Starting phenix.real_space_refine
on Tue Aug  4 16:16:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9urm_64461/08_2026/9urm_64461.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9urm_64461/08_2026/9urm_64461.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9urm_64461/08_2026/9urm_64461.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9urm_64461/08_2026/9urm_64461.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9urm_64461/08_2026/9urm_64461.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9urm_64461/08_2026/9urm_64461.map"
  }
  resolution = 4.24
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      75      5.49       5
     S      15      5.16       5
     C    2678      2.51       5
     N     812      2.21       5
     O    1142      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4722
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1382
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 179, 1382
          Classifications: {'peptide': 179}
          Link IDs: {'PTRANS': 5, 'TRANS': 173}
    Chain: "B"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 973
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 2, 'TRANS': 124}
    Chain: "C"
      Number of atoms: 780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 780
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 7, 'TRANS': 97}
    Chain: "R"
      Number of atoms: 1587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1587
          Classifications: {'RNA': 75}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 36}
          Link IDs: {'rna2p': 8, 'rna3p': 66}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.30, per 1000 atoms: 0.28
  Number of scatterers: 4722
  At special positions: 0
  Unit cell: (92.16, 78.72, 127.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      15     16.00
     P      75     15.00
     O    1142      8.00
     N     812      7.00
     C    2678      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.41
  Conformation dependent library (CDL) restraints added in 130.2 milliseconds
  

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  730

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 8 sheets defined
      11.4% alpha, 47.2% beta
      23 base pairs and 48 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 14
    Processing helix  chain 'A' and resid 38 through 42
    Processing helix  chain 'A' and resid 86 through 90
      removed outlier: 3.686A  pdb=" N   ILE A  90 " --> pdb=" O   ARG A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 146
      removed outlier: 3.775A  pdb=" N   GLN A 145 " --> pdb=" O   LYS A 142 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   CYS A 146 " --> pdb=" O   THR A 143 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 142 through 146'
    Processing helix  chain 'A' and resid 174 through 178
      removed outlier: 3.559A  pdb=" N   TYR A 177 " --> pdb=" O   LYS A 174 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   PHE A 178 " --> pdb=" O   LYS A 175 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 174 through 178'
    Processing helix  chain 'B' and resid 30 through 34
      removed outlier: 3.623A  pdb=" N   SER B  33 " --> pdb=" O   THR B  30 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   TYR B  34 " --> pdb=" O   PHE B  31 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 30 through 34'
    Processing helix  chain 'C' and resid 26 through 30
      removed outlier: 3.643A  pdb=" N   ASP C  29 " --> pdb=" O   LYS C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 82
      removed outlier: 3.798A  pdb=" N   ASP C  81 " --> pdb=" O   GLN C  78 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   GLU C  82 " --> pdb=" O   ALA C  79 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 78 through 82'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 20
      removed outlier: 3.519A  pdb=" N   LEU A  28 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   VAL A  34 " --> pdb=" O   ILE A  30 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   LEU A  72 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ASP A  58 " --> pdb=" O   THR A  76 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   ASP A  78 " --> pdb=" O   VAL A  56 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   VAL A  56 " --> pdb=" O   ASP A  78 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 126
      removed outlier: 6.980A  pdb=" N   MET A 120 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ILE A 135 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   GLY A 122 " --> pdb=" O   ARG A 133 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ARG A 133 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
      removed outlier: 7.895A  pdb=" N   ARG A 133 " --> pdb=" O   GLN A 172 " (cutoff:3.500A)
      removed outlier: 5.590A  pdb=" N   ALA A 171 " --> pdb=" O   HIS A 160 " (cutoff:3.500A)
      removed outlier: 5.887A  pdb=" N   HIS A 160 " --> pdb=" O   ALA A 171 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   LEU A 150 " --> pdb=" O   PHE A 157 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ALA A  99 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL A 115 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   SER A 105 " --> pdb=" O   THR A 109 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   THR A 109 " --> pdb=" O   SER A 105 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 10
    Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 14
      removed outlier: 6.098A  pdb=" N   ARG B  40 " --> pdb=" O   TRP B  49 " (cutoff:3.500A)
      removed outlier: 5.241A  pdb=" N   TRP B  49 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 13 through 14
      removed outlier: 4.339A  pdb=" N   VAL B 117 " --> pdb=" O   ARG B 100 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 9 through 10
    Processing sheet with id=AA7, first strand: chain 'C' and resid 17 through 23
    Processing sheet with id=AA8, first strand: chain 'C' and resid 44 through 47
      removed outlier: 6.847A  pdb=" N   TRP C  34 " --> pdb=" O   VAL C  46 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   THR C  94 " --> pdb=" O   ASP C  91 " (cutoff:3.500A)

    126 hydrogen bonds defined for protein.
    315 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      59 hydrogen bonds
      114 hydrogen bond angles
      0 basepair planarities
      23 basepair parallelities
      48 stacking parallelities
  Total time for adding SS restraints: 0.71

  Time building geometry restraints manager: 0.50 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1203
        1.33 -     1.45: 1331
        1.45 -     1.57: 2262
        1.57 -     1.69: 148
        1.69 -     1.81: 22
  Bond restraints: 4966
  Sorted by residual:
  bond pdb=" CA  ARG A  84 "
       pdb=" C   ARG A  84 "
    ideal  model  delta    sigma   weight residual
    1.523  1.481  0.042 1.24e-02 6.50e+03 1.16e+01
  bond pdb=" P     A R   8 "
       pdb=" O5'   A R   8 "
    ideal  model  delta    sigma   weight residual
    1.593  1.622 -0.029 1.00e-02 1.00e+04 8.60e+00
  bond pdb=" C4    C R  26 "
       pdb=" C5    C R  26 "
    ideal  model  delta    sigma   weight residual
    1.425  1.404  0.021 8.00e-03 1.56e+04 7.14e+00
  bond pdb=" P     G R  16 "
       pdb=" O5'   G R  16 "
    ideal  model  delta    sigma   weight residual
    1.593  1.619 -0.026 1.00e-02 1.00e+04 6.79e+00
  bond pdb=" P     U R  42 "
       pdb=" O5'   U R  42 "
    ideal  model  delta    sigma   weight residual
    1.593  1.617 -0.024 1.00e-02 1.00e+04 5.75e+00
  ... (remaining 4961 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 6607
        1.71 -     3.41: 369
        3.41 -     5.12: 62
        5.12 -     6.83: 32
        6.83 -     8.54: 9
  Bond angle restraints: 7079
  Sorted by residual:
  angle pdb=" C3'   G R   9 "
        pdb=" C2'   G R   9 "
        pdb=" C1'   G R   9 "
      ideal   model   delta    sigma   weight residual
     101.30  105.00   -3.70 7.00e-01 2.04e+00 2.79e+01
  angle pdb=" O3'   A R   6 "
        pdb=" P     C R   7 "
        pdb=" O5'   C R   7 "
      ideal   model   delta    sigma   weight residual
     104.00   96.68    7.32 1.90e+00 2.77e-01 1.49e+01
  angle pdb=" C3'   C R   7 "
        pdb=" O3'   C R   7 "
        pdb=" P     A R   8 "
      ideal   model   delta    sigma   weight residual
     119.70  124.02   -4.32 1.20e+00 6.94e-01 1.30e+01
  angle pdb=" C3'   U R  14 "
        pdb=" O3'   U R  14 "
        pdb=" P     G R  15 "
      ideal   model   delta    sigma   weight residual
     119.70  123.99   -4.29 1.20e+00 6.94e-01 1.28e+01
  angle pdb=" C1'   C R  57 "
        pdb=" N1    C R  57 "
        pdb=" C2    C R  57 "
      ideal   model   delta    sigma   weight residual
     118.80  122.59   -3.79 1.10e+00 8.26e-01 1.18e+01
  ... (remaining 7074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.91: 2655
       22.91 -    45.83: 245
       45.83 -    68.74: 135
       68.74 -    91.65: 22
       91.65 -   114.57: 1
  Dihedral angle restraints: 3058
    sinusoidal: 1901
      harmonic: 1157
  Sorted by residual:
  dihedral pdb=" O4'   A R  59 "
           pdb=" C1'   A R  59 "
           pdb=" N9    A R  59 "
           pdb=" C4    A R  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
     254.00  178.29   75.71     1      1.70e+01 3.46e-03 2.50e+01
  dihedral pdb=" O4'   U R  60 "
           pdb=" C1'   U R  60 "
           pdb=" N1    U R  60 "
           pdb=" C2    U R  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00  178.73   53.27     1      1.70e+01 3.46e-03 1.34e+01
  dihedral pdb=" O4'   A R   4 "
           pdb=" C1'   A R   4 "
           pdb=" N9    A R   4 "
           pdb=" C4    A R   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -154.63   48.63     1      1.70e+01 3.46e-03 1.13e+01
  ... (remaining 3055 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.110: 712
       0.110 -    0.219: 112
       0.219 -    0.329: 17
       0.329 -    0.439: 3
       0.439 -    0.548: 13
  Chirality restraints: 857
  Sorted by residual:
  chirality pdb=" P     C R  25 "
            pdb=" OP1   C R  25 "
            pdb=" OP2   C R  25 "
            pdb=" O5'   C R  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.96   -0.55 2.00e-01 2.50e+01 7.52e+00
  chirality pdb=" P     G R   9 "
            pdb=" OP1   G R   9 "
            pdb=" OP2   G R   9 "
            pdb=" O5'   G R   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.94   -0.53 2.00e-01 2.50e+01 6.89e+00
  chirality pdb=" P     G R  12 "
            pdb=" OP1   G R  12 "
            pdb=" OP2   G R  12 "
            pdb=" O5'   G R  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.92   -0.51 2.00e-01 2.50e+01 6.62e+00
  ... (remaining 854 not shown)

  Planarity restraints: 632
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A  83 "    0.019 2.00e-02 2.50e+03   3.86e-02 1.49e+01
        pdb=" C   PHE A  83 "   -0.067 2.00e-02 2.50e+03
        pdb=" O   PHE A  83 "    0.026 2.00e-02 2.50e+03
        pdb=" N   ARG A  84 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C   7 "   -0.042 5.00e-02 4.00e+02   6.41e-02 6.57e+00
        pdb=" N   PRO C   8 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO C   8 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO C   8 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A  71 "    0.008 2.00e-02 2.50e+03   1.71e-02 2.91e+00
        pdb=" C   GLU A  71 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   GLU A  71 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU A  72 "    0.010 2.00e-02 2.50e+03
  ... (remaining 629 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 851
        2.77 -     3.30: 3861
        3.30 -     3.84: 7960
        3.84 -     4.37: 9539
        4.37 -     4.90: 15026
  Nonbonded interactions: 37237
  Sorted by model distance:
  nonbonded pdb=" O2'   U R  14 "
            pdb=" OP1   G R  15 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OH  TYR C   2 "
            pdb=" O   ASP C  25 "
     model   vdw
     2.344 3.040
  nonbonded pdb=" NH1 ARG B  69 "
            pdb=" O   SER B  87 "
     model   vdw
     2.372 3.120
  nonbonded pdb=" O   SER B  54 "
            pdb=" NH1 ARG B  74 "
     model   vdw
     2.397 3.120
  nonbonded pdb=" N   ASP B 116 "
            pdb=" OD1 ASP B 116 "
     model   vdw
     2.426 3.120
  ... (remaining 37232 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:                  0.000
  Normalize map: mean=0, sd=1:             1.590
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     6.600
  Find NCS groups from input model:        0.020
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3306
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   4966  Z= 0.437
  Angle     :  0.944   8.537   7079  Z= 0.561
  Chirality :  0.099   0.548    857
  Planarity :  0.005   0.064    632
  Dihedral  : 20.314 114.566   2328
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 14.87 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.43), residues: 405
  helix:  1.98 (1.79), residues: 11
  sheet:  1.08 (0.40), residues: 185
  loop : -0.91 (0.43), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  84 
 TYR   0.011   0.001   TYR B  97 
 PHE   0.011   0.001   PHE B  70 
 TRP   0.012   0.001   TRP C  90 
 HIS   0.002   0.001   HIS A 160 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00610 /  0.44 ( 4966)
  covalent geometry    : angle       0.94417 /  0.56 ( 7079)
  hydrogen bonds       : bond        0.15143 /  9.37 (  180)
  hydrogen bonds       : angle       5.77581 /  4.08 (  429)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1213
  time to fit residues: 11.8125
Evaluate side-chains
  33 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:    8.9990
   chunk 16 optimal weight:    8.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    2.5584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 172 GLN
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  79 ASN
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4609 r_free = 0.4609 target = 0.139968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.120896 restraints weight = 32660.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.119166 restraints weight = 33141.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.118915 restraints weight = 37441.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.118772 restraints weight = 35703.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.118782 restraints weight = 34839.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.4258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5455
moved from start:          0.3122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   4966  Z= 0.228
  Angle     :  0.732   7.822   7079  Z= 0.407
  Chirality :  0.045   0.260    857
  Planarity :  0.007   0.055    632
  Dihedral  : 20.939 121.527   1622
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 17.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.40), residues: 405
  helix:  3.10 (1.48), residues: 11
  sheet:  0.78 (0.38), residues: 178
  loop : -1.05 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  18 
 TYR   0.021   0.002   TYR C  31 
 PHE   0.030   0.003   PHE A 169 
 TRP   0.020   0.002   TRP C  90 
 HIS   0.004   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00459 /  0.23 ( 4966)
  covalent geometry    : angle       0.73205 /  0.41 ( 7079)
  hydrogen bonds       : bond        0.06215 /  4.21 (  180)
  hydrogen bonds       : angle       4.71295 /  3.39 (  429)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.083 
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   68 ILE cc_start: 0.5676 (mt) cc_final: 0.5215 (mt)
REVERT: A  166 ARG cc_start: 0.8037 (mpt180) cc_final: 0.7051 (ptp90)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.0899
  time to fit residues: 5.4315
Evaluate side-chains
  34 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 40 optimal weight:   20.0000
   chunk 30 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 42 optimal weight:   20.0000
   chunk 17 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9990
   chunk 1 optimal weight:    8.9990
   chunk 39 optimal weight:   20.0000
   chunk 43 optimal weight:   20.0000
   chunk 11 optimal weight:    3.9990
   overall best weight:    2.1986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 145 GLN
** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  59 ASN
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  41 GLN
** C  88 GLN ** 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 = 0.4547 r_free = 0.4547 target = 0.134734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.105796 restraints weight = 35563.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.106103 restraints weight = 33882.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.106183 restraints weight = 32821.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.106185 restraints weight = 32528.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.106185 restraints weight = 32519.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5891
moved from start:          0.4120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   4966  Z= 0.189
  Angle     :  0.625   7.607   7079  Z= 0.346
  Chirality :  0.040   0.304    857
  Planarity :  0.006   0.045    632
  Dihedral  : 21.142 126.055   1622
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  3.21 %
    Favored  : 96.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.40), residues: 405
  helix:  4.26 (1.48), residues: 11
  sheet:  0.58 (0.40), residues: 159
  loop : -1.19 (0.37), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  18 
 TYR   0.024   0.003   TYR C  86 
 PHE   0.014   0.002   PHE B  31 
 TRP   0.017   0.003   TRP B 109 
 HIS   0.005   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00405 /  0.19 ( 4966)
  covalent geometry    : angle       0.62528 /  0.35 ( 7079)
  hydrogen bonds       : bond        0.05504 /  3.42 (  180)
  hydrogen bonds       : angle       4.83571 /  3.39 (  429)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.080 
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  166 ARG cc_start: 0.8283 (mpt180) cc_final: 0.7246 (ptp90)
  outliers start: 1
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0746
  time to fit residues: 4.4960
Evaluate side-chains
  36 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:   40.0000
   chunk 0 optimal weight:    9.9990
   chunk 14 optimal weight:    8.9990
   chunk 19 optimal weight:    8.9990
   chunk 38 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   overall best weight:    2.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 172 GLN
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  41 GLN
** C  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.129362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.099891 restraints weight = 34397.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.099917 restraints weight = 29606.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.099917 restraints weight = 30232.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.099917 restraints weight = 30232.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.099917 restraints weight = 30232.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6021
moved from start:          0.5143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.087   4966  Z= 0.218
  Angle     :  0.673   6.241   7079  Z= 0.379
  Chirality :  0.044   0.305    857
  Planarity :  0.006   0.055    632
  Dihedral  : 21.406 127.479   1622
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 17.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  3.79 %
    Favored  : 95.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.41), residues: 405
  helix:  4.05 (1.48), residues: 11
  sheet:  0.40 (0.37), residues: 175
  loop : -1.21 (0.41), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  18 
 TYR   0.022   0.003   TYR B  62 
 PHE   0.020   0.003   PHE B  31 
 TRP   0.020   0.003   TRP B 109 
 HIS   0.005   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00466 /  0.22 ( 4966)
  covalent geometry    : angle       0.67285 /  0.38 ( 7079)
  hydrogen bonds       : bond        0.06942 /  4.52 (  180)
  hydrogen bonds       : angle       5.22632 /  3.77 (  429)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 ARG cc_start: 0.8226 (mpt180) cc_final: 0.7128 (mmp-170)
REVERT: B   36 MET cc_start: 0.7747 (mmp) cc_final: 0.7471 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 44
  average time/residue: 0.1100
  time to fit residues: 5.8689
Evaluate side-chains
  33 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 40 optimal weight:   20.0000
   chunk 23 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0040
   chunk 37 optimal weight:   10.0000
   chunk 10 optimal weight:    5.9990
   chunk 44 optimal weight:   20.0000
   chunk 5 optimal weight:    0.2980
   chunk 26 optimal weight:    4.9990
   overall best weight:    0.6194

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  37 GLN
C  41 GLN
** C  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.132662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.104328 restraints weight = 34315.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.104328 restraints weight = 31728.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.104328 restraints weight = 31728.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.104328 restraints weight = 31728.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.104328 restraints weight = 31728.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.4135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5854
moved from start:          0.5103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   4966  Z= 0.116
  Angle     :  0.558   5.692   7079  Z= 0.306
  Chirality :  0.040   0.302    857
  Planarity :  0.005   0.043    632
  Dihedral  : 21.189 125.327   1622
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  0.29 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.41), residues: 405
  helix:  4.23 (1.53), residues: 11
  sheet:  0.65 (0.39), residues: 173
  loop : -1.05 (0.41), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  53 
 TYR   0.012   0.001   TYR A  60 
 PHE   0.010   0.002   PHE B  31 
 TRP   0.012   0.002   TRP C  90 
 HIS   0.002   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00237 /  0.12 ( 4966)
  covalent geometry    : angle       0.55772 /  0.31 ( 7079)
  hydrogen bonds       : bond        0.04801 /  3.09 (  180)
  hydrogen bonds       : angle       4.91982 /  3.54 (  429)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.097 
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  166 ARG cc_start: 0.8049 (mpt180) cc_final: 0.6839 (mmp-170)
REVERT: B   36 MET cc_start: 0.7659 (mmp) cc_final: 0.7232 (mmm)
REVERT: C   37 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8905 (pp30)
  outliers start: 2
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1065
  time to fit residues: 5.2886
Evaluate side-chains
  32 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 39 optimal weight:   20.0000
   chunk 30 optimal weight:    0.5980
   chunk 14 optimal weight:    6.9990
   chunk 40 optimal weight:   20.0000
   chunk 13 optimal weight:    0.8980
   chunk 5 optimal weight:   10.0000
   chunk 19 optimal weight:   20.0000
   chunk 17 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 21 optimal weight:    0.4980
   chunk 31 optimal weight:    8.9990
   overall best weight:    2.5984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   6 GLN
** C  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  88 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 = 0.4463 r_free = 0.4463 target = 0.127635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.098458 restraints weight = 35112.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.098832 restraints weight = 33051.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 16)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.098832 restraints weight = 31004.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.098832 restraints weight = 31003.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.098832 restraints weight = 31003.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6068
moved from start:          0.5809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4966  Z= 0.180
  Angle     :  0.629  11.212   7079  Z= 0.349
  Chirality :  0.040   0.298    857
  Planarity :  0.005   0.050    632
  Dihedral  : 21.244 126.636   1622
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 17.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  2.33 %
    Favored  : 97.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.42), residues: 405
  helix:  4.11 (1.44), residues: 11
  sheet:  0.27 (0.39), residues: 177
  loop : -1.08 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  18 
 TYR   0.015   0.003   TYR A  60 
 PHE   0.015   0.002   PHE B  31 
 TRP   0.016   0.002   TRP B 109 
 HIS   0.005   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.18 ( 4966)
  covalent geometry    : angle       0.62935 /  0.35 ( 7079)
  hydrogen bonds       : bond        0.06283 /  4.05 (  180)
  hydrogen bonds       : angle       5.02486 /  3.60 (  429)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.082 
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  166 ARG cc_start: 0.8225 (mpt180) cc_final: 0.7163 (mmp-170)
REVERT: B   36 MET cc_start: 0.7811 (mmp) cc_final: 0.7474 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 41
  average time/residue: 0.0856
  time to fit residues: 4.2215
Evaluate side-chains
  30 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 29
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 41 optimal weight:   20.0000
   chunk 33 optimal weight:    0.9980
   chunk 10 optimal weight:    8.9990
   chunk 42 optimal weight:   20.0000
   chunk 17 optimal weight:    5.9990
   chunk 21 optimal weight:    0.5980
   chunk 40 optimal weight:    8.9990
   chunk 45 optimal weight:   30.0000
   chunk 11 optimal weight:    0.0870
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    0.0470
   overall best weight:    1.5458

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 145 GLN
** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  41 GLN
** C  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.128714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.100398 restraints weight = 34516.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.100456 restraints weight = 29429.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.100456 restraints weight = 30088.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.100456 restraints weight = 30088.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.100456 restraints weight = 30088.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.4074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5976
moved from start:          0.6048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4966  Z= 0.135
  Angle     :  0.582   5.696   7079  Z= 0.320
  Chirality :  0.040   0.298    857
  Planarity :  0.005   0.043    632
  Dihedral  : 21.242 124.838   1622
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 15.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  1.75 %
    Favored  : 97.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.42), residues: 405
  helix:  4.09 (1.46), residues: 11
  sheet:  0.33 (0.39), residues: 174
  loop : -1.06 (0.41), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  18 
 TYR   0.014   0.002   TYR A  60 
 PHE   0.011   0.002   PHE A 178 
 TRP   0.012   0.002   TRP C  90 
 HIS   0.003   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.13 ( 4966)
  covalent geometry    : angle       0.58176 /  0.32 ( 7079)
  hydrogen bonds       : bond        0.05297 /  3.38 (  180)
  hydrogen bonds       : angle       4.98532 /  3.59 (  429)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 ARG cc_start: 0.7974 (mpt180) cc_final: 0.6891 (mmp-170)
REVERT: B   36 MET cc_start: 0.7746 (mmp) cc_final: 0.7414 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1086
  time to fit residues: 4.9161
Evaluate side-chains
  28 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 15 optimal weight:   20.0000
   chunk 13 optimal weight:    9.9990
   chunk 34 optimal weight:    7.9990
   chunk 18 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0870
   chunk 6 optimal weight:    0.9980
   chunk 42 optimal weight:   20.0000
   chunk 1 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    2.4164

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  59 ASN
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  88 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.122807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.092311 restraints weight = 35707.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.092978 restraints weight = 33093.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.092992 restraints weight = 30852.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.092992 restraints weight = 30834.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.092992 restraints weight = 30834.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.4005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6170
moved from start:          0.6930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   4966  Z= 0.188
  Angle     :  0.633   7.531   7079  Z= 0.358
  Chirality :  0.042   0.302    857
  Planarity :  0.005   0.049    632
  Dihedral  : 21.352 124.446   1622
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 20.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  0.87 %
    Favored  : 98.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.41), residues: 405
  helix:  3.50 (1.39), residues: 11
  sheet: -0.07 (0.39), residues: 166
  loop : -0.99 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  18 
 TYR   0.017   0.003   TYR C  31 
 PHE   0.022   0.003   PHE A 108 
 TRP   0.021   0.003   TRP B 109 
 HIS   0.006   0.002   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.19 ( 4966)
  covalent geometry    : angle       0.63304 /  0.36 ( 7079)
  hydrogen bonds       : bond        0.06850 /  4.39 (  180)
  hydrogen bonds       : angle       5.19766 /  3.72 (  429)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 35
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 ARG cc_start: 0.8321 (mmt180) cc_final: 0.7693 (mmp-170)
REVERT: B   36 MET cc_start: 0.7919 (mmp) cc_final: 0.7595 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0762
  time to fit residues: 3.3310
Evaluate side-chains
  24 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 33 optimal weight:    0.5980
   chunk 22 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 43 optimal weight:   30.0000
   chunk 8 optimal weight:    7.9990
   chunk 28 optimal weight:    0.7980
   chunk 37 optimal weight:   10.0000
   chunk 38 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.6584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  80 ASN
** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  15 GLN
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.123916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.094529 restraints weight = 34633.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.095230 restraints weight = 31812.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.095579 restraints weight = 30436.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.096160 restraints weight = 29264.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.096092 restraints weight = 26600.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.4075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6076
moved from start:          0.7159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4966  Z= 0.136
  Angle     :  0.588   6.149   7079  Z= 0.325
  Chirality :  0.039   0.292    857
  Planarity :  0.005   0.043    632
  Dihedral  : 21.321 121.840   1622
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 16.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.41), residues: 405
  helix:  3.83 (1.45), residues: 11
  sheet: -0.23 (0.39), residues: 167
  loop : -0.90 (0.41), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  18 
 TYR   0.016   0.002   TYR A  60 
 PHE   0.010   0.002   PHE A 178 
 TRP   0.014   0.002   TRP C  90 
 HIS   0.003   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.14 ( 4966)
  covalent geometry    : angle       0.58784 /  0.33 ( 7079)
  hydrogen bonds       : bond        0.05717 /  3.60 (  180)
  hydrogen bonds       : angle       5.15039 /  3.69 (  429)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 MET cc_start: 0.7589 (tmm) cc_final: 0.7286 (tmm)
REVERT: A  166 ARG cc_start: 0.8357 (mmt180) cc_final: 0.7697 (mmp-170)
REVERT: B   36 MET cc_start: 0.7832 (mmp) cc_final: 0.7491 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0918
  time to fit residues: 3.9952
Evaluate side-chains
  26 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 25 optimal weight:    0.5980
   chunk 35 optimal weight:    8.9990
   chunk 28 optimal weight:    6.9990
   chunk 44 optimal weight:   20.0000
   chunk 15 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 30 optimal weight:    7.9990
   chunk 5 optimal weight:    4.9990
   chunk 7 optimal weight:    9.9990
   overall best weight:    2.9188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.118801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.089040 restraints weight = 35307.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.089687 restraints weight = 32289.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.089979 restraints weight = 30603.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.090053 restraints weight = 29907.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.090056 restraints weight = 29073.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6226
moved from start:          0.7830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4966  Z= 0.201
  Angle     :  0.711   9.570   7079  Z= 0.394
  Chirality :  0.044   0.299    857
  Planarity :  0.006   0.052    632
  Dihedral  : 21.494 122.273   1622
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 23.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.41), residues: 405
  helix:  3.10 (1.37), residues: 11
  sheet: -0.49 (0.37), residues: 178
  loop : -1.07 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 100 
 TYR   0.024   0.004   TYR B 114 
 PHE   0.014   0.003   PHE B  31 
 TRP   0.023   0.003   TRP B 109 
 HIS   0.016   0.003   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00401 /  0.20 ( 4966)
  covalent geometry    : angle       0.71132 /  0.39 ( 7079)
  hydrogen bonds       : bond        0.07477 /  4.75 (  180)
  hydrogen bonds       : angle       5.53713 /  3.96 (  429)

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

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

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  810 Ramachandran restraints generated.
    405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 ARG cc_start: 0.8220 (mmt180) cc_final: 0.7467 (mmp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0933
  time to fit residues: 4.4223
Evaluate side-chains
  27 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 40 optimal weight:   30.0000
   chunk 15 optimal weight:   20.0000
   chunk 25 optimal weight:    8.9990
   chunk 20 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 41 optimal weight:   20.0000
   chunk 0 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 29 optimal weight:   10.0000
   overall best weight:    1.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 HIS
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  88 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 = 0.4407 r_free = 0.4407 target = 0.120479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.091117 restraints weight = 33598.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.091683 restraints weight = 31495.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.092353 restraints weight = 29991.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.092303 restraints weight = 26979.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.092303 restraints weight = 27066.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.4016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6097
moved from start:          0.7969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4966  Z= 0.137
  Angle     :  0.600   7.168   7079  Z= 0.332
  Chirality :  0.040   0.291    857
  Planarity :  0.005   0.044    632
  Dihedral  : 21.441 119.594   1622
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 18.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.41), residues: 405
  helix:  0.16 (1.44), residues: 17
  sheet: -0.46 (0.38), residues: 177
  loop : -1.12 (0.43), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 136 
 TYR   0.018   0.003   TYR A  60 
 PHE   0.020   0.002   PHE A 178 
 TRP   0.016   0.002   TRP C  90 
 HIS   0.004   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.14 ( 4966)
  covalent geometry    : angle       0.60030 /  0.33 ( 7079)
  hydrogen bonds       : bond        0.05933 /  3.71 (  180)
  hydrogen bonds       : angle       5.44987 /  3.88 (  429)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1211.23 seconds
wall clock time: 21 minutes 28.79 seconds (1288.79 seconds total)