Starting phenix.real_space_refine
on Thu Mar  6 04:28:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8poc_17788/03_2025/8poc_17788.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8poc_17788/03_2025/8poc_17788.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8poc_17788/03_2025/8poc_17788.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8poc_17788/03_2025/8poc_17788.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8poc_17788/03_2025/8poc_17788.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8poc_17788/03_2025/8poc_17788.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.027
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: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    3108      2.51       5
     N     880      2.21       5
     O     908      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4924
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1231
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 6, 'TRANS': 147}
    Chain: "B"
      Number of atoms: 1231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1231
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 6, 'TRANS': 147}
    Chain: "C"
      Number of atoms: 1231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1231
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 6, 'TRANS': 147}
    Chain: "D"
      Number of atoms: 1231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1231
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 6, 'TRANS': 147}
  Time building chain proxies: 3.51, per 1000 atoms: 0.71
  Number of scatterers: 4924
  At special positions: 0
  Unit cell: (86.49, 76.26, 77.19, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O     908      8.00
     N     880      7.00
     C    3108      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.15
  Conformation dependent library (CDL) restraints added in 577.3 milliseconds
  

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1136

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 4 sheets defined
      60.1% alpha, 11.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 15
    Processing helix  chain 'A' and resid 20 through 37
    Processing helix  chain 'A' and resid 38 through 56
      removed outlier: 3.539A  pdb=" N   ARG A  55 " --> pdb=" O   GLN A  51 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   TYR A  56 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 4.100A  pdb=" N   LEU A  77 " --> pdb=" O   ARG A  73 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   PHE A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 131
      removed outlier: 3.896A  pdb=" N   GLY A 131 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 15
    Processing helix  chain 'B' and resid 20 through 37
    Processing helix  chain 'B' and resid 38 through 56
      removed outlier: 3.574A  pdb=" N   ARG B  55 " --> pdb=" O   GLN B  51 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   TYR B  56 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 79
      removed outlier: 4.039A  pdb=" N   LEU B  77 " --> pdb=" O   ARG B  73 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   PHE B  78 " --> pdb=" O   VAL B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 130
    Processing helix  chain 'C' and resid 2 through 15
    Processing helix  chain 'C' and resid 20 through 37
    Processing helix  chain 'C' and resid 38 through 56
      removed outlier: 3.596A  pdb=" N   ARG C  55 " --> pdb=" O   GLN C  51 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   TYR C  56 " --> pdb=" O   LEU C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 79
      removed outlier: 4.027A  pdb=" N   LEU C  77 " --> pdb=" O   ARG C  73 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   PHE C  78 " --> pdb=" O   VAL C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 107 through 130
    Processing helix  chain 'D' and resid 2 through 15
    Processing helix  chain 'D' and resid 20 through 37
    Processing helix  chain 'D' and resid 38 through 56
      removed outlier: 3.548A  pdb=" N   ARG D  55 " --> pdb=" O   GLN D  51 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   TYR D  56 " --> pdb=" O   LEU D  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 63 through 79
      removed outlier: 4.039A  pdb=" N   LEU D  77 " --> pdb=" O   ARG D  73 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   PHE D  78 " --> pdb=" O   VAL D  74 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 107 through 131
      removed outlier: 3.905A  pdb=" N   GLY D 131 " --> pdb=" O   LEU D 127 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 87
    Processing sheet with id=AA2, first strand: chain 'B' and resid 82 through 87
    Processing sheet with id=AA3, first strand: chain 'C' and resid 82 through 87
    Processing sheet with id=AA4, first strand: chain 'D' and resid 82 through 87

    336 hydrogen bonds defined for protein.
    966 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.19

  Time building geometry restraints manager: 1.38 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1680
        1.34 -     1.46: 1134
        1.46 -     1.58: 2174
        1.58 -     1.70: 0
        1.70 -     1.81: 48
  Bond restraints: 5036
  Sorted by residual:
  bond pdb=" CG1 ILE A  94 "
       pdb=" CD1 ILE A  94 "
    ideal  model  delta    sigma   weight residual
    1.513  1.470  0.043 3.90e-02 6.57e+02 1.20e+00
  bond pdb=" CB  GLN B  14 "
       pdb=" CG  GLN B  14 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.15e+00
  bond pdb=" CG1 ILE D  94 "
       pdb=" CD1 ILE D  94 "
    ideal  model  delta    sigma   weight residual
    1.513  1.472  0.041 3.90e-02 6.57e+02 1.13e+00
  bond pdb=" CB  GLN C  14 "
       pdb=" CG  GLN C  14 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.11e+00
  bond pdb=" CG  LEU A  85 "
       pdb=" CD2 LEU A  85 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.51e-01
  ... (remaining 5031 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 6663
        1.71 -     3.41: 129
        3.41 -     5.12: 27
        5.12 -     6.83: 10
        6.83 -     8.53: 3
  Bond angle restraints: 6832
  Sorted by residual:
  angle pdb=" C   GLN D  16 "
        pdb=" N   LEU D  17 "
        pdb=" CA  LEU D  17 "
      ideal   model   delta    sigma   weight residual
     122.31  113.78    8.53 2.34e+00 1.83e-01 1.33e+01
  angle pdb=" C   GLN C  16 "
        pdb=" N   LEU C  17 "
        pdb=" CA  LEU C  17 "
      ideal   model   delta    sigma   weight residual
     122.31  114.00    8.31 2.34e+00 1.83e-01 1.26e+01
  angle pdb=" C   GLN B  16 "
        pdb=" N   LEU B  17 "
        pdb=" CA  LEU B  17 "
      ideal   model   delta    sigma   weight residual
     122.31  114.55    7.76 2.34e+00 1.83e-01 1.10e+01
  angle pdb=" CA  GLN C  14 "
        pdb=" CB  GLN C  14 "
        pdb=" CG  GLN C  14 "
      ideal   model   delta    sigma   weight residual
     114.10  119.51   -5.41 2.00e+00 2.50e-01 7.32e+00
  angle pdb=" CA  GLN B  14 "
        pdb=" CB  GLN B  14 "
        pdb=" CG  GLN B  14 "
      ideal   model   delta    sigma   weight residual
     114.10  119.51   -5.41 2.00e+00 2.50e-01 7.30e+00
  ... (remaining 6827 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 2649
       17.13 -    34.26: 276
       34.26 -    51.39: 35
       51.39 -    68.52: 6
       68.52 -    85.65: 18
  Dihedral angle restraints: 2984
    sinusoidal: 1208
      harmonic: 1776
  Sorted by residual:
  dihedral pdb=" CA  ASN B  35 "
           pdb=" C   ASN B  35 "
           pdb=" N   ALA B  36 "
           pdb=" CA  ALA B  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.77  -15.23     0      5.00e+00 4.00e-02 9.27e+00
  dihedral pdb=" CA  ARG A  13 "
           pdb=" CB  ARG A  13 "
           pdb=" CG  ARG A  13 "
           pdb=" CD  ARG A  13 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.88   53.88     3      1.50e+01 4.44e-03 9.24e+00
  dihedral pdb=" CA  ARG B  13 "
           pdb=" CB  ARG B  13 "
           pdb=" CG  ARG B  13 "
           pdb=" CD  ARG B  13 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.61   53.61     3      1.50e+01 4.44e-03 9.22e+00
  ... (remaining 2981 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 569
       0.038 -    0.075: 151
       0.075 -    0.113: 4
       0.113 -    0.150: 0
       0.150 -    0.188: 4
  Chirality restraints: 728
  Sorted by residual:
  chirality pdb=" CA  ILE A  94 "
            pdb=" N   ILE A  94 "
            pdb=" C   ILE A  94 "
            pdb=" CB  ILE A  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.82e-01
  chirality pdb=" CA  ILE D  94 "
            pdb=" N   ILE D  94 "
            pdb=" C   ILE D  94 "
            pdb=" CB  ILE D  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.40e-01
  chirality pdb=" CA  ILE C  94 "
            pdb=" N   ILE C  94 "
            pdb=" C   ILE C  94 "
            pdb=" CB  ILE C  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.65e-01
  ... (remaining 725 not shown)

  Planarity restraints: 896
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C  99 "   -0.024 5.00e-02 4.00e+02   3.64e-02 2.12e+00
        pdb=" N   PRO C 100 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO C 100 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C 100 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  11 "    0.008 2.00e-02 2.50e+03   1.03e-02 2.11e+00
        pdb=" CG  TYR B  11 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  11 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  11 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  11 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  11 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  11 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B  11 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  99 "    0.024 5.00e-02 4.00e+02   3.62e-02 2.09e+00
        pdb=" N   PRO B 100 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B 100 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 100 "    0.020 5.00e-02 4.00e+02
  ... (remaining 893 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 1472
        2.84 -     3.35: 4800
        3.35 -     3.87: 7565
        3.87 -     4.38: 7525
        4.38 -     4.90: 14384
  Nonbonded interactions: 35746
  Sorted by model distance:
  nonbonded pdb=" O   GLU D  68 "
            pdb=" ND2 ASN D  72 "
     model   vdw
     2.324 3.120
  nonbonded pdb=" N   GLU A  89 "
            pdb=" OE1 GLU A  89 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" N   GLU C  89 "
            pdb=" OE1 GLU C  89 "
     model   vdw
     2.343 3.120
  nonbonded pdb=" O   GLU B  68 "
            pdb=" ND2 ASN B  72 "
     model   vdw
     2.346 3.120
  nonbonded pdb=" NH2 ARG C 112 "
            pdb=" OE1 GLU C 142 "
     model   vdw
     2.382 3.120
  ... (remaining 35741 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  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:             1.350
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.270
  Find NCS groups from input model:        0.150
  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:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
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      :  0.003   0.043   5036  Z= 0.221
  Angle     :  0.667   8.532   6832  Z= 0.349
  Chirality :  0.034   0.188    728
  Planarity :  0.004   0.037    896
  Dihedral  : 14.858  85.653   1848
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.33), residues: 608
  helix:  2.97 (0.27), residues: 344
  sheet:  0.47 (0.44), residues: 96
  loop : -1.49 (0.42), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C 126 
 HIS   0.006   0.002   HIS A  96 
 PHE   0.007   0.001   PHE D  44 
 TYR   0.025   0.001   TYR B  11 
 ARG   0.009   0.001   ARG D  39 

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.499 
Fit side-chains
REVERT: C   93 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8035 (mt-10)
REVERT: D    1 MET cc_start: 0.7142 (mpp) cc_final: 0.6579 (mpp)
REVERT: D   89 GLU cc_start: 0.8233 (pm20) cc_final: 0.7990 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1588
  time to fit residues: 27.4881
Evaluate side-chains
  108 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    0.0980
   chunk 45 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 28 optimal weight:    8.9990
   chunk 35 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
B  79 HIS
B 104 ASN
** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  96 HIS
** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.157915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.114057 restraints weight = 6710.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.116103 restraints weight = 5702.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.117298 restraints weight = 5129.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5036  Z= 0.272
  Angle     :  0.588   5.074   6832  Z= 0.298
  Chirality :  0.035   0.181    728
  Planarity :  0.004   0.034    896
  Dihedral  :  3.466  15.374    692
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 11.15 %
    Favored  : 85.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.26 (0.34), residues: 608
  helix:  2.93 (0.27), residues: 356
  sheet:  0.75 (0.48), residues: 96
  loop : -1.59 (0.45), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 126 
 HIS   0.003   0.001   HIS B  96 
 PHE   0.009   0.002   PHE B  25 
 TYR   0.006   0.001   TYR B  95 
 ARG   0.003   0.000   ARG D  39 

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.515 
Fit side-chains
REVERT: A   93 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8131 (mt-10)
REVERT: B    1 MET cc_start: 0.7288 (mmm) cc_final: 0.7070 (mpp)
REVERT: B   68 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8167 (pt0)
REVERT: B   93 GLU cc_start: 0.8475 (tt0) cc_final: 0.7910 (mt-10)
REVERT: C   93 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8036 (mt-10)
  outliers start: 18
  outliers final: 11
  residues processed: 135
  average time/residue: 0.1689
  time to fit residues: 28.9201
Evaluate side-chains
  134 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain B residue    3 ASP
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue  140 CYS
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  140 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0040
   chunk 51 optimal weight:    2.9990
   chunk 20 optimal weight:    0.3980
   chunk 2 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
B  79 HIS
C  79 HIS
C  96 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.159625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.114956 restraints weight = 6806.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.117424 restraints weight = 5648.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.119184 restraints weight = 4995.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5036  Z= 0.186
  Angle     :  0.536   4.764   6832  Z= 0.268
  Chirality :  0.034   0.174    728
  Planarity :  0.004   0.036    896
  Dihedral  :  3.322  14.668    692
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.15 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.51 (0.34), residues: 608
  helix:  3.12 (0.27), residues: 356
  sheet:  0.76 (0.47), residues: 96
  loop : -1.42 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D  21 
 HIS   0.004   0.001   HIS B  79 
 PHE   0.004   0.001   PHE B  78 
 TYR   0.011   0.001   TYR B  11 
 ARG   0.003   0.000   ARG D 152 

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.535 
Fit side-chains
REVERT: A   93 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8094 (mt-10)
REVERT: B   93 GLU cc_start: 0.8559 (tt0) cc_final: 0.8014 (mt-10)
REVERT: C   93 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8074 (mt-10)
REVERT: C  152 ARG cc_start: 0.8755 (tpp80) cc_final: 0.8135 (mtt90)
REVERT: D    1 MET cc_start: 0.7888 (mpp) cc_final: 0.7621 (mpp)
REVERT: D   89 GLU cc_start: 0.8290 (pm20) cc_final: 0.8022 (pm20)
REVERT: D   93 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8145 (mt-10)
  outliers start: 12
  outliers final: 6
  residues processed: 127
  average time/residue: 0.1681
  time to fit residues: 27.1784
Evaluate side-chains
  125 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 119
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue  140 CYS
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  140 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 52 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   chunk 45 optimal weight:    0.0970
   chunk 57 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.155613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.110455 restraints weight = 7003.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.112932 restraints weight = 5782.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.114466 restraints weight = 5099.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5036  Z= 0.232
  Angle     :  0.549   5.719   6832  Z= 0.272
  Chirality :  0.034   0.170    728
  Planarity :  0.004   0.035    896
  Dihedral  :  3.299  14.779    692
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 15.19 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.60 (0.34), residues: 608
  helix:  3.16 (0.27), residues: 356
  sheet:  0.75 (0.46), residues: 96
  loop : -1.26 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 126 
 HIS   0.004   0.001   HIS D  96 
 PHE   0.008   0.002   PHE D  25 
 TYR   0.007   0.001   TYR B  11 
 ARG   0.003   0.000   ARG D 152 

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.545 
Fit side-chains
REVERT: A   17 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8509 (pp)
REVERT: A   68 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8114 (pt0)
REVERT: A   93 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8171 (mt-10)
REVERT: B   93 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8050 (mt-10)
REVERT: C  152 ARG cc_start: 0.8781 (tpp80) cc_final: 0.8105 (mtt90)
REVERT: D   17 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8503 (pp)
REVERT: D   93 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8140 (mt-10)
  outliers start: 26
  outliers final: 14
  residues processed: 125
  average time/residue: 0.1670
  time to fit residues: 26.5830
Evaluate side-chains
  131 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   38 GLU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain B residue    3 ASP
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue  140 CYS
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  140 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0370
   chunk 48 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.160110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.116625 restraints weight = 6801.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.119018 restraints weight = 5650.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 17)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.120425 restraints weight = 5007.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5036  Z= 0.189
  Angle     :  0.523   6.479   6832  Z= 0.257
  Chirality :  0.033   0.178    728
  Planarity :  0.004   0.035    896
  Dihedral  :  3.220  14.670    692
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 16.35 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.75 (0.34), residues: 608
  helix:  3.26 (0.26), residues: 356
  sheet:  0.78 (0.45), residues: 96
  loop : -1.11 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C  21 
 HIS   0.003   0.001   HIS B  96 
 PHE   0.004   0.001   PHE B  78 
 TYR   0.006   0.001   TYR B  11 
 ARG   0.003   0.000   ARG D 152 

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.524 
Fit side-chains
REVERT: A   17 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8480 (pp)
REVERT: A   93 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8301 (mt-10)
REVERT: B   93 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8035 (mt-10)
REVERT: C  152 ARG cc_start: 0.8764 (tpp80) cc_final: 0.8099 (mtt90)
REVERT: D   17 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8514 (pp)
REVERT: D   89 GLU cc_start: 0.8346 (pm20) cc_final: 0.7996 (pm20)
REVERT: D   93 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8082 (mt-10)
  outliers start: 20
  outliers final: 12
  residues processed: 129
  average time/residue: 0.2053
  time to fit residues: 34.0243
Evaluate side-chains
  127 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  140 CYS
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  140 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 4 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0980
   chunk 16 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.160896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.116703 restraints weight = 6878.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.119187 restraints weight = 5700.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.120735 restraints weight = 5035.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5036  Z= 0.219
  Angle     :  0.540   5.253   6832  Z= 0.266
  Chirality :  0.034   0.174    728
  Planarity :  0.004   0.035    896
  Dihedral  :  3.219  15.025    692
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 16.92 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.81 (0.34), residues: 608
  helix:  3.27 (0.26), residues: 356
  sheet:  0.81 (0.45), residues: 96
  loop : -1.00 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  21 
 HIS   0.003   0.001   HIS B  96 
 PHE   0.006   0.001   PHE D  25 
 TYR   0.005   0.001   TYR A  95 
 ARG   0.003   0.000   ARG D 152 

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 0.511 
Fit side-chains
REVERT: A   17 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8470 (pp)
REVERT: A   93 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8254 (mt-10)
REVERT: B   17 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8538 (pp)
REVERT: C   17 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8479 (pp)
REVERT: C   93 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8064 (mt-10)
REVERT: C  152 ARG cc_start: 0.8781 (tpp80) cc_final: 0.8110 (mtt90)
REVERT: D   17 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8486 (pp)
REVERT: D   93 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8064 (mt-10)
  outliers start: 28
  outliers final: 18
  residues processed: 136
  average time/residue: 0.2010
  time to fit residues: 35.6434
Evaluate side-chains
  137 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 1.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  140 CYS
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  140 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   chunk 27 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0070
   chunk 4 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.4998

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

Flipped N/Q/H residues before XYZ refinement:
C  30 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.162682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.119329 restraints weight = 6660.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.121708 restraints weight = 5511.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.123514 restraints weight = 4869.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5036  Z= 0.185
  Angle     :  0.542   7.304   6832  Z= 0.264
  Chirality :  0.033   0.184    728
  Planarity :  0.004   0.035    896
  Dihedral  :  3.175  15.095    692
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 18.46 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.90 (0.34), residues: 608
  helix:  3.36 (0.26), residues: 356
  sheet:  0.78 (0.44), residues: 96
  loop : -0.96 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D  21 
 HIS   0.003   0.001   HIS B  96 
 PHE   0.003   0.001   PHE D 151 
 TYR   0.005   0.001   TYR B  11 
 ARG   0.003   0.000   ARG D 152 

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.675 
Fit side-chains
REVERT: A   68 GLU cc_start: 0.8232 (pt0) cc_final: 0.7995 (pt0)
REVERT: A   93 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8169 (mt-10)
REVERT: B   17 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8521 (pp)
REVERT: B   93 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8034 (mt-10)
REVERT: C   14 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8713 (tp40)
REVERT: C   17 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8463 (pp)
REVERT: C   93 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8032 (mt-10)
REVERT: C  146 GLU cc_start: 0.7382 (mp0) cc_final: 0.7175 (mp0)
REVERT: C  152 ARG cc_start: 0.8796 (tpp80) cc_final: 0.8392 (mtt90)
REVERT: D   93 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8048 (mt-10)
  outliers start: 23
  outliers final: 16
  residues processed: 128
  average time/residue: 0.1950
  time to fit residues: 32.5430
Evaluate side-chains
  132 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   65 VAL
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  140 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 0 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 52 optimal weight:    0.6980
   chunk 48 optimal weight:    6.9990
   chunk 19 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.156943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.113265 restraints weight = 6785.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.115385 restraints weight = 5602.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.117276 restraints weight = 4921.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5036  Z= 0.225
  Angle     :  0.565   7.635   6832  Z= 0.270
  Chirality :  0.034   0.173    728
  Planarity :  0.004   0.034    896
  Dihedral  :  3.160  15.272    692
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 18.08 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.92 (0.34), residues: 608
  helix:  3.39 (0.27), residues: 356
  sheet:  0.81 (0.43), residues: 96
  loop : -0.98 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 111 
 HIS   0.003   0.001   HIS B  79 
 PHE   0.006   0.001   PHE B  25 
 TYR   0.004   0.001   TYR A  95 
 ARG   0.004   0.000   ARG D 152 

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.564 
Fit side-chains
REVERT: A   93 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8205 (mt-10)
REVERT: B   17 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8463 (pp)
REVERT: B   93 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8056 (mt-10)
REVERT: C   17 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8509 (pp)
REVERT: C   93 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8179 (mt-10)
REVERT: C  146 GLU cc_start: 0.7420 (mp0) cc_final: 0.7213 (mp0)
REVERT: C  152 ARG cc_start: 0.8798 (tpp80) cc_final: 0.8404 (mtt90)
  outliers start: 24
  outliers final: 17
  residues processed: 127
  average time/residue: 0.2074
  time to fit residues: 34.0100
Evaluate side-chains
  138 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 1.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   65 VAL
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  140 CYS
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  140 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 55 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 1 optimal weight:    0.3980
   chunk 46 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.158116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.114712 restraints weight = 6674.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.116889 restraints weight = 5467.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.118995 restraints weight = 4805.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.2922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5036  Z= 0.195
  Angle     :  0.571   7.955   6832  Z= 0.272
  Chirality :  0.033   0.179    728
  Planarity :  0.004   0.034    896
  Dihedral  :  3.149  15.228    692
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 18.08 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.95 (0.34), residues: 608
  helix:  3.39 (0.26), residues: 356
  sheet:  0.81 (0.43), residues: 96
  loop : -0.91 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D  21 
 HIS   0.004   0.001   HIS B  96 
 PHE   0.004   0.001   PHE B  78 
 TYR   0.009   0.001   TYR D  11 
 ARG   0.004   0.000   ARG D 152 

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.578 
Fit side-chains
REVERT: A   93 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8189 (mt-10)
REVERT: B   17 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8464 (pp)
REVERT: B   93 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8037 (mt-10)
REVERT: C   14 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8752 (tp40)
REVERT: C   17 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8474 (pp)
REVERT: C   93 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8086 (mt-10)
REVERT: C  152 ARG cc_start: 0.8797 (tpp80) cc_final: 0.8380 (mtt90)
  outliers start: 21
  outliers final: 17
  residues processed: 129
  average time/residue: 0.1965
  time to fit residues: 32.7744
Evaluate side-chains
  139 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 HIS
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   65 VAL
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  140 CYS
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  140 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 21 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0870
   chunk 25 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    6.9990
   chunk 9 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.158183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.114785 restraints weight = 6787.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.117369 restraints weight = 5531.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.119235 restraints weight = 4829.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5036  Z= 0.206
  Angle     :  0.596   8.436   6832  Z= 0.283
  Chirality :  0.034   0.175    728
  Planarity :  0.004   0.034    896
  Dihedral  :  3.130  15.484    692
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 17.88 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.99 (0.34), residues: 608
  helix:  3.45 (0.26), residues: 356
  sheet:  0.81 (0.42), residues: 96
  loop : -0.95 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C  21 
 HIS   0.003   0.001   HIS B  96 
 PHE   0.005   0.001   PHE A  44 
 TYR   0.017   0.001   TYR D  11 
 ARG   0.004   0.000   ARG D 152 

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.514 
Fit side-chains
REVERT: A   93 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8216 (mt-10)
REVERT: B   17 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8506 (pp)
REVERT: B   93 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8037 (mt-10)
REVERT: C   14 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8744 (tp40)
REVERT: C   17 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8493 (pp)
REVERT: C   93 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8081 (mt-10)
REVERT: C  152 ARG cc_start: 0.8784 (tpp80) cc_final: 0.8373 (mtt90)
  outliers start: 21
  outliers final: 17
  residues processed: 128
  average time/residue: 0.1505
  time to fit residues: 25.1191
Evaluate side-chains
  129 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 HIS
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   65 VAL
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  140 CYS
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  140 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  79 HIS
** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.157087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.114498 restraints weight = 6836.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.116400 restraints weight = 5879.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.117620 restraints weight = 5318.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.3106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5036  Z= 0.228
  Angle     :  0.604   8.224   6832  Z= 0.288
  Chirality :  0.034   0.173    728
  Planarity :  0.004   0.034    896
  Dihedral  :  3.164  15.220    692
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 18.27 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.01 (0.34), residues: 608
  helix:  3.45 (0.27), residues: 356
  sheet:  0.79 (0.42), residues: 96
  loop : -0.88 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  21 
 HIS   0.004   0.001   HIS B  79 
 PHE   0.006   0.001   PHE D  25 
 TYR   0.016   0.001   TYR D  11 
 ARG   0.004   0.000   ARG D 152 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1843.79 seconds
wall clock time: 34 minutes 15.72 seconds (2055.72 seconds total)