.3687 target = 0.065821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.049550 restraints weight = 64581.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.051403 restraints weight = 38406.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.052718 restraints weight = 26820.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11812  Z= 0.190
  Angle     :  0.741  11.324  16997  Z= 0.419
  Chirality :  0.041   0.253   1964
  Planarity :  0.006   0.067   1276
  Dihedral  : 30.975 172.746   3544
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 16.05
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.85 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 11.61 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.28), residues: 790
  helix:  0.05 (0.22), residues: 514
  sheet:  None (None), residues: 0
  loop : -2.61 (0.32), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.001   HIS D 197 
 PHE   0.014   0.002   PHE A  61 
 TYR   0.024   0.002   TYR B 172 
 ARG   0.006   0.001   ARG C 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05210 (  709)
  hydrogen bonds       : angle       4.61982 ( 1790)
  covalent geometry    : bond        0.00409 (11812)
  covalent geometry    : angle       0.74083 (16997)

*********************** 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: 18
    poor density    : 142
  time to evaluate  : 0.848 
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   59 ARG cc_start: 0.8731 (mtm180) cc_final: 0.8039 (mtt-85)
REVERT: A   61 PHE cc_start: 0.8519 (m-80) cc_final: 0.8202 (m-80)
REVERT: A  142 MET cc_start: 0.8943 (ptm) cc_final: 0.8643 (ptp)
REVERT: B   45 MET cc_start: 0.8516 (mmm) cc_final: 0.8213 (mmm)
REVERT: B  121 TYR cc_start: 0.8915 (t80) cc_final: 0.8300 (t80)
REVERT: B  149 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9323 (mm)
REVERT: B  166 LEU cc_start: 0.9527 (tp) cc_final: 0.9278 (tp)
REVERT: B  187 ASP cc_start: 0.9150 (m-30) cc_final: 0.8904 (m-30)
REVERT: C   64 MET cc_start: 0.8637 (mmt) cc_final: 0.8293 (mmt)
REVERT: C   71 GLN cc_start: 0.9366 (mt0) cc_final: 0.9008 (mt0)
REVERT: C   77 MET cc_start: 0.9368 (ppp) cc_final: 0.9015 (ppp)
REVERT: C   82 ARG cc_start: 0.8897 (tpm170) cc_final: 0.8363 (mmm160)
REVERT: C  116 PHE cc_start: 0.7320 (t80) cc_final: 0.6999 (t80)
REVERT: C  139 ARG cc_start: 0.8566 (mmm160) cc_final: 0.7977 (mpt-90)
REVERT: C  142 MET cc_start: 0.8105 (ptt) cc_final: 0.7639 (ppp)
REVERT: C  199 TYR cc_start: 0.9267 (m-10) cc_final: 0.8795 (m-80)
REVERT: C  216 MET cc_start: 0.8796 (tpt) cc_final: 0.8214 (tpp)
REVERT: D   62 GLU cc_start: 0.9306 (mm-30) cc_final: 0.9083 (mm-30)
REVERT: D   69 PHE cc_start: 0.9378 (t80) cc_final: 0.9166 (t80)
REVERT: D  174 MET cc_start: 0.9643 (mmp) cc_final: 0.9379 (mmp)
  outliers start: 18
  outliers final: 12
  residues processed: 149
  average time/residue: 0.2292
  time to fit residues: 48.3367
Evaluate side-chains
  139 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
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  149 LEU
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  115 THR
Chi-restraints excluded: chain D residue  166 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 84 optimal weight:    7.9990
   chunk 78 optimal weight:   10.0000
   chunk 65 optimal weight:    0.7980
   chunk 68 optimal weight:    4.9990
   chunk 41 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 87 optimal weight:    6.9990
   chunk 34 optimal weight:    9.9990
   overall best weight:    2.9586

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

Flipped N/Q/H residues before XYZ refinement:
B  65 ASN
C  32 GLN
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  65 ASN
** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.062630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.046438 restraints weight = 68579.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.048137 restraints weight = 40836.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.049339 restraints weight = 28583.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  11812  Z= 0.243
  Angle     :  0.711   9.814  16997  Z= 0.412
  Chirality :  0.040   0.160   1964
  Planarity :  0.006   0.073   1276
  Dihedral  : 30.807 174.450   3544
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 18.13
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.22 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 15.94 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.28), residues: 790
  helix:  0.11 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -2.57 (0.32), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D 109 
 PHE   0.013   0.002   PHE D 209 
 TYR   0.013   0.002   TYR B 121 
 ARG   0.006   0.001   ARG D  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06645 (  709)
  hydrogen bonds       : angle       4.66416 ( 1790)
  covalent geometry    : bond        0.00517 (11812)
  covalent geometry    : angle       0.71116 (16997)

*********************** 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
  149 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.922 
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   59 ARG cc_start: 0.8814 (mtm180) cc_final: 0.8139 (mtt-85)
REVERT: A   61 PHE cc_start: 0.8464 (m-80) cc_final: 0.8155 (m-80)
REVERT: A  177 ASP cc_start: 0.9096 (m-30) cc_final: 0.8890 (m-30)
REVERT: A  180 GLN cc_start: 0.9505 (OUTLIER) cc_final: 0.9278 (tp40)
REVERT: B  121 TYR cc_start: 0.8970 (t80) cc_final: 0.8344 (t80)
REVERT: B  187 ASP cc_start: 0.9198 (m-30) cc_final: 0.8985 (m-30)
REVERT: C   64 MET cc_start: 0.8660 (mmt) cc_final: 0.8418 (mmt)
REVERT: C   77 MET cc_start: 0.9467 (ppp) cc_final: 0.8951 (ppp)
REVERT: C  216 MET cc_start: 0.8840 (tpt) cc_final: 0.8281 (tpp)
  outliers start: 24
  outliers final: 16
  residues processed: 138
  average time/residue: 0.2025
  time to fit residues: 41.0121
Evaluate side-chains
  128 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  180 GLN
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   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   44 ASN
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
Chi-restraints excluded: chain D residue  148 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 18 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 84 optimal weight:    6.9990
   chunk 101 optimal weight:   10.0000
   chunk 54 optimal weight:    0.6980
   chunk 97 optimal weight:    7.9990
   chunk 56 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
A  32 GLN
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 219 HIS
** D 183 ASN ** 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 = 0.3674 r_free = 0.3674 target = 0.064727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.048209 restraints weight = 65747.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.050045 restraints weight = 39107.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.051341 restraints weight = 27359.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11812  Z= 0.178
  Angle     :  0.685   7.150  16997  Z= 0.393
  Chirality :  0.039   0.221   1964
  Planarity :  0.005   0.073   1276
  Dihedral  : 30.782 174.375   3544
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 15.56
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.33 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 18.11 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.28), residues: 790
  helix:  0.31 (0.22), residues: 506
  sheet:  None (None), residues: 0
  loop : -2.43 (0.33), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 109 
 PHE   0.021   0.002   PHE D 173 
 TYR   0.012   0.002   TYR B 172 
 ARG   0.004   0.001   ARG D  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04923 (  709)
  hydrogen bonds       : angle       4.50975 ( 1790)
  covalent geometry    : bond        0.00383 (11812)
  covalent geometry    : angle       0.68470 (16997)

*********************** 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
  142 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.786 
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   58 ILE cc_start: 0.9443 (pp) cc_final: 0.9043 (pp)
REVERT: A   61 PHE cc_start: 0.8362 (m-80) cc_final: 0.7413 (m-80)
REVERT: A   71 GLN cc_start: 0.9637 (mt0) cc_final: 0.9390 (mt0)
REVERT: A   95 GLU cc_start: 0.9284 (pp20) cc_final: 0.8858 (tp30)
REVERT: B   45 MET cc_start: 0.8268 (mmm) cc_final: 0.7935 (mmm)
REVERT: B  121 TYR cc_start: 0.8942 (t80) cc_final: 0.8398 (t80)
REVERT: B  149 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9378 (mm)
REVERT: B  187 ASP cc_start: 0.9160 (m-30) cc_final: 0.8945 (m-30)
REVERT: C   64 MET cc_start: 0.8550 (mmt) cc_final: 0.7941 (mmt)
REVERT: C   71 GLN cc_start: 0.9379 (mt0) cc_final: 0.9050 (mt0)
REVERT: C   77 MET cc_start: 0.9409 (ppp) cc_final: 0.9073 (ppp)
REVERT: C  116 PHE cc_start: 0.7527 (t80) cc_final: 0.7317 (t80)
REVERT: C  154 PHE cc_start: 0.9138 (t80) cc_final: 0.8931 (t80)
REVERT: C  216 MET cc_start: 0.8845 (tpt) cc_final: 0.8269 (tpp)
  outliers start: 21
  outliers final: 11
  residues processed: 132
  average time/residue: 0.2007
  time to fit residues: 38.7924
Evaluate side-chains
  124 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain B residue   65 ASN
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 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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 100 optimal weight:    6.9990
   chunk 8 optimal weight:   20.0000
   chunk 56 optimal weight:    0.9990
   chunk 84 optimal weight:    7.9990
   chunk 71 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 99 optimal weight:    7.9990
   chunk 92 optimal weight:    7.9990
   chunk 83 optimal weight:    7.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  40 HIS
** D 183 ASN ** 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 = 0.3659 r_free = 0.3659 target = 0.064095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.047658 restraints weight = 66286.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.049443 restraints weight = 39767.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.050710 restraints weight = 27975.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.3345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  11812  Z= 0.189
  Angle     :  0.670   7.596  16997  Z= 0.387
  Chirality :  0.038   0.219   1964
  Planarity :  0.005   0.075   1276
  Dihedral  : 30.728 174.666   3544
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 15.71
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.70 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 20.90 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.29), residues: 790
  helix:  0.31 (0.22), residues: 510
  sheet:  None (None), residues: 0
  loop : -2.39 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 152 
 PHE   0.019   0.002   PHE D 173 
 TYR   0.013   0.002   TYR D 172 
 ARG   0.005   0.001   ARG C 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05170 (  709)
  hydrogen bonds       : angle       4.46560 ( 1790)
  covalent geometry    : bond        0.00406 (11812)
  covalent geometry    : angle       0.66993 (16997)

*********************** 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
  138 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.9152 (mtp85) cc_final: 0.8890 (mtp180)
REVERT: A   61 PHE cc_start: 0.8281 (m-80) cc_final: 0.7893 (m-80)
REVERT: A   71 GLN cc_start: 0.9620 (mt0) cc_final: 0.9387 (mt0)
REVERT: A   95 GLU cc_start: 0.9279 (pp20) cc_final: 0.8872 (tp30)
REVERT: A  154 PHE cc_start: 0.9246 (t80) cc_final: 0.9003 (t80)
REVERT: B  109 HIS cc_start: 0.9180 (t70) cc_final: 0.8467 (t-90)
REVERT: B  121 TYR cc_start: 0.9016 (t80) cc_final: 0.8451 (t80)
REVERT: B  187 ASP cc_start: 0.9170 (m-30) cc_final: 0.8963 (m-30)
REVERT: C   64 MET cc_start: 0.8557 (mmt) cc_final: 0.7799 (mmt)
REVERT: C   77 MET cc_start: 0.9458 (ppp) cc_final: 0.9038 (ppp)
REVERT: C  154 PHE cc_start: 0.9196 (t80) cc_final: 0.8872 (t80)
REVERT: C  216 MET cc_start: 0.8796 (tpt) cc_final: 0.8215 (tpp)
REVERT: D  139 GLN cc_start: 0.9251 (tt0) cc_final: 0.8957 (tt0)
REVERT: D  174 MET cc_start: 0.9600 (mmm) cc_final: 0.9399 (mmp)
  outliers start: 18
  outliers final: 12
  residues processed: 129
  average time/residue: 0.2103
  time to fit residues: 39.4096
Evaluate side-chains
  121 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  207 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  204 THR
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain D residue   45 MET
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain D residue  148 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 51 optimal weight:    0.5980
   chunk 10 optimal weight:    3.9990
   chunk 88 optimal weight:   10.0000
   chunk 98 optimal weight:    7.9990
   chunk 60 optimal weight:   10.0000
   chunk 81 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9990
   chunk 83 optimal weight:    7.9990
   chunk 2 optimal weight:   10.0000
   chunk 70 optimal weight:    2.9990
   overall best weight:    2.9188

-------------------------------------------------------------------------------
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**
D  65 ASN
D 139 GLN
** D 183 ASN ** 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 = 0.3609 r_free = 0.3609 target = 0.061591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.045434 restraints weight = 67845.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.047179 restraints weight = 40324.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.048281 restraints weight = 28122.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.3678

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= 0.234
  Angle     :  0.695   8.470  16997  Z= 0.403
  Chirality :  0.039   0.184   1964
  Planarity :  0.006   0.076   1276
  Dihedral  : 30.889 176.580   3544
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 18.57
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.72 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 23.07 %
    Favored  : 74.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.29), residues: 790
  helix:  0.36 (0.23), residues: 508
  sheet:  None (None), residues: 0
  loop : -2.29 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A 167 
 PHE   0.049   0.003   PHE C 116 
 TYR   0.013   0.002   TYR B 121 
 ARG   0.006   0.001   ARG C 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06409 (  709)
  hydrogen bonds       : angle       4.51135 ( 1790)
  covalent geometry    : bond        0.00501 (11812)
  covalent geometry    : angle       0.69532 (16997)

*********************** 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: 17
    poor density    : 117
  time to evaluate  : 0.790 
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: 0.8188 (m-80) cc_final: 0.7806 (m-80)
REVERT: A   71 GLN cc_start: 0.9613 (mt0) cc_final: 0.9379 (mt0)
REVERT: A   95 GLU cc_start: 0.9325 (pp20) cc_final: 0.9017 (tp30)
REVERT: A  177 ASP cc_start: 0.9113 (m-30) cc_final: 0.8905 (m-30)
REVERT: B   45 MET cc_start: 0.8006 (mmm) cc_final: 0.7610 (mmm)
REVERT: B  109 HIS cc_start: 0.9158 (t70) cc_final: 0.8359 (t70)
REVERT: B  121 TYR cc_start: 0.8937 (t80) cc_final: 0.8414 (t80)
REVERT: C   64 MET cc_start: 0.8574 (mmt) cc_final: 0.7868 (mmt)
REVERT: C   77 MET cc_start: 0.9441 (ppp) cc_final: 0.9055 (ppp)
REVERT: C   95 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7571 (tp30)
REVERT: C  216 MET cc_start: 0.8782 (tpt) cc_final: 0.8213 (tpp)
REVERT: D   82 LEU cc_start: 0.8684 (mm) cc_final: 0.8437 (mm)
REVERT: D  139 GLN cc_start: 0.9251 (tt0) cc_final: 0.8894 (tt0)
  outliers start: 17
  outliers final: 9
  residues processed: 129
  average time/residue: 0.2047
  time to fit residues: 38.6970
Evaluate side-chains
  120 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  207 THR
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  204 THR
Chi-restraints excluded: chain D residue   45 MET
Chi-restraints excluded: chain D residue  148 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 68 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 17 optimal weight:    0.3980
   chunk 67 optimal weight:    6.9990
   chunk 76 optimal weight:    3.9990
   chunk 63 optimal weight:    7.9990
   chunk 38 optimal weight:   10.0000
   chunk 75 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 23 optimal weight:    8.9990
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 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 = 0.3622 r_free = 0.3622 target = 0.062264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.046274 restraints weight = 67027.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.048062 restraints weight = 39452.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.049287 restraints weight = 27298.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.4039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11812  Z= 0.202
  Angle     :  0.704  10.372  16997  Z= 0.401
  Chirality :  0.039   0.178   1964
  Planarity :  0.005   0.077   1276
  Dihedral  : 30.963 177.299   3544
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 16.89
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.46 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 25.70 %
    Favored  : 71.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.29), residues: 790
  helix:  0.39 (0.23), residues: 508
  sheet:  None (None), residues: 0
  loop : -2.31 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 167 
 PHE   0.026   0.002   PHE C 116 
 TYR   0.012   0.002   TYR B 121 
 ARG   0.007   0.001   ARG A  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05308 (  709)
  hydrogen bonds       : angle       4.50446 ( 1790)
  covalent geometry    : bond        0.00436 (11812)
  covalent geometry    : angle       0.70353 (16997)

*********************** 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: 15
    poor density    : 112
  time to evaluate  : 0.856 
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   71 GLN cc_start: 0.9631 (mt0) cc_final: 0.9413 (mt0)
REVERT: A   95 GLU cc_start: 0.9290 (pp20) cc_final: 0.8985 (tp30)
REVERT: A  177 ASP cc_start: 0.9085 (m-30) cc_final: 0.8871 (m-30)
REVERT: B  109 HIS cc_start: 0.9221 (t70) cc_final: 0.8424 (t70)
REVERT: B  121 TYR cc_start: 0.8940 (t80) cc_final: 0.8464 (t80)
REVERT: C   64 MET cc_start: 0.8596 (mmt) cc_final: 0.7858 (mmt)
REVERT: C   77 MET cc_start: 0.9455 (ppp) cc_final: 0.9017 (ppp)
REVERT: C  154 PHE cc_start: 0.9053 (t80) cc_final: 0.8697 (t80)
REVERT: C  210 ASP cc_start: 0.8667 (m-30) cc_final: 0.7926 (t0)
REVERT: C  216 MET cc_start: 0.8778 (tpt) cc_final: 0.8224 (tpp)
REVERT: D   82 LEU cc_start: 0.8717 (mm) cc_final: 0.8512 (mm)
REVERT: D  139 GLN cc_start: 0.9177 (tt0) cc_final: 0.8753 (tt0)
  outliers start: 15
  outliers final: 11
  residues processed: 123
  average time/residue: 0.2074
  time to fit residues: 37.4253
Evaluate side-chains
  120 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  207 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  161 ILE
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain C residue  207 THR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 78 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 94 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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**
** D 183 ASN ** 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 = 0.3570 r_free = 0.3570 target = 0.059807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.043907 restraints weight = 69715.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.045546 restraints weight = 41373.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.046696 restraints weight = 28938.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.4394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  11812  Z= 0.263
  Angle     :  0.731  10.197  16997  Z= 0.421
  Chirality :  0.041   0.188   1964
  Planarity :  0.006   0.076   1276
  Dihedral  : 31.171 179.601   3544
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 20.40
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.35 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 26.47 %
    Favored  : 70.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.29), residues: 790
  helix:  0.16 (0.22), residues: 514
  sheet:  None (None), residues: 0
  loop : -2.37 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS A 167 
 PHE   0.018   0.002   PHE A 154 
 TYR   0.014   0.002   TYR B 121 
 ARG   0.007   0.001   ARG B 186 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07190 (  709)
  hydrogen bonds       : angle       4.63410 ( 1790)
  covalent geometry    : bond        0.00563 (11812)
  covalent geometry    : angle       0.73109 (16997)

*********************** 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: 19
    poor density    : 108
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9523 (pp) cc_final: 0.9081 (pp)
REVERT: A   61 PHE cc_start: 0.8274 (m-10) cc_final: 0.7673 (m-80)
REVERT: A   71 GLN cc_start: 0.9625 (mt0) cc_final: 0.9397 (mt0)
REVERT: A   95 GLU cc_start: 0.9315 (pp20) cc_final: 0.8971 (tp30)
REVERT: A  177 ASP cc_start: 0.9182 (m-30) cc_final: 0.8961 (m-30)
REVERT: B   45 MET cc_start: 0.8012 (mmm) cc_final: 0.7584 (mmm)
REVERT: B  121 TYR cc_start: 0.8964 (t80) cc_final: 0.8494 (t80)
REVERT: C   64 MET cc_start: 0.8627 (mmt) cc_final: 0.8084 (mmt)
REVERT: C   77 MET cc_start: 0.9458 (ppp) cc_final: 0.8944 (ppp)
REVERT: C   82 ARG cc_start: 0.9023 (tpm170) cc_final: 0.8582 (mmm160)
REVERT: C   95 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7584 (tp30)
REVERT: C  154 PHE cc_start: 0.9047 (t80) cc_final: 0.8843 (t80)
REVERT: C  216 MET cc_start: 0.8733 (tpt) cc_final: 0.8204 (tpp)
  outliers start: 19
  outliers final: 15
  residues processed: 122
  average time/residue: 0.1910
  time to fit residues: 34.5836
Evaluate side-chains
  120 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  207 THR
Chi-restraints excluded: chain B residue  149 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  204 THR
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain D residue   45 MET
Chi-restraints excluded: chain D residue   70 LEU
Chi-restraints excluded: chain D residue  148 LEU
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 37 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 96 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 42 optimal weight:    0.5980
   chunk 9 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 81 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0870
   chunk 70 optimal weight:   10.0000
   overall best weight:    1.3362

-------------------------------------------------------------------------------
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  71 GLN
** C 141 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 = 0.3632 r_free = 0.3632 target = 0.062935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.046875 restraints weight = 66740.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.048621 restraints weight = 39596.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.049790 restraints weight = 27632.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.4709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  11812  Z= 0.175
  Angle     :  0.711  10.986  16997  Z= 0.402
  Chirality :  0.040   0.225   1964
  Planarity :  0.005   0.072   1276
  Dihedral  : 31.081 179.844   3544
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 16.35
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.06 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 28.02 %
    Favored  : 70.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.52 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.29), residues: 790
  helix:  0.45 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.23 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 167 
 PHE   0.010   0.002   PHE B  38 
 TYR   0.009   0.002   TYR B 121 
 ARG   0.005   0.001   ARG C  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04667 (  709)
  hydrogen bonds       : angle       4.50514 ( 1790)
  covalent geometry    : bond        0.00381 (11812)
  covalent geometry    : angle       0.71100 (16997)

*********************** 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
  127 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.980 
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: 0.7998 (ttm) cc_final: 0.7501 (tpp)
REVERT: A   71 GLN cc_start: 0.9630 (mt0) cc_final: 0.9363 (mt0)
REVERT: A   95 GLU cc_start: 0.9249 (pp20) cc_final: 0.8986 (tp30)
REVERT: A  154 PHE cc_start: 0.9259 (t80) cc_final: 0.8963 (t80)
REVERT: A  177 ASP cc_start: 0.9084 (m-30) cc_final: 0.8867 (m-30)
REVERT: B   39 ARG cc_start: 0.8301 (mpt-90) cc_final: 0.8083 (mtt90)
REVERT: B   45 MET cc_start: 0.8073 (mmm) cc_final: 0.7649 (mmm)
REVERT: B  121 TYR cc_start: 0.9023 (t80) cc_final: 0.8683 (t80)
REVERT: B  126 GLU cc_start: 0.9438 (pt0) cc_final: 0.9199 (pp20)
REVERT: C   64 MET cc_start: 0.8628 (mmt) cc_final: 0.7839 (mmt)
REVERT: C   77 MET cc_start: 0.9446 (ppp) cc_final: 0.8968 (ppp)
REVERT: C  154 PHE cc_start: 0.8955 (t80) cc_final: 0.8578 (t80)
REVERT: C  210 ASP cc_start: 0.8633 (m-30) cc_final: 0.7881 (t0)
REVERT: C  216 MET cc_start: 0.8712 (tpt) cc_final: 0.8181 (tpp)
REVERT: D  139 GLN cc_start: 0.9098 (tt0) cc_final: 0.8766 (tt0)
REVERT: D  204 ASN cc_start: 0.9035 (OUTLIER) cc_final: 0.8799 (p0)
REVERT: D  217 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.8390 (p90)
  outliers start: 12
  outliers final: 7
  residues processed: 124
  average time/residue: 0.2159
  time to fit residues: 39.2160
Evaluate side-chains
  114 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 C residue  161 ILE
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain C residue  207 THR
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 72 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 95 optimal weight:    9.9990
   chunk 99 optimal weight:    7.9990
   chunk 21 optimal weight:    6.9990
   chunk 89 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 96 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   chunk 71 optimal weight:    6.9990
   overall best weight:    2.3984

-------------------------------------------------------------------------------
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 109 HIS
D 204 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.061397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.045575 restraints weight = 67556.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.047251 restraints weight = 39811.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.048425 restraints weight = 27747.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.4853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  11812  Z= 0.213
  Angle     :  0.723  11.126  16997  Z= 0.410
  Chirality :  0.040   0.267   1964
  Planarity :  0.006   0.074   1276
  Dihedral  : 31.100 179.632   3544
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 19.26
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.47 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 28.79 %
    Favored  : 69.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.52 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.29), residues: 790
  helix:  0.41 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.24 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.018   0.001   HIS B 109 
 PHE   0.016   0.002   PHE A  61 
 TYR   0.011   0.002   TYR B 121 
 ARG   0.007   0.001   ARG D 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05717 (  709)
  hydrogen bonds       : angle       4.54133 ( 1790)
  covalent geometry    : bond        0.00460 (11812)
  covalent geometry    : angle       0.72341 (16997)

********************** 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
  112 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 MET cc_start: 0.8063 (ttm) cc_final: 0.7793 (tpp)
REVERT: A   71 GLN cc_start: 0.9592 (mt0) cc_final: 0.9381 (mt0)
REVERT: A   95 GLU cc_start: 0.9254 (pp20) cc_final: 0.8927 (tp30)
REVERT: A  177 ASP cc_start: 0.9129 (m-30) cc_final: 0.8900 (m-30)
REVERT: B  105 ASP cc_start: 0.9405 (p0) cc_final: 0.9112 (p0)
REVERT: B  121 TYR cc_start: 0.9030 (t80) cc_final: 0.8718 (t80)
REVERT: C   64 MET cc_start: 0.8680 (mmt) cc_final: 0.8103 (mmt)
REVERT: C   77 MET cc_start: 0.9441 (ppp) cc_final: 0.9025 (ppp)
REVERT: C  154 PHE cc_start: 0.8956 (t80) cc_final: 0.8581 (t80)
REVERT: C  210 ASP cc_start: 0.8647 (m-30) cc_final: 0.7962 (t0)
REVERT: C  216 MET cc_start: 0.8692 (tpt) cc_final: 0.8155 (tpp)
REVERT: D  139 GLN cc_start: 0.9129 (tt0) cc_final: 0.8843 (tt0)
REVERT: D  204 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8863 (p0)
  outliers start: 11
  outliers final: 8
  residues processed: 109
  average time/residue: 0.2062
  time to fit residues: 33.2598
Evaluate side-chains
  108 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 C residue  161 ILE
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain C residue  207 THR
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 90 optimal weight:   20.0000
   chunk 68 optimal weight:    6.9990
   chunk 4 optimal weight:    0.7980
   chunk 98 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9990
   chunk 41 optimal weight:    9.9990
   chunk 3 optimal weight:    0.6980
   chunk 100 optimal weight:    6.9990
   chunk 81 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 9 optimal weight:    9.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
A  32 GLN
** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 141 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 = 0.3595 r_free = 0.3595 target = 0.061183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.045349 restraints weight = 67672.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.047006 restraints weight = 40099.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.048172 restraints weight = 28131.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.5011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  11812  Z= 0.214
  Angle     :  0.725  11.017  16997  Z= 0.412
  Chirality :  0.040   0.232   1964
  Planarity :  0.006   0.076   1276
  Dihedral  : 31.221 178.466   3544
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 18.96
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.84 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 28.02 %
    Favored  : 69.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.52 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.29), residues: 790
  helix:  0.30 (0.23), residues: 508
  sheet:  None (None), residues: 0
  loop : -2.28 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 167 
 PHE   0.016   0.002   PHE A  61 
 TYR   0.010   0.002   TYR B 121 
 ARG   0.007   0.001   ARG C 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05717 (  709)
  hydrogen bonds       : angle       4.58792 ( 1790)
  covalent geometry    : bond        0.00463 (11812)
  covalent geometry    : angle       0.72544 (16997)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3645.32 seconds
wall clock time: 64 minutes 0.47 seconds (3840.47 seconds total)