Starting phenix.real_space_refine
on Fri Sep 11 18:51:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n8n_24238/09_2026/7n8n_24238.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n8n_24238/09_2026/7n8n_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_2026/7n8n_24238.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n8n_24238/09_2026/7n8n_24238.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n8n_24238/09_2026/7n8n_24238.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n8n_24238/09_2026/7n8n_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-2.2.1-6174/lib/python3.11/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: 2.19, per 1000 atoms: 0.20
  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: 0.88
  Conformation dependent library (CDL) restraints added in 246.1 milliseconds
  

  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: 1.45
  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: 1.67

  Time building geometry restraints manager: 1.19 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=" C3'  DA I -25 "
       pdb=" O3'  DA I -25 "
    ideal  model  delta    sigma   weight residual
    1.435  1.396  0.039 1.30e-02 5.92e+03 9.15e+00
  bond pdb=" C3'  DT I  30 "
       pdb=" C2'  DT I  30 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.04e+00
  bond pdb=" C3'  DT I -16 "
       pdb=" O3'  DT I -16 "
    ideal  model  delta    sigma   weight residual
    1.435  1.396  0.039 1.30e-02 5.92e+03 8.99e+00
  bond pdb=" C3'  DA I -15 "
       pdb=" C2'  DA I -15 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.92e+00
  bond pdb=" C3'  DT J -16 "
       pdb=" O3'  DT J -16 "
    ideal  model  delta    sigma   weight residual
    1.435  1.397  0.038 1.30e-02 5.92e+03 8.73e+00
  ... (remaining 11807 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 16283
        2.25 -     4.51: 670
        4.51 -     6.76: 40
        6.76 -     9.02: 0
        9.02 -    11.27: 4
  Bond angle restraints: 16997
  Sorted by residual:
  angle pdb=" O4'  DG J  38 "
        pdb=" C1'  DG J  38 "
        pdb=" N9   DG J  38 "
      ideal   model   delta    sigma   weight residual
     108.00  112.80   -4.80 7.00e-01 2.04e+00 4.71e+01
  angle pdb=" N3   DT I  38 "
        pdb=" C4   DT I  38 "
        pdb=" O4   DT I  38 "
      ideal   model   delta    sigma   weight residual
     119.90  123.12   -3.22 6.00e-01 2.78e+00 2.88e+01
  angle pdb=" O4'  DG I -40 "
        pdb=" C4'  DG I -40 "
        pdb=" C3'  DG I -40 "
      ideal   model   delta    sigma   weight residual
     106.00  102.86    3.14 6.00e-01 2.78e+00 2.73e+01
  angle pdb=" O4'  DC I  36 "
        pdb=" C4'  DC I  36 "
        pdb=" C3'  DC I  36 "
      ideal   model   delta    sigma   weight residual
     106.00  103.09    2.91 6.00e-01 2.78e+00 2.36e+01
  angle pdb=" O4   DT I  38 "
        pdb=" C4   DT I  38 "
        pdb=" C5   DT I  38 "
      ideal   model   delta    sigma   weight residual
     124.90  121.54    3.36 7.00e-01 2.04e+00 2.31e+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 -    0.043: 1266
       0.043 -    0.086: 463
       0.086 -    0.129: 195
       0.129 -    0.172: 36
       0.172 -    0.215: 4
  Chirality restraints: 1964
  Sorted by residual:
  chirality pdb=" C3'  DT J -17 "
            pdb=" C4'  DT J -17 "
            pdb=" O3'  DT J -17 "
            pdb=" C2'  DT J -17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.52   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" C3'  DG I -41 "
            pdb=" C4'  DG I -41 "
            pdb=" O3'  DG I -41 "
            pdb=" C2'  DG I -41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.54   -0.19 2.00e-01 2.50e+01 8.79e-01
  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
  ... (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:             1.030
  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:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     10.850
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
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      :  0.007   0.039  11812  Z= 0.622
  Angle     :  0.955  11.271  16997  Z= 0.750
  Chirality :  0.053   0.215   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 are 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/Z
  covalent geometry    : bond        0.00712 /  0.62 (11812)
  covalent geometry    : angle       0.95472 /  0.75 (16997)
  hydrogen bonds       : bond        0.13569 /  9.39 (  709)
  hydrogen bonds       : angle       5.49303 /  3.86 ( 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  : 0.292 
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: 0.8660 (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: 0.9012 (tpt)
REVERT: B   45 MET cc_start: 0.8391 (mmm) cc_final: 0.8030 (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: 0.9111 (ppp)
REVERT: C  157 MET cc_start: 0.9086 (mtt) cc_final: 0.8544 (mmm)
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: 0.0992
  time to fit residues: 26.2262
Evaluate side-chains
  113 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
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:   20.0000
   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:    0.9980
   chunk 100 optimal weight:   20.0000
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9990
   overall best weight:    2.3986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  40 HIS
** A  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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
D  65 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.063497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.047405 restraints weight = 66228.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.049199 restraints weight = 39059.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.050433 restraints weight = 27160.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.051279 restraints weight = 21038.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.051881 restraints weight = 17601.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.1601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  11812  Z= 0.212
  Angle     :  0.852  11.111  16997  Z= 0.479
  Chirality :  0.050   0.409   1964
  Planarity :  0.007   0.075   1276
  Dihedral  : 31.394 176.216   3544
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 20.64
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.73 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 12.07 %
    Favored  : 84.37 %
  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 are not related in a simple way.
  whole: -1.48 (0.28), residues: 790
  helix: -0.03 (0.22), residues: 512
  sheet:  None (None), residues: 0
  loop : -2.80 (0.32), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 157 
 TYR   0.022   0.003   TYR B 172 
 PHE   0.013   0.002   PHE A  61 
 HIS   0.005   0.001   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00394 /  0.21 (11812)
  covalent geometry    : angle       0.85241 /  0.48 (16997)
  hydrogen bonds       : bond        0.07478 /  5.07 (  709)
  hydrogen bonds       : angle       4.90351 /  3.44 ( 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
  159 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 136
  time to evaluate  : 0.527 
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: 0.8555 (m-80) cc_final: 0.8250 (m-80)
REVERT: A   77 MET cc_start: 0.9548 (ttp) cc_final: 0.9330 (tmm)
REVERT: A  142 MET cc_start: 0.8960 (ptm) cc_final: 0.8628 (ptp)
REVERT: A  216 MET cc_start: 0.9128 (tpt) cc_final: 0.8911 (tpt)
REVERT: B   45 MET cc_start: 0.8505 (mmm) cc_final: 0.8131 (mmm)
REVERT: B  121 TYR cc_start: 0.8824 (t80) cc_final: 0.8226 (t80)
REVERT: B  187 ASP cc_start: 0.9209 (m-30) cc_final: 0.8986 (m-30)
REVERT: C   64 MET cc_start: 0.8691 (mmt) cc_final: 0.8478 (mmt)
REVERT: C   71 GLN cc_start: 0.9420 (mt0) cc_final: 0.9207 (mm-40)
REVERT: C   77 MET cc_start: 0.9404 (ppp) cc_final: 0.8921 (ppp)
REVERT: C  199 TYR cc_start: 0.9297 (m-10) cc_final: 0.8893 (m-80)
REVERT: C  216 MET cc_start: 0.8868 (tpt) cc_final: 0.8273 (tpp)
REVERT: D   69 PHE cc_start: 0.9357 (t80) cc_final: 0.9119 (t80)
REVERT: D  108 ARG cc_start: 0.8645 (mtm110) cc_final: 0.8240 (ttp80)
REVERT: D  174 MET cc_start: 0.9648 (mmp) cc_final: 0.9377 (mmp)
  outliers start: 23
  outliers final: 17
  residues processed: 147
  average time/residue: 0.0866
  time to fit residues: 19.2382
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  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  207 THR
Chi-restraints excluded: chain B residue   33 ASP
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 C residue  207 THR
Chi-restraints excluded: chain D residue   44 ASN
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   74 ILE
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:    7.9990
   chunk 46 optimal weight:    0.7980
   chunk 67 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9990
   chunk 3 optimal weight:    0.2980
   chunk 49 optimal weight:   20.0000
   chunk 4 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 88 optimal weight:   30.0000
   overall best weight:    1.6186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  40 HIS
B  65 ASN
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  44 ASN
D  65 ASN
D 204 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.064076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.048015 restraints weight = 66125.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.049760 restraints weight = 38767.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.050915 restraints weight = 26988.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.051780 restraints weight = 21110.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.052327 restraints weight = 17652.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.2079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  11812  Z= 0.185
  Angle     :  0.795   9.756  16997  Z= 0.450
  Chirality :  0.048   0.404   1964
  Planarity :  0.006   0.075   1276
  Dihedral  : 31.220 176.333   3544
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 18.08
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.47 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 15.63 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.28), residues: 790
  helix: -0.01 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -2.63 (0.32), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  32 
 TYR   0.018   0.002   TYR D 121 
 PHE   0.021   0.002   PHE C 154 
 HIS   0.006   0.001   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.19 (11812)
  covalent geometry    : angle       0.79498 /  0.45 (16997)
  hydrogen bonds       : bond        0.06274 /  4.29 (  709)
  hydrogen bonds       : angle       4.75653 /  3.34 ( 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
  148 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 0.280 
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: 0.8763 (mtm180) cc_final: 0.8212 (mtt180)
REVERT: A   61 PHE cc_start: 0.8404 (m-80) cc_final: 0.8037 (m-80)
REVERT: A   77 MET cc_start: 0.9583 (ttp) cc_final: 0.9379 (tmm)
REVERT: B   45 MET cc_start: 0.8356 (mmm) cc_final: 0.8068 (mmm)
REVERT: B  121 TYR cc_start: 0.8888 (t80) cc_final: 0.8269 (t80)
REVERT: B  187 ASP cc_start: 0.9160 (m-30) cc_final: 0.8929 (m-30)
REVERT: C   64 MET cc_start: 0.8610 (mmt) cc_final: 0.8158 (mmt)
REVERT: C   71 GLN cc_start: 0.9421 (mt0) cc_final: 0.9169 (mm-40)
REVERT: C   77 MET cc_start: 0.9417 (ppp) cc_final: 0.9020 (ppp)
REVERT: C  180 GLN cc_start: 0.9394 (OUTLIER) cc_final: 0.9174 (mm110)
REVERT: C  199 TYR cc_start: 0.9291 (m-10) cc_final: 0.8890 (m-80)
REVERT: C  216 MET cc_start: 0.8830 (tpt) cc_final: 0.8232 (tpp)
REVERT: D  170 ILE cc_start: 0.9463 (mm) cc_final: 0.9224 (mm)
REVERT: D  174 MET cc_start: 0.9668 (mmp) cc_final: 0.9341 (mmp)
  outliers start: 26
  outliers final: 14
  residues processed: 135
  average time/residue: 0.0887
  time to fit residues: 18.1053
Evaluate side-chains
  130 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
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  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  180 GLN
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain D residue   44 ASN
Chi-restraints excluded: chain D residue   70 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 94 optimal weight:   30.0000
   chunk 97 optimal weight:   20.0000
   chunk 79 optimal weight:   30.0000
   chunk 35 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 74 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   chunk 100 optimal weight:   20.0000
   chunk 83 optimal weight:   20.0000
   overall best weight:    2.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  40 HIS
** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 ASN
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  44 ASN
D  65 ASN
D 109 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.062641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.046652 restraints weight = 67345.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.048447 restraints weight = 39737.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.049667 restraints weight = 27682.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.050526 restraints weight = 21428.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.051121 restraints weight = 17774.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  11812  Z= 0.207
  Angle     :  0.775   8.400  16997  Z= 0.444
  Chirality :  0.046   0.389   1964
  Planarity :  0.006   0.076   1276
  Dihedral  : 31.163 177.646   3544
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 18.37
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.23 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 16.56 %
    Favored  : 79.41 %
  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 are not related in a simple way.
  whole: -1.40 (0.28), residues: 790
  helix: -0.03 (0.22), residues: 506
  sheet:  None (None), residues: 0
  loop : -2.56 (0.33), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 203 
 TYR   0.025   0.003   TYR D 121 
 PHE   0.020   0.002   PHE C 154 
 HIS   0.011   0.001   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.21 (11812)
  covalent geometry    : angle       0.77487 /  0.44 (16997)
  hydrogen bonds       : bond        0.06986 /  4.80 (  709)
  hydrogen bonds       : angle       4.74815 /  3.33 ( 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
  143 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.248 
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   58 ILE cc_start: 0.9503 (pp) cc_final: 0.9030 (pp)
REVERT: A   59 ARG cc_start: 0.8773 (mtm180) cc_final: 0.8193 (mtt180)
REVERT: A   61 PHE cc_start: 0.8443 (m-80) cc_final: 0.7425 (m-80)
REVERT: A  216 MET cc_start: 0.9181 (tpt) cc_final: 0.8979 (tpt)
REVERT: B   45 MET cc_start: 0.8423 (mmm) cc_final: 0.8138 (mmm)
REVERT: B  121 TYR cc_start: 0.8958 (t80) cc_final: 0.8265 (t80)
REVERT: B  187 ASP cc_start: 0.9178 (m-30) cc_final: 0.8949 (m-30)
REVERT: C   71 GLN cc_start: 0.9434 (mt0) cc_final: 0.9147 (mm-40)
REVERT: C   77 MET cc_start: 0.9456 (ppp) cc_final: 0.9068 (ppp)
REVERT: C  199 TYR cc_start: 0.9323 (m-10) cc_final: 0.9122 (m-80)
REVERT: C  216 MET cc_start: 0.8842 (tpt) cc_final: 0.8258 (tpp)
REVERT: D  174 MET cc_start: 0.9696 (mmp) cc_final: 0.9456 (mmp)
  outliers start: 26
  outliers final: 17
  residues processed: 131
  average time/residue: 0.0756
  time to fit residues: 15.2075
Evaluate side-chains
  132 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
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  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   48 GLN
Chi-restraints excluded: chain D residue   69 PHE
Chi-restraints excluded: chain D residue   70 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 98 optimal weight:   30.0000
   chunk 91 optimal weight:   40.0000
   chunk 8 optimal weight:    7.9990
   chunk 99 optimal weight:   20.0000
   chunk 33 optimal weight:    6.9990
   chunk 52 optimal weight:    7.9990
   chunk 14 optimal weight:   10.0000
   chunk 88 optimal weight:   30.0000
   chunk 22 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    3.5786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  40 HIS
** A 134 ASN ** 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**
D  44 ASN

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 = 0.061655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.045603 restraints weight = 68033.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.047311 restraints weight = 40606.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.048490 restraints weight = 28506.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.049299 restraints weight = 22270.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.049799 restraints weight = 18742.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2621

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= 0.225
  Angle     :  0.778   8.726  16997  Z= 0.447
  Chirality :  0.046   0.377   1964
  Planarity :  0.006   0.077   1276
  Dihedral  : 31.197 178.387   3544
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 19.36
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.23 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 18.89 %
    Favored  : 76.63 %
  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 are not related in a simple way.
  whole: -1.33 (0.28), residues: 790
  helix: -0.01 (0.22), residues: 506
  sheet:  None (None), residues: 0
  loop : -2.48 (0.34), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 203 
 TYR   0.024   0.003   TYR D 121 
 PHE   0.045   0.003   PHE A 154 
 HIS   0.009   0.001   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00406 /  0.23 (11812)
  covalent geometry    : angle       0.77787 /  0.45 (16997)
  hydrogen bonds       : bond        0.07284 /  5.00 (  709)
  hydrogen bonds       : angle       4.79831 /  3.38 ( 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
  144 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 0.305 
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: 0.9514 (pp) cc_final: 0.9141 (pp)
REVERT: A   61 PHE cc_start: 0.8421 (m-80) cc_final: 0.7457 (m-80)
REVERT: A   95 GLU cc_start: 0.9293 (pp20) cc_final: 0.8770 (tp30)
REVERT: B   45 MET cc_start: 0.8485 (mmm) cc_final: 0.8203 (mmm)
REVERT: B  121 TYR cc_start: 0.8977 (t80) cc_final: 0.8298 (t80)
REVERT: B  174 MET cc_start: 0.9493 (mmm) cc_final: 0.9054 (mmm)
REVERT: B  187 ASP cc_start: 0.9181 (m-30) cc_final: 0.8962 (m-30)
REVERT: C   64 MET cc_start: 0.8626 (mmt) cc_final: 0.8325 (mmt)
REVERT: C   77 MET cc_start: 0.9489 (ppp) cc_final: 0.9140 (ppp)
REVERT: C   95 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7335 (tp30)
REVERT: C  184 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8384 (mt-10)
REVERT: C  216 MET cc_start: 0.8841 (tpt) cc_final: 0.8294 (tpp)
REVERT: D  205 ASP cc_start: 0.8209 (t0) cc_final: 0.7979 (t70)
  outliers start: 29
  outliers final: 18
  residues processed: 132
  average time/residue: 0.0893
  time to fit residues: 17.9537
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  : 0.331 
-------------------------------------------------------------------------------
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  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   95 GLU
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  167 HIS
Chi-restraints excluded: chain C residue  179 LEU
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   69 PHE
Chi-restraints excluded: chain D residue   70 LEU
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   95 LEU
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 94 optimal weight:   20.0000
   chunk 88 optimal weight:   30.0000
   chunk 77 optimal weight:   20.0000
   chunk 90 optimal weight:   50.0000
   chunk 99 optimal weight:   20.0000
   chunk 61 optimal weight:    1.9990
   chunk 71 optimal weight:    6.9990
   chunk 87 optimal weight:   20.0000
   chunk 15 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   overall best weight:    2.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  32 GLN
A  40 HIS
** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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**
D  65 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.062352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.046016 restraints weight = 67663.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.047771 restraints weight = 40336.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.049012 restraints weight = 28367.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.049870 restraints weight = 22082.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.050381 restraints weight = 18451.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11812  Z= 0.188
  Angle     :  0.770  11.304  16997  Z= 0.437
  Chirality :  0.046   0.373   1964
  Planarity :  0.005   0.077   1276
  Dihedral  : 31.186 178.487   3544
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 18.82
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.59 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 20.90 %
    Favored  : 75.08 %
  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 are not related in a simple way.
  whole: -1.28 (0.29), residues: 790
  helix:  0.03 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -2.45 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  59 
 TYR   0.021   0.003   TYR B 172 
 PHE   0.032   0.003   PHE A 154 
 HIS   0.008   0.001   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.19 (11812)
  covalent geometry    : angle       0.76972 /  0.44 (16997)
  hydrogen bonds       : bond        0.06274 /  4.29 (  709)
  hydrogen bonds       : angle       4.71622 /  3.32 ( 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
  142 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 0.336 
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   59 ARG cc_start: 0.9130 (mtm180) cc_final: 0.8836 (mtp180)
REVERT: A   61 PHE cc_start: 0.8310 (m-80) cc_final: 0.7943 (m-80)
REVERT: A   71 GLN cc_start: 0.9615 (mt0) cc_final: 0.9389 (mt0)
REVERT: A   95 GLU cc_start: 0.9289 (pp20) cc_final: 0.8824 (tp30)
REVERT: B   40 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8593 (mm)
REVERT: B   45 MET cc_start: 0.8410 (mmm) cc_final: 0.8132 (mmm)
REVERT: B  109 HIS cc_start: 0.9034 (t70) cc_final: 0.8235 (t-90)
REVERT: B  121 TYR cc_start: 0.8952 (t80) cc_final: 0.8398 (t80)
REVERT: B  187 ASP cc_start: 0.9157 (m-30) cc_final: 0.8931 (m-30)
REVERT: C   64 MET cc_start: 0.8623 (mmt) cc_final: 0.8289 (mmt)
REVERT: C   77 MET cc_start: 0.9474 (ppp) cc_final: 0.9101 (ppp)
REVERT: C   95 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7472 (tp30)
REVERT: C  184 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8333 (mt-10)
REVERT: C  216 MET cc_start: 0.8816 (tpt) cc_final: 0.8262 (tpp)
REVERT: D   43 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8994 (tpt170)
REVERT: D   44 ASN cc_start: 0.8986 (OUTLIER) cc_final: 0.8769 (p0)
  outliers start: 26
  outliers final: 15
  residues processed: 132
  average time/residue: 0.0988
  time to fit residues: 19.2778
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  : 0.226 
-------------------------------------------------------------------------------
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   40 LEU
Chi-restraints excluded: chain B residue   65 ASN
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   95 GLU
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain D residue   43 ARG
Chi-restraints excluded: chain D residue   44 ASN
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain D residue   69 PHE
Chi-restraints excluded: chain D residue   70 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
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:    9.9990
   chunk 83 optimal weight:   20.0000
   chunk 57 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   chunk 2 optimal weight:    9.9990
   chunk 34 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 88 optimal weight:   30.0000
   chunk 50 optimal weight:    2.9990
   overall best weight:    2.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  40 HIS
** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 170 HIS
C 219 HIS
D  44 ASN
D  65 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.061863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.045565 restraints weight = 67904.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.047323 restraints weight = 40226.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.048563 restraints weight = 28115.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.049423 restraints weight = 21866.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.049981 restraints weight = 18263.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.3075

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= 0.203
  Angle     :  0.768  10.539  16997  Z= 0.438
  Chirality :  0.046   0.362   1964
  Planarity :  0.006   0.079   1276
  Dihedral  : 31.182 179.069   3544
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 18.96
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.34 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 21.52 %
    Favored  : 74.15 %
  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 are not related in a simple way.
  whole: -1.19 (0.29), residues: 790
  helix:  0.13 (0.22), residues: 506
  sheet:  None (None), residues: 0
  loop : -2.49 (0.34), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 203 
 TYR   0.021   0.003   TYR D 121 
 PHE   0.030   0.003   PHE A 154 
 HIS   0.006   0.001   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.20 (11812)
  covalent geometry    : angle       0.76806 /  0.44 (16997)
  hydrogen bonds       : bond        0.06634 /  4.55 (  709)
  hydrogen bonds       : angle       4.74443 /  3.35 ( 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
  138 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 110
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8340 (m-80) cc_final: 0.7926 (m-80)
REVERT: A   71 GLN cc_start: 0.9612 (mt0) cc_final: 0.9387 (mt0)
REVERT: A   77 MET cc_start: 0.9405 (tmm) cc_final: 0.9193 (tmm)
REVERT: A   95 GLU cc_start: 0.9286 (pp20) cc_final: 0.8830 (tp30)
REVERT: B   40 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8579 (mm)
REVERT: B  109 HIS cc_start: 0.9073 (t70) cc_final: 0.8305 (t-90)
REVERT: B  121 TYR cc_start: 0.8958 (t80) cc_final: 0.8435 (t80)
REVERT: B  172 TYR cc_start: 0.8616 (t80) cc_final: 0.8408 (t80)
REVERT: B  187 ASP cc_start: 0.9167 (m-30) cc_final: 0.8951 (m-30)
REVERT: C   64 MET cc_start: 0.8627 (mmt) cc_final: 0.8274 (mmt)
REVERT: C   71 GLN cc_start: 0.9456 (mt0) cc_final: 0.9204 (mm-40)
REVERT: C   77 MET cc_start: 0.9473 (ppp) cc_final: 0.9122 (ppp)
REVERT: C   95 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7415 (tp30)
REVERT: C  184 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8275 (mt-10)
REVERT: C  216 MET cc_start: 0.8826 (tpt) cc_final: 0.8278 (tpp)
  outliers start: 28
  outliers final: 20
  residues processed: 127
  average time/residue: 0.0951
  time to fit residues: 18.2865
Evaluate side-chains
  127 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
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   40 LEU
Chi-restraints excluded: chain B residue   65 ASN
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  115 THR
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  167 HIS
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   69 PHE
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  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 63 optimal weight:    8.9990
   chunk 69 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 68 optimal weight:    0.7980
   chunk 60 optimal weight:   10.0000
   chunk 77 optimal weight:    5.9990
   chunk 74 optimal weight:    0.0670
   chunk 76 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   overall best weight:    1.3724

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.063153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.047030 restraints weight = 65823.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.048796 restraints weight = 38735.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.050049 restraints weight = 27077.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.050911 restraints weight = 20933.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.051512 restraints weight = 17460.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.3306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11812  Z= 0.168
  Angle     :  0.768  11.615  16997  Z= 0.432
  Chirality :  0.047   0.363   1964
  Planarity :  0.005   0.072   1276
  Dihedral  : 31.119 178.499   3544
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 16.74
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.71 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 23.53 %
    Favored  : 73.37 %
  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 are not related in a simple way.
  whole: -1.25 (0.29), residues: 790
  helix:  0.09 (0.22), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.50 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  59 
 TYR   0.021   0.003   TYR D 121 
 PHE   0.028   0.002   PHE D 173 
 HIS   0.008   0.001   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.17 (11812)
  covalent geometry    : angle       0.76826 /  0.43 (16997)
  hydrogen bonds       : bond        0.05402 /  3.70 (  709)
  hydrogen bonds       : angle       4.69305 /  3.29 ( 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
  141 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8221 (m-10) cc_final: 0.7776 (m-80)
REVERT: A   71 GLN cc_start: 0.9611 (mt0) cc_final: 0.9379 (mt0)
REVERT: A   77 MET cc_start: 0.9364 (tmm) cc_final: 0.9096 (tmm)
REVERT: A   95 GLU cc_start: 0.9281 (pp20) cc_final: 0.8880 (tp30)
REVERT: B   40 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8583 (mm)
REVERT: B  109 HIS cc_start: 0.9101 (t70) cc_final: 0.8287 (t-90)
REVERT: B  121 TYR cc_start: 0.8903 (t80) cc_final: 0.8261 (t80)
REVERT: B  172 TYR cc_start: 0.8604 (t80) cc_final: 0.8401 (t80)
REVERT: B  187 ASP cc_start: 0.9140 (m-30) cc_final: 0.8937 (m-30)
REVERT: C   64 MET cc_start: 0.8593 (mmt) cc_final: 0.8234 (mmt)
REVERT: C   77 MET cc_start: 0.9445 (ppp) cc_final: 0.9083 (ppp)
REVERT: C   95 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7540 (tp30)
REVERT: C  184 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8253 (mt-10)
REVERT: C  216 MET cc_start: 0.8806 (tpt) cc_final: 0.8255 (tpp)
  outliers start: 20
  outliers final: 14
  residues processed: 133
  average time/residue: 0.0968
  time to fit residues: 19.2880
Evaluate side-chains
  127 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   65 ASN
Chi-restraints excluded: chain B residue   80 THR
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  204 THR
Chi-restraints excluded: chain D residue   45 MET
Chi-restraints excluded: chain D residue   80 THR
Chi-restraints excluded: chain D residue   96 LEU
Chi-restraints excluded: chain D residue  115 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:   20.0000
   chunk 15 optimal weight:    0.0970
   chunk 82 optimal weight:   20.0000
   chunk 77 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   chunk 21 optimal weight:    0.1980
   chunk 84 optimal weight:   30.0000
   chunk 47 optimal weight:    9.9990
   chunk 44 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 49 optimal weight:   50.0000
   overall best weight:    3.4584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  40 HIS
** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.060885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.044969 restraints weight = 67684.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.046675 restraints weight = 40191.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.047856 restraints weight = 28088.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.048629 restraints weight = 21877.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.049188 restraints weight = 18459.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.3481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  11812  Z= 0.222
  Angle     :  0.794  10.228  16997  Z= 0.451
  Chirality :  0.046   0.336   1964
  Planarity :  0.006   0.075   1276
  Dihedral  : 31.149 179.854   3544
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 20.45
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.22 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 25.85 %
    Favored  : 70.74 %
  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 are not related in a simple way.
  whole: -1.27 (0.29), residues: 790
  helix:  0.10 (0.23), residues: 508
  sheet:  None (None), residues: 0
  loop : -2.61 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG D 108 
 TYR   0.023   0.003   TYR D 121 
 PHE   0.033   0.003   PHE A 154 
 HIS   0.006   0.001   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00403 /  0.22 (11812)
  covalent geometry    : angle       0.79380 /  0.45 (16997)
  hydrogen bonds       : bond        0.07354 /  5.05 (  709)
  hydrogen bonds       : angle       4.77865 /  3.39 ( 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
  127 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8339 (m-10) cc_final: 0.7940 (m-80)
REVERT: A   71 GLN cc_start: 0.9605 (mt0) cc_final: 0.9384 (mt0)
REVERT: A   77 MET cc_start: 0.9457 (tmm) cc_final: 0.9218 (tmm)
REVERT: A   95 GLU cc_start: 0.9287 (pp20) cc_final: 0.8868 (tp30)
REVERT: A  212 GLU cc_start: 0.9499 (mp0) cc_final: 0.8898 (pm20)
REVERT: B   40 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8595 (mm)
REVERT: B   45 MET cc_start: 0.8187 (mmm) cc_final: 0.7802 (mmm)
REVERT: B  109 HIS cc_start: 0.9113 (t70) cc_final: 0.8257 (t-90)
REVERT: B  121 TYR cc_start: 0.8909 (t80) cc_final: 0.8346 (t80)
REVERT: B  172 TYR cc_start: 0.8645 (t80) cc_final: 0.8436 (t80)
REVERT: B  187 ASP cc_start: 0.9175 (m-30) cc_final: 0.8956 (m-30)
REVERT: C   64 MET cc_start: 0.8651 (mmt) cc_final: 0.7963 (mmt)
REVERT: C   77 MET cc_start: 0.9471 (ppp) cc_final: 0.9104 (ppp)
REVERT: C   95 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7591 (tp30)
REVERT: C  216 MET cc_start: 0.8825 (tpt) cc_final: 0.8259 (tpp)
  outliers start: 22
  outliers final: 16
  residues processed: 121
  average time/residue: 0.0868
  time to fit residues: 16.3250
Evaluate side-chains
  125 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 THR
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   65 ASN
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  141 SER
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  167 HIS
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain D residue   45 MET
Chi-restraints excluded: chain D residue   96 LEU
Chi-restraints excluded: chain D residue  115 THR
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 14 optimal weight:    8.9990
   chunk 59 optimal weight:    9.9990
   chunk 87 optimal weight:   20.0000
   chunk 38 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 22 optimal weight:    6.9990
   chunk 77 optimal weight:    8.9990
   chunk 79 optimal weight:   30.0000
   chunk 26 optimal weight:    0.0870
   chunk 69 optimal weight:    3.9990
   chunk 101 optimal weight:   30.0000
   overall best weight:    2.7564

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  40 HIS
** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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  40 HIS
D 109 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.061103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.045090 restraints weight = 67817.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.046817 restraints weight = 39866.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.048018 restraints weight = 27807.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.048836 restraints weight = 21586.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.049331 restraints weight = 18089.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.3648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  11812  Z= 0.196
  Angle     :  0.788  12.965  16997  Z= 0.444
  Chirality :  0.046   0.336   1964
  Planarity :  0.006   0.075   1276
  Dihedral  : 31.176 179.931   3544
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 19.51
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.22 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 26.63 %
    Favored  : 70.43 %
  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 are not related in a simple way.
  whole: -1.30 (0.29), residues: 790
  helix:  0.09 (0.23), residues: 508
  sheet:  None (None), residues: 0
  loop : -2.64 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  82 
 TYR   0.022   0.002   TYR D 121 
 PHE   0.031   0.003   PHE C 154 
 HIS   0.011   0.001   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.20 (11812)
  covalent geometry    : angle       0.78823 /  0.44 (16997)
  hydrogen bonds       : bond        0.06291 /  4.29 (  709)
  hydrogen bonds       : angle       4.79455 /  3.37 ( 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
  130 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8310 (m-10) cc_final: 0.7886 (m-80)
REVERT: A   71 GLN cc_start: 0.9619 (mt0) cc_final: 0.9380 (mt0)
REVERT: A   77 MET cc_start: 0.9448 (tmm) cc_final: 0.9193 (tmm)
REVERT: A   95 GLU cc_start: 0.9276 (pp20) cc_final: 0.8896 (tp30)
REVERT: B   40 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8616 (mm)
REVERT: B   45 MET cc_start: 0.8162 (mmm) cc_final: 0.7798 (mmm)
REVERT: B  109 HIS cc_start: 0.9117 (t70) cc_final: 0.8532 (t70)
REVERT: B  121 TYR cc_start: 0.8943 (t80) cc_final: 0.8385 (t80)
REVERT: B  187 ASP cc_start: 0.9174 (m-30) cc_final: 0.8973 (m-30)
REVERT: C   64 MET cc_start: 0.8660 (mmt) cc_final: 0.7961 (mmt)
REVERT: C   77 MET cc_start: 0.9476 (ppp) cc_final: 0.9108 (ppp)
REVERT: C   95 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7545 (tp30)
REVERT: C  184 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8499 (mt-10)
REVERT: C  216 MET cc_start: 0.8813 (tpt) cc_final: 0.8240 (tpp)
  outliers start: 19
  outliers final: 16
  residues processed: 124
  average time/residue: 0.0921
  time to fit residues: 17.2880
Evaluate side-chains
  121 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   65 ASN
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  141 SER
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  167 HIS
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   96 LEU
Chi-restraints excluded: chain D residue  115 THR
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:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 34 optimal weight:    9.9990
   chunk 23 optimal weight:    6.9990
   chunk 67 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 89 optimal weight:   30.0000
   chunk 13 optimal weight:    3.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  40 HIS
** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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  71 GLN
** D 139 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 = 0.3617 r_free = 0.3617 target = 0.062071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.045876 restraints weight = 67856.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.047651 restraints weight = 39834.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.048855 restraints weight = 27652.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.049684 restraints weight = 21486.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.050240 restraints weight = 18004.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.3897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081  11812  Z= 0.177
  Angle     :  0.776  11.804  16997  Z= 0.437
  Chirality :  0.046   0.327   1964
  Planarity :  0.006   0.075   1276
  Dihedral  : 31.133 179.863   3544
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 18.13
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.71 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 26.63 %
    Favored  : 70.28 %
  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 are not related in a simple way.
  whole: -1.26 (0.29), residues: 790
  helix:  0.14 (0.23), residues: 506
  sheet:  None (None), residues: 0
  loop : -2.64 (0.33), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  59 
 TYR   0.022   0.002   TYR D 121 
 PHE   0.026   0.002   PHE C 154 
 HIS   0.004   0.001   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.18 (11812)
  covalent geometry    : angle       0.77617 /  0.44 (16997)
  hydrogen bonds       : bond        0.05568 /  3.77 (  709)
  hydrogen bonds       : angle       4.72771 /  3.32 ( 1790)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2063.68 seconds
wall clock time: 36 minutes 33.18 seconds (2193.18 seconds total)