Starting phenix.real_space_refine
on Thu Mar  6 04:24:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p2q_13172/03_2025/7p2q_13172_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p2q_13172/03_2025/7p2q_13172.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p2q_13172/03_2025/7p2q_13172.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p2q_13172/03_2025/7p2q_13172.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p2q_13172/03_2025/7p2q_13172_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p2q_13172/03_2025/7p2q_13172_neut.cif"
  }
  resolution = 4.9
  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=   0.002
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      23      5.16       5
     C    3106      2.51       5
     N     778      2.21       5
     O     873      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4780
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1186
          Classifications: {'peptide': 148}
          Link IDs: {'PTRANS': 6, 'TRANS': 141}
    Chain: "B"
      Number of atoms: 1426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 179, 1426
          Classifications: {'peptide': 179}
          Link IDs: {'PTRANS': 7, 'TRANS': 171}
    Chain: "C"
      Number of atoms: 1411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1411
          Classifications: {'peptide': 174}
          Link IDs: {'PTRANS': 6, 'TRANS': 167}
    Chain: "D"
      Number of atoms: 696
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 696
          Classifications: {'peptide': 86}
          Link IDs: {'PTRANS': 6, 'TRANS': 79}
    Chain: "E"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 3.42, per 1000 atoms: 0.72
  Number of scatterers: 4780
  At special positions: 0
  Unit cell: (81.81, 84.24, 126.36, 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      23     16.00
     O     873      8.00
     N     778      7.00
     C    3106      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
  Links applied
    ALPHA1-3
      " BMA E   3 " - " MAN E   4 "
    ALPHA1-6
      " BMA E   3 " - " MAN E   5 "
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG E   1 " - " ASN B 141 "
  Time building additional restraints: 1.47
  Conformation dependent library (CDL) restraints added in 551.1 milliseconds
  

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1102

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 6 sheets defined
      41.4% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 56
      removed outlier: 4.288A  pdb=" N   LEU A  30 " --> pdb=" O   ASN A  26 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   GLY A  56 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 171
      removed outlier: 3.782A  pdb=" N   VAL A 164 " --> pdb=" O   TYR A 160 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   TYR A 171 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 33
    Processing helix  chain 'C' and resid 52 through 72
    Processing helix  chain 'C' and resid 79 through 105
    Processing helix  chain 'C' and resid 106 through 109
      removed outlier: 3.516A  pdb=" N   GLU C 109 " --> pdb=" O   PRO C 106 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 106 through 109'
    Processing helix  chain 'C' and resid 110 through 136
      removed outlier: 3.720A  pdb=" N   LEU C 114 " --> pdb=" O   SER C 110 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LYS C 135 " --> pdb=" O   TYR C 131 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 194 through 196
      No H-bonds generated for 'chain 'C' and resid 194 through 196'
    Processing helix  chain 'C' and resid 207 through 224
      removed outlier: 3.700A  pdb=" N   GLU C 211 " --> pdb=" O   ALA C 207 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 73
      removed outlier: 3.653A  pdb=" N   LEU D  72 " --> pdb=" O   MET D  68 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   SER D  73 " --> pdb=" O   LEU D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 80 through 109
    Processing helix  chain 'D' and resid 112 through 131
    Processing helix  chain 'D' and resid 135 through 140
    Processing helix  chain 'D' and resid 140 through 145
      removed outlier: 3.601A  pdb=" N   LEU D 145 " --> pdb=" O   PRO D 141 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64
      removed outlier: 3.983A  pdb=" N   ASP A  77 " --> pdb=" O   VAL A  64 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 99
      removed outlier: 5.282A  pdb=" N   VAL A 110 " --> pdb=" O   LYS A 126 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   LYS A 126 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LYS A 112 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55
      removed outlier: 4.094A  pdb=" N   VAL B  51 " --> pdb=" O   LEU B  63 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LEU B  63 " --> pdb=" O   VAL B  51 " (cutoff:3.500A)
      removed outlier: 5.060A  pdb=" N   ASP B  53 " --> pdb=" O   SER B  61 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   SER B  61 " --> pdb=" O   ASP B  53 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   PHE B 129 " --> pdb=" O   GLY B  64 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 108 through 111
      removed outlier: 3.679A  pdb=" N   GLN B  84 " --> pdb=" O   VAL B 151 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 104
    Processing sheet with id=AA6, first strand: chain 'C' and resid 75 through 76
      removed outlier: 6.622A  pdb=" N   LEU C 159 " --> pdb=" O   PHE C 140 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   VAL C 142 " --> pdb=" O   TRP C 157 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   TRP C 157 " --> pdb=" O   VAL C 142 " (cutoff:3.500A)

    241 hydrogen bonds defined for protein.
    693 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: 1.08

  Time building geometry restraints manager: 1.52 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1460
        1.34 -     1.46: 971
        1.46 -     1.58: 2424
        1.58 -     1.69: 0
        1.69 -     1.81: 41
  Bond restraints: 4896
  Sorted by residual:
  bond pdb=" C1  BMA E   3 "
       pdb=" C2  BMA E   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.567 -0.048 2.00e-02 2.50e+03 5.76e+00
  bond pdb=" C1  MAN E   4 "
       pdb=" C2  MAN E   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.563 -0.037 2.00e-02 2.50e+03 3.45e+00
  bond pdb=" C1  BMA E   3 "
       pdb=" O5  BMA E   3 "
    ideal  model  delta    sigma   weight residual
    1.410  1.445 -0.035 2.00e-02 2.50e+03 2.99e+00
  bond pdb=" C5  MAN E   4 "
       pdb=" O5  MAN E   4 "
    ideal  model  delta    sigma   weight residual
    1.418  1.452 -0.034 2.00e-02 2.50e+03 2.94e+00
  bond pdb=" C   LEU D 131 "
       pdb=" N   PRO D 132 "
    ideal  model  delta    sigma   weight residual
    1.329  1.349 -0.020 1.18e-02 7.18e+03 2.88e+00
  ... (remaining 4891 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 6412
        1.91 -     3.81: 165
        3.81 -     5.72: 31
        5.72 -     7.63: 15
        7.63 -     9.53: 6
  Bond angle restraints: 6629
  Sorted by residual:
  angle pdb=" C   LYS B 121 "
        pdb=" N   ASP B 122 "
        pdb=" CA  ASP B 122 "
      ideal   model   delta    sigma   weight residual
     121.54  131.00   -9.46 1.91e+00 2.74e-01 2.45e+01
  angle pdb=" C   GLY B 133 "
        pdb=" N   ASN B 134 "
        pdb=" CA  ASN B 134 "
      ideal   model   delta    sigma   weight residual
     121.54  130.70   -9.16 1.91e+00 2.74e-01 2.30e+01
  angle pdb=" C   GLU A  58 "
        pdb=" N   SER A  59 "
        pdb=" CA  SER A  59 "
      ideal   model   delta    sigma   weight residual
     121.80  130.19   -8.39 2.44e+00 1.68e-01 1.18e+01
  angle pdb=" N   SER A  59 "
        pdb=" CA  SER A  59 "
        pdb=" C   SER A  59 "
      ideal   model   delta    sigma   weight residual
     109.81  116.82   -7.01 2.21e+00 2.05e-01 1.00e+01
  angle pdb=" CA  LEU D  75 "
        pdb=" CB  LEU D  75 "
        pdb=" CG  LEU D  75 "
      ideal   model   delta    sigma   weight residual
     116.30  125.83   -9.53 3.50e+00 8.16e-02 7.42e+00
  ... (remaining 6624 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.22: 2892
       21.22 -    42.44: 61
       42.44 -    63.66: 4
       63.66 -    84.89: 7
       84.89 -   106.11: 4
  Dihedral angle restraints: 2968
    sinusoidal: 1260
      harmonic: 1708
  Sorted by residual:
  dihedral pdb=" CA  ASP C 154 "
           pdb=" C   ASP C 154 "
           pdb=" N   ASP C 155 "
           pdb=" CA  ASP C 155 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.34   20.66     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  TYR B 174 "
           pdb=" C   TYR B 174 "
           pdb=" N   GLU B 175 "
           pdb=" CA  GLU B 175 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.01  -18.99     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" O4  BMA E   3 "
           pdb=" C4  BMA E   3 "
           pdb=" C5  BMA E   3 "
           pdb=" O5  BMA E   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -177.40  106.11     1      3.00e+01 1.11e-03 1.36e+01
  ... (remaining 2965 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 590
       0.057 -    0.114: 138
       0.114 -    0.171: 22
       0.171 -    0.228: 5
       0.228 -    0.285: 1
  Chirality restraints: 756
  Sorted by residual:
  chirality pdb=" C5  BMA E   3 "
            pdb=" C4  BMA E   3 "
            pdb=" C6  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.56    0.28 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CB  ILE B 109 "
            pdb=" CA  ILE B 109 "
            pdb=" CG1 ILE B 109 "
            pdb=" CG2 ILE B 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CA  ASN B 134 "
            pdb=" N   ASN B 134 "
            pdb=" C   ASN B 134 "
            pdb=" CB  ASN B 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 753 not shown)

  Planarity restraints: 822
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS D 140 "   -0.038 5.00e-02 4.00e+02   5.70e-02 5.20e+00
        pdb=" N   PRO D 141 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO D 141 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO D 141 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A  70 "    0.033 5.00e-02 4.00e+02   4.93e-02 3.88e+00
        pdb=" N   PRO A  71 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A  71 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A  71 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  37 "   -0.031 5.00e-02 4.00e+02   4.76e-02 3.63e+00
        pdb=" N   PRO B  38 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO B  38 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B  38 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 819 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1005
        2.79 -     3.32: 4108
        3.32 -     3.85: 7306
        3.85 -     4.37: 7850
        4.37 -     4.90: 13680
  Nonbonded interactions: 33949
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 109 "
            pdb=" CE1 PHE B  86 "
     model   vdw
     2.264 3.420
  nonbonded pdb=" O   LYS B 121 "
            pdb=" OD1 ASP B 122 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" NH1 ARG C  84 "
            pdb=" OE2 GLU C 136 "
     model   vdw
     2.352 3.120
  nonbonded pdb=" OG  SER B  90 "
            pdb=" O   THR B 145 "
     model   vdw
     2.357 3.040
  nonbonded pdb=" OD1 ASP A 120 "
            pdb=" NZ  LYS A 147 "
     model   vdw
     2.401 3.120
  ... (remaining 33944 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:                  0.010
  Normalize map: mean=0, sd=1:             0.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.190
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
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      :  0.004   0.048   4896  Z= 0.243
  Angle     :  0.840   9.532   6629  Z= 0.432
  Chirality :  0.051   0.285    756
  Planarity :  0.007   0.057    821
  Dihedral  : 11.107 106.107   1866
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  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: -3.09 (0.29), residues: 579
  helix: -1.26 (0.24), residues: 220
  sheet: -1.18 (0.47), residues: 120
  loop : -3.26 (0.32), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 157 
 HIS   0.009   0.002   HIS C 144 
 PHE   0.024   0.002   PHE A  80 
 TYR   0.023   0.002   TYR B 174 
 ARG   0.005   0.000   ARG B 112 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 TYR cc_start: 0.8489 (m-10) cc_final: 0.7727 (m-80)
REVERT: A   47 ILE cc_start: 0.8986 (mt) cc_final: 0.8784 (mt)
REVERT: A   52 ILE cc_start: 0.8925 (pt) cc_final: 0.8577 (pt)
REVERT: A   90 ARG cc_start: 0.7608 (mtm110) cc_final: 0.7112 (mmt90)
REVERT: A  134 ASP cc_start: 0.8211 (m-30) cc_final: 0.7242 (t0)
REVERT: A  146 GLU cc_start: 0.6990 (tt0) cc_final: 0.6722 (tt0)
REVERT: A  158 LEU cc_start: 0.8953 (mm) cc_final: 0.8742 (mm)
REVERT: B   42 HIS cc_start: 0.8714 (m-70) cc_final: 0.8397 (t-170)
REVERT: B   49 LYS cc_start: 0.8171 (ptmt) cc_final: 0.7918 (ptpp)
REVERT: B   59 GLU cc_start: 0.7296 (tp30) cc_final: 0.6952 (tp30)
REVERT: B   73 ASP cc_start: 0.8255 (t0) cc_final: 0.7370 (t70)
REVERT: B   78 PHE cc_start: 0.7880 (m-80) cc_final: 0.7513 (m-80)
REVERT: B   80 TRP cc_start: 0.6359 (m100) cc_final: 0.5855 (p-90)
REVERT: B  128 PHE cc_start: 0.7994 (m-10) cc_final: 0.7730 (m-10)
REVERT: C   70 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8536 (tm-30)
REVERT: C  102 ASP cc_start: 0.8659 (m-30) cc_final: 0.8314 (m-30)
REVERT: C  174 LEU cc_start: 0.8449 (mm) cc_final: 0.7380 (mm)
REVERT: C  208 TYR cc_start: 0.9118 (t80) cc_final: 0.8689 (t80)
REVERT: D   68 MET cc_start: 0.9152 (mtt) cc_final: 0.8800 (tmm)
REVERT: D  128 LEU cc_start: 0.8645 (mt) cc_final: 0.8394 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 270
  average time/residue: 0.2159
  time to fit residues: 69.1460
Evaluate side-chains
  153 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 14 optimal weight:    0.5980
   chunk 28 optimal weight:    7.9990
   chunk 22 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 105 HIS
** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 158 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 = 0.3648 r_free = 0.3648 target = 0.078934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.062846 restraints weight = 27236.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.064506 restraints weight = 21166.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.065763 restraints weight = 17355.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.4402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4896  Z= 0.209
  Angle     :  0.711   9.181   6629  Z= 0.360
  Chirality :  0.046   0.184    756
  Planarity :  0.006   0.060    821
  Dihedral  : 10.479  84.926    731
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.34 %
    Favored  : 98.46 %
  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: -1.51 (0.33), residues: 579
  helix:  0.62 (0.31), residues: 220
  sheet: -0.74 (0.48), residues: 126
  loop : -2.81 (0.34), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 101 
 HIS   0.007   0.001   HIS C 144 
 PHE   0.018   0.002   PHE A  37 
 TYR   0.018   0.002   TYR C 208 
 ARG   0.006   0.001   ARG C 145 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 191
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TYR cc_start: 0.8964 (m-80) cc_final: 0.8635 (m-80)
REVERT: A   32 TYR cc_start: 0.8140 (m-10) cc_final: 0.7841 (m-80)
REVERT: A   33 GLN cc_start: 0.8995 (mm110) cc_final: 0.8610 (mm-40)
REVERT: A   46 MET cc_start: 0.7864 (ttp) cc_final: 0.7516 (ttp)
REVERT: A   51 LEU cc_start: 0.9482 (mt) cc_final: 0.9278 (mt)
REVERT: A  121 ILE cc_start: 0.6637 (mm) cc_final: 0.5811 (mm)
REVERT: A  134 ASP cc_start: 0.7569 (m-30) cc_final: 0.7368 (t0)
REVERT: A  146 GLU cc_start: 0.6862 (tt0) cc_final: 0.6562 (tt0)
REVERT: A  158 LEU cc_start: 0.9084 (mm) cc_final: 0.8494 (mm)
REVERT: B   42 HIS cc_start: 0.8720 (m-70) cc_final: 0.8429 (t-170)
REVERT: B   73 ASP cc_start: 0.8455 (t0) cc_final: 0.7603 (t70)
REVERT: B   80 TRP cc_start: 0.6351 (m100) cc_final: 0.5694 (p-90)
REVERT: C   94 PHE cc_start: 0.8621 (m-10) cc_final: 0.8316 (m-10)
REVERT: C  102 ASP cc_start: 0.8526 (m-30) cc_final: 0.8279 (m-30)
REVERT: C  174 LEU cc_start: 0.8144 (mm) cc_final: 0.7821 (mm)
REVERT: C  208 TYR cc_start: 0.9057 (t80) cc_final: 0.8782 (t80)
REVERT: D  131 LEU cc_start: 0.8878 (mt) cc_final: 0.8427 (mt)
REVERT: D  139 ARG cc_start: 0.8377 (ttt180) cc_final: 0.8039 (ptt180)
  outliers start: 1
  outliers final: 1
  residues processed: 192
  average time/residue: 0.1805
  time to fit residues: 42.6640
Evaluate side-chains
  138 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 34 optimal weight:    0.6980
   chunk 19 optimal weight:   30.0000
   chunk 23 optimal weight:   10.0000
   chunk 41 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 38 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
** C 144 HIS ** 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 = 0.3594 r_free = 0.3594 target = 0.076378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.060013 restraints weight = 28857.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.061443 restraints weight = 22790.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.062550 restraints weight = 19043.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.5373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4896  Z= 0.210
  Angle     :  0.685   8.413   6629  Z= 0.347
  Chirality :  0.045   0.235    756
  Planarity :  0.004   0.050    821
  Dihedral  :  9.718  76.750    731
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.88 %
    Favored  : 96.93 %
  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: -0.84 (0.34), residues: 579
  helix:  1.25 (0.34), residues: 225
  sheet: -0.45 (0.49), residues: 130
  loop : -2.59 (0.35), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 148 
 HIS   0.005   0.001   HIS D  71 
 PHE   0.016   0.002   PHE A  37 
 TYR   0.018   0.002   TYR C 121 
 ARG   0.004   0.000   ARG A 109 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 0.512 
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   31 TYR cc_start: 0.9033 (m-80) cc_final: 0.8686 (m-80)
REVERT: A   32 TYR cc_start: 0.8218 (m-10) cc_final: 0.7878 (m-80)
REVERT: A   33 GLN cc_start: 0.9102 (mm110) cc_final: 0.8684 (mm-40)
REVERT: A   36 ASN cc_start: 0.9078 (m110) cc_final: 0.8816 (m110)
REVERT: A   46 MET cc_start: 0.7968 (ttp) cc_final: 0.7354 (ttp)
REVERT: A   74 HIS cc_start: 0.8744 (m-70) cc_final: 0.8224 (m-70)
REVERT: A  121 ILE cc_start: 0.7042 (mm) cc_final: 0.6821 (mm)
REVERT: A  133 ASP cc_start: 0.6767 (t70) cc_final: 0.6431 (t70)
REVERT: A  134 ASP cc_start: 0.7609 (m-30) cc_final: 0.7221 (t0)
REVERT: A  146 GLU cc_start: 0.6683 (tt0) cc_final: 0.6440 (tt0)
REVERT: B   42 HIS cc_start: 0.8786 (m-70) cc_final: 0.8482 (m-70)
REVERT: B   73 ASP cc_start: 0.8522 (t0) cc_final: 0.7280 (p0)
REVERT: B   92 GLU cc_start: 0.8092 (tt0) cc_final: 0.7889 (tt0)
REVERT: C   94 PHE cc_start: 0.8779 (m-10) cc_final: 0.8461 (m-10)
REVERT: C  102 ASP cc_start: 0.8571 (m-30) cc_final: 0.8312 (m-30)
REVERT: C  121 TYR cc_start: 0.8141 (t80) cc_final: 0.7686 (t80)
REVERT: C  162 SER cc_start: 0.8209 (t) cc_final: 0.7995 (t)
REVERT: C  167 ASP cc_start: 0.8283 (t0) cc_final: 0.7766 (t0)
REVERT: C  168 ASP cc_start: 0.8498 (t0) cc_final: 0.8031 (t0)
REVERT: C  193 ILE cc_start: 0.9206 (pt) cc_final: 0.8963 (mp)
REVERT: C  208 TYR cc_start: 0.9034 (t80) cc_final: 0.8722 (t80)
REVERT: D   71 HIS cc_start: 0.7223 (m90) cc_final: 0.6867 (m90)
  outliers start: 1
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1575
  time to fit residues: 35.0972
Evaluate side-chains
  142 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 29 optimal weight:    8.9990
   chunk 19 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 28 optimal weight:   20.0000
   chunk 21 optimal weight:    9.9990
   chunk 48 optimal weight:    6.9990
   chunk 3 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 144 HIS ** 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 = 0.3536 r_free = 0.3536 target = 0.073485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.057259 restraints weight = 29140.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.058724 restraints weight = 22749.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.059846 restraints weight = 18746.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.5921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4896  Z= 0.239
  Angle     :  0.724  10.454   6629  Z= 0.361
  Chirality :  0.045   0.195    756
  Planarity :  0.005   0.045    821
  Dihedral  :  8.947  67.364    731
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  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: -0.60 (0.35), residues: 579
  helix:  1.50 (0.35), residues: 225
  sheet: -0.25 (0.50), residues: 130
  loop : -2.57 (0.36), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 148 
 HIS   0.004   0.001   HIS C 216 
 PHE   0.017   0.002   PHE B  86 
 TYR   0.022   0.002   TYR B  88 
 ARG   0.003   0.001   ARG C 165 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.504 
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   31 TYR cc_start: 0.9031 (m-80) cc_final: 0.8666 (m-80)
REVERT: A   32 TYR cc_start: 0.8189 (m-10) cc_final: 0.7981 (m-80)
REVERT: A   33 GLN cc_start: 0.9110 (mm110) cc_final: 0.8726 (mm110)
REVERT: A   46 MET cc_start: 0.8002 (ttp) cc_final: 0.7394 (ttp)
REVERT: A  112 LYS cc_start: 0.9011 (mmmm) cc_final: 0.8723 (mmmm)
REVERT: A  134 ASP cc_start: 0.7748 (m-30) cc_final: 0.7511 (p0)
REVERT: A  146 GLU cc_start: 0.6679 (tt0) cc_final: 0.6361 (tt0)
REVERT: A  158 LEU cc_start: 0.9328 (mm) cc_final: 0.8862 (mm)
REVERT: B   42 HIS cc_start: 0.8807 (m-70) cc_final: 0.8472 (m-70)
REVERT: B   47 MET cc_start: 0.7011 (tmm) cc_final: 0.6687 (tmm)
REVERT: C   70 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8276 (tm-30)
REVERT: C  102 ASP cc_start: 0.8595 (m-30) cc_final: 0.8337 (m-30)
REVERT: C  124 MET cc_start: 0.8106 (ppp) cc_final: 0.7683 (ptt)
REVERT: C  188 GLU cc_start: 0.8915 (pp20) cc_final: 0.8641 (pp20)
REVERT: C  208 TYR cc_start: 0.9042 (t80) cc_final: 0.8712 (t80)
REVERT: D   71 HIS cc_start: 0.7152 (m90) cc_final: 0.6894 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.1613
  time to fit residues: 35.2133
Evaluate side-chains
  139 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 53 optimal weight:    7.9990
   chunk 44 optimal weight:    4.9990
   chunk 21 optimal weight:    9.9990
   chunk 39 optimal weight:    9.9990
   chunk 38 optimal weight:    7.9990
   chunk 12 optimal weight:    0.7980
   chunk 33 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 114 HIS
A 129 ASN
A 143 ASN
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  58 ASN
** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.071645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.056166 restraints weight = 30040.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.057613 restraints weight = 23390.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.058714 restraints weight = 19170.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.6477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4896  Z= 0.261
  Angle     :  0.723   7.760   6629  Z= 0.369
  Chirality :  0.046   0.193    756
  Planarity :  0.004   0.048    821
  Dihedral  :  8.359  57.425    731
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  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: -0.51 (0.35), residues: 579
  helix:  1.52 (0.34), residues: 219
  sheet: -0.22 (0.50), residues: 130
  loop : -2.35 (0.37), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 134 
 HIS   0.004   0.001   HIS C 216 
 PHE   0.026   0.002   PHE C  94 
 TYR   0.015   0.002   TYR B  88 
 ARG   0.004   0.001   ARG B 112 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.629 
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   31 TYR cc_start: 0.9010 (m-80) cc_final: 0.8630 (m-80)
REVERT: A   32 TYR cc_start: 0.8126 (m-10) cc_final: 0.7879 (m-80)
REVERT: A  112 LYS cc_start: 0.9089 (mmmm) cc_final: 0.8795 (mmmt)
REVERT: A  128 ASP cc_start: 0.8719 (t0) cc_final: 0.8499 (t0)
REVERT: A  146 GLU cc_start: 0.6665 (tt0) cc_final: 0.6198 (tt0)
REVERT: B   42 HIS cc_start: 0.8727 (m-70) cc_final: 0.8434 (m90)
REVERT: B   49 LYS cc_start: 0.7408 (mttt) cc_final: 0.7089 (mptt)
REVERT: C  102 ASP cc_start: 0.8603 (m-30) cc_final: 0.8340 (m-30)
REVERT: C  188 GLU cc_start: 0.8929 (pp20) cc_final: 0.8623 (pp20)
REVERT: C  208 TYR cc_start: 0.9013 (t80) cc_final: 0.8709 (t80)
REVERT: D   71 HIS cc_start: 0.7106 (m90) cc_final: 0.6820 (m-70)
REVERT: D  139 ARG cc_start: 0.8494 (ttt180) cc_final: 0.8193 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1736
  time to fit residues: 36.0950
Evaluate side-chains
  124 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 54 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   chunk 43 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 144 HIS ** 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 = 0.3463 r_free = 0.3463 target = 0.070080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.055314 restraints weight = 29864.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.056629 restraints weight = 23327.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.057633 restraints weight = 19289.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.6902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   4896  Z= 0.265
  Angle     :  0.732   7.549   6629  Z= 0.373
  Chirality :  0.045   0.173    756
  Planarity :  0.005   0.046    821
  Dihedral  :  7.753  58.915    731
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  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: -0.68 (0.35), residues: 579
  helix:  1.35 (0.34), residues: 219
  sheet: -0.44 (0.49), residues: 129
  loop : -2.31 (0.37), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 144 
 HIS   0.004   0.001   HIS B  42 
 PHE   0.016   0.002   PHE A  37 
 TYR   0.015   0.002   TYR B  88 
 ARG   0.003   0.001   ARG A 109 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.9469 (mmm) cc_final: 0.9224 (mmm)
REVERT: A   93 GLU cc_start: 0.6357 (pm20) cc_final: 0.6108 (pm20)
REVERT: A  112 LYS cc_start: 0.9094 (mmmm) cc_final: 0.8728 (mmmt)
REVERT: A  128 ASP cc_start: 0.8871 (t0) cc_final: 0.8607 (t0)
REVERT: A  146 GLU cc_start: 0.6730 (tt0) cc_final: 0.6105 (tt0)
REVERT: A  158 LEU cc_start: 0.9343 (mm) cc_final: 0.8823 (mm)
REVERT: B   42 HIS cc_start: 0.8680 (m-70) cc_final: 0.8412 (m90)
REVERT: B   49 LYS cc_start: 0.7252 (mttt) cc_final: 0.7050 (mttp)
REVERT: B   65 PHE cc_start: 0.8599 (m-80) cc_final: 0.8358 (m-10)
REVERT: C  102 ASP cc_start: 0.8634 (m-30) cc_final: 0.8373 (m-30)
REVERT: C  188 GLU cc_start: 0.8951 (pp20) cc_final: 0.8631 (pp20)
REVERT: D   71 HIS cc_start: 0.7067 (m90) cc_final: 0.6841 (m-70)
REVERT: D   85 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8732 (mmtt)
REVERT: D  139 ARG cc_start: 0.8532 (ttt180) cc_final: 0.8210 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.2161
  time to fit residues: 45.7539
Evaluate side-chains
  129 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 43 optimal weight:   10.0000
   chunk 20 optimal weight:   20.0000
   chunk 46 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 52 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 12 optimal weight:    9.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  26 ASN
B  50 ASN
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.069172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.054214 restraints weight = 28734.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.055618 restraints weight = 22140.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.056677 restraints weight = 18098.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.7246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4896  Z= 0.267
  Angle     :  0.743  12.129   6629  Z= 0.375
  Chirality :  0.045   0.160    756
  Planarity :  0.005   0.041    821
  Dihedral  :  6.663  54.906    731
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  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: -0.75 (0.35), residues: 579
  helix:  1.31 (0.34), residues: 219
  sheet: -0.50 (0.46), residues: 137
  loop : -2.41 (0.38), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D 134 
 HIS   0.004   0.001   HIS C 216 
 PHE   0.015   0.002   PHE A  84 
 TYR   0.041   0.002   TYR A  32 
 ARG   0.011   0.001   ARG A  28 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.562 
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   32 TYR cc_start: 0.8109 (m-80) cc_final: 0.7755 (m-80)
REVERT: A   33 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8902 (mm110)
REVERT: A   69 MET cc_start: 0.9502 (mmm) cc_final: 0.9265 (mmm)
REVERT: A   93 GLU cc_start: 0.6316 (pm20) cc_final: 0.5829 (pm20)
REVERT: A  112 LYS cc_start: 0.9091 (mmmm) cc_final: 0.8877 (mmmt)
REVERT: A  128 ASP cc_start: 0.8876 (t0) cc_final: 0.8577 (t0)
REVERT: A  146 GLU cc_start: 0.6637 (tt0) cc_final: 0.6216 (tt0)
REVERT: A  158 LEU cc_start: 0.9332 (mm) cc_final: 0.8889 (mm)
REVERT: B   42 HIS cc_start: 0.8689 (m-70) cc_final: 0.8363 (m90)
REVERT: B   47 MET cc_start: 0.7072 (tmm) cc_final: 0.6700 (tmm)
REVERT: B   65 PHE cc_start: 0.8610 (m-80) cc_final: 0.8380 (m-10)
REVERT: B  122 ASP cc_start: 0.8882 (p0) cc_final: 0.8621 (p0)
REVERT: B  124 LYS cc_start: 0.8900 (mttt) cc_final: 0.8561 (tmmt)
REVERT: C   96 ILE cc_start: 0.9450 (mm) cc_final: 0.9095 (tp)
REVERT: C  102 ASP cc_start: 0.8616 (m-30) cc_final: 0.8318 (m-30)
REVERT: C  188 GLU cc_start: 0.8928 (pp20) cc_final: 0.8605 (pp20)
REVERT: D   71 HIS cc_start: 0.7179 (m90) cc_final: 0.6897 (m90)
REVERT: D  139 ARG cc_start: 0.8537 (ttt180) cc_final: 0.8221 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1897
  time to fit residues: 40.0709
Evaluate side-chains
  128 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 8 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   chunk 4 optimal weight:   10.0000
   chunk 20 optimal weight:    9.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  77 ASN
** C 144 HIS ** 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 = 0.3464 r_free = 0.3464 target = 0.069668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.055332 restraints weight = 29142.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.056713 restraints weight = 22338.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.057744 restraints weight = 18243.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.7428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4896  Z= 0.224
  Angle     :  0.740  10.780   6629  Z= 0.376
  Chirality :  0.045   0.183    756
  Planarity :  0.004   0.039    821
  Dihedral  :  6.503  55.385    731
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  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: -0.84 (0.35), residues: 579
  helix:  1.28 (0.34), residues: 220
  sheet: -0.64 (0.47), residues: 131
  loop : -2.41 (0.37), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 134 
 HIS   0.004   0.001   HIS C 199 
 PHE   0.014   0.002   PHE A  37 
 TYR   0.042   0.002   TYR C 121 
 ARG   0.004   0.000   ARG A 109 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 1.318 
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   32 TYR cc_start: 0.8106 (m-80) cc_final: 0.7728 (m-80)
REVERT: A   33 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8738 (mm-40)
REVERT: A   69 MET cc_start: 0.9502 (mmm) cc_final: 0.9257 (mmm)
REVERT: A   93 GLU cc_start: 0.6059 (pm20) cc_final: 0.5790 (pm20)
REVERT: A  128 ASP cc_start: 0.8903 (t0) cc_final: 0.8593 (t0)
REVERT: A  146 GLU cc_start: 0.6624 (tt0) cc_final: 0.5996 (tt0)
REVERT: A  158 LEU cc_start: 0.9371 (mm) cc_final: 0.8902 (mm)
REVERT: B   42 HIS cc_start: 0.8680 (m-70) cc_final: 0.8382 (m-70)
REVERT: B   65 PHE cc_start: 0.8545 (m-80) cc_final: 0.8307 (m-10)
REVERT: B  122 ASP cc_start: 0.8903 (p0) cc_final: 0.8627 (p0)
REVERT: B  124 LYS cc_start: 0.8857 (mttt) cc_final: 0.8528 (tmmt)
REVERT: C   96 ILE cc_start: 0.9462 (mm) cc_final: 0.9150 (tp)
REVERT: C  102 ASP cc_start: 0.8555 (m-30) cc_final: 0.8262 (m-30)
REVERT: C  174 LEU cc_start: 0.8383 (mm) cc_final: 0.8016 (mm)
REVERT: C  188 GLU cc_start: 0.8912 (pp20) cc_final: 0.8601 (pp20)
REVERT: C  203 LEU cc_start: 0.8066 (tp) cc_final: 0.7669 (tp)
REVERT: D   71 HIS cc_start: 0.7157 (m90) cc_final: 0.6876 (m-70)
REVERT: D   82 LYS cc_start: 0.7988 (mppt) cc_final: 0.7260 (mmmt)
REVERT: D   85 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8715 (mmtt)
REVERT: D  134 TRP cc_start: 0.7338 (m100) cc_final: 0.7075 (m100)
REVERT: D  139 ARG cc_start: 0.8563 (ttt180) cc_final: 0.8237 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.2018
  time to fit residues: 43.6980
Evaluate side-chains
  122 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 1.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 28 optimal weight:    8.9990
   chunk 48 optimal weight:    0.4980
   chunk 31 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 42 optimal weight:    0.4980
   chunk 49 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0870
   chunk 46 optimal weight:    9.9990
   overall best weight:    0.7960

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

Flipped N/Q/H residues before XYZ refinement:
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 144 HIS ** 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 = 0.3512 r_free = 0.3512 target = 0.072098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.057212 restraints weight = 28866.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.058635 restraints weight = 22339.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.059695 restraints weight = 18298.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.7419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4896  Z= 0.175
  Angle     :  0.716  11.324   6629  Z= 0.352
  Chirality :  0.044   0.163    756
  Planarity :  0.004   0.034    821
  Dihedral  :  6.101  56.478    731
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  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: -0.64 (0.35), residues: 579
  helix:  1.44 (0.35), residues: 221
  sheet: -0.26 (0.48), residues: 125
  loop : -2.45 (0.36), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 148 
 HIS   0.003   0.001   HIS C 199 
 PHE   0.012   0.001   PHE A  37 
 TYR   0.027   0.002   TYR A  32 
 ARG   0.005   0.001   ARG C 223 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.450 
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   32 TYR cc_start: 0.8060 (m-80) cc_final: 0.7574 (m-80)
REVERT: A   33 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8684 (mm110)
REVERT: A   93 GLU cc_start: 0.6165 (pm20) cc_final: 0.5907 (pm20)
REVERT: A  112 LYS cc_start: 0.9015 (mmtm) cc_final: 0.8643 (mmmt)
REVERT: A  121 ILE cc_start: 0.6915 (mm) cc_final: 0.6698 (mm)
REVERT: A  146 GLU cc_start: 0.6433 (tt0) cc_final: 0.5918 (tt0)
REVERT: A  158 LEU cc_start: 0.9409 (mm) cc_final: 0.8938 (mm)
REVERT: B   42 HIS cc_start: 0.8561 (m-70) cc_final: 0.8297 (m-70)
REVERT: B   88 TYR cc_start: 0.7202 (m-80) cc_final: 0.6462 (m-10)
REVERT: B  122 ASP cc_start: 0.8852 (p0) cc_final: 0.8583 (t0)
REVERT: C   91 SER cc_start: 0.7671 (p) cc_final: 0.7403 (p)
REVERT: C   96 ILE cc_start: 0.9465 (mm) cc_final: 0.9103 (tp)
REVERT: C  102 ASP cc_start: 0.8482 (m-30) cc_final: 0.8147 (m-30)
REVERT: C  174 LEU cc_start: 0.8580 (mm) cc_final: 0.8115 (mp)
REVERT: C  188 GLU cc_start: 0.8902 (pp20) cc_final: 0.8662 (pp20)
REVERT: C  193 ILE cc_start: 0.9302 (pt) cc_final: 0.8983 (mt)
REVERT: C  203 LEU cc_start: 0.7765 (tp) cc_final: 0.7444 (tp)
REVERT: D   71 HIS cc_start: 0.7184 (m90) cc_final: 0.6881 (m-70)
REVERT: D   82 LYS cc_start: 0.7904 (mppt) cc_final: 0.7148 (mmmt)
REVERT: D   85 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8760 (mmtt)
REVERT: D  139 ARG cc_start: 0.8434 (ttt180) cc_final: 0.8125 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.2101
  time to fit residues: 45.4286
Evaluate side-chains
  129 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 3 optimal weight:    0.8980
   chunk 42 optimal weight:   10.0000
   chunk 46 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   chunk 21 optimal weight:    0.7980
   chunk 36 optimal weight:    0.4980
   chunk 53 optimal weight:    7.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 144 HIS ** 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 = 0.3503 r_free = 0.3503 target = 0.071471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.057156 restraints weight = 28799.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.058548 restraints weight = 22396.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.059605 restraints weight = 18382.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.7595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4896  Z= 0.195
  Angle     :  0.757  11.201   6629  Z= 0.369
  Chirality :  0.044   0.170    756
  Planarity :  0.004   0.035    821
  Dihedral  :  6.144  56.144    731
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -0.66 (0.35), residues: 579
  helix:  1.49 (0.35), residues: 221
  sheet: -0.24 (0.48), residues: 123
  loop : -2.55 (0.36), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 148 
 HIS   0.003   0.001   HIS C 199 
 PHE   0.020   0.002   PHE C  94 
 TYR   0.032   0.002   TYR D  81 
 ARG   0.004   0.000   ARG A 109 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.871 
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   32 TYR cc_start: 0.8165 (m-80) cc_final: 0.7761 (m-80)
REVERT: A   33 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8748 (mm-40)
REVERT: A   93 GLU cc_start: 0.6184 (pm20) cc_final: 0.5923 (pm20)
REVERT: A  112 LYS cc_start: 0.8984 (mmtm) cc_final: 0.8576 (mmmt)
REVERT: A  121 ILE cc_start: 0.6898 (mm) cc_final: 0.6673 (mm)
REVERT: A  146 GLU cc_start: 0.6356 (tt0) cc_final: 0.5722 (tt0)
REVERT: A  158 LEU cc_start: 0.9367 (mm) cc_final: 0.8931 (mm)
REVERT: B   42 HIS cc_start: 0.8631 (m-70) cc_final: 0.8301 (m-70)
REVERT: B   88 TYR cc_start: 0.7412 (m-80) cc_final: 0.6832 (m-10)
REVERT: B  122 ASP cc_start: 0.8910 (p0) cc_final: 0.8609 (t0)
REVERT: C   96 ILE cc_start: 0.9465 (mm) cc_final: 0.9146 (tp)
REVERT: C  102 ASP cc_start: 0.8550 (m-30) cc_final: 0.8225 (m-30)
REVERT: C  174 LEU cc_start: 0.8482 (mm) cc_final: 0.8127 (mp)
REVERT: C  188 GLU cc_start: 0.8876 (pp20) cc_final: 0.8619 (pp20)
REVERT: D   71 HIS cc_start: 0.7177 (m90) cc_final: 0.6899 (m-70)
REVERT: D   82 LYS cc_start: 0.7941 (mppt) cc_final: 0.7239 (mmmt)
REVERT: D   85 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8836 (mmtt)
REVERT: D  134 TRP cc_start: 0.7339 (m100) cc_final: 0.6892 (m100)
REVERT: D  139 ARG cc_start: 0.8480 (ttt180) cc_final: 0.8159 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1858
  time to fit residues: 38.7166
Evaluate side-chains
  123 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 52 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9980
   chunk 0 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 31 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0020
   chunk 40 optimal weight:    9.9990
   chunk 20 optimal weight:    9.9990
   chunk 19 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    1.5392

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

Flipped N/Q/H residues before XYZ refinement:
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 144 HIS ** 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 = 0.3499 r_free = 0.3499 target = 0.071247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.056996 restraints weight = 28894.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.058439 restraints weight = 22144.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.059550 restraints weight = 17921.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.7670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4896  Z= 0.183
  Angle     :  0.729  11.287   6629  Z= 0.357
  Chirality :  0.045   0.283    756
  Planarity :  0.004   0.035    821
  Dihedral  :  6.046  56.214    731
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  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: -0.65 (0.35), residues: 579
  helix:  1.48 (0.35), residues: 221
  sheet: -0.21 (0.49), residues: 121
  loop : -2.53 (0.35), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 148 
 HIS   0.003   0.001   HIS C 199 
 PHE   0.013   0.001   PHE A  37 
 TYR   0.023   0.002   TYR A  32 
 ARG   0.004   0.001   ARG A 153 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2038.83 seconds
wall clock time: 37 minutes 7.71 seconds (2227.71 seconds total)