Starting phenix.real_space_refine
on Thu Jul  2 00:42:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9urm_64461/07_2026/9urm_64461.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9urm_64461/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9urm_64461/07_2026/9urm_64461.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9urm_64461/07_2026/9urm_64461.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9urm_64461/07_2026/9urm_64461.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9urm_64461/07_2026/9urm_64461.cif"
  }
  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-dev-6108/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: 0.96, per 1000 atoms: 0.20
  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: 0.33
  Conformation dependent library (CDL) restraints added in 82.7 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: 0.40
  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: 0.44

  Time building geometry restraints manager: 0.39 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=" 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=" N   LYS C 102 "
       pdb=" CA  LYS C 102 "
    ideal  model  delta    sigma   weight residual
    1.456  1.482 -0.026 1.21e-02 6.83e+03 4.60e+00
  bond pdb=" N   LEU C 103 "
       pdb=" CA  LEU C 103 "
    ideal  model  delta    sigma   weight residual
    1.455  1.480 -0.025 1.21e-02 6.83e+03 4.28e+00
  ... (remaining 4961 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 6597
        1.71 -     3.41: 376
        3.41 -     5.12: 65
        5.12 -     6.83: 32
        6.83 -     8.54: 9
  Bond angle restraints: 7079
  Sorted by residual:
  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 1.50e+00 4.44e-01 2.38e+01
  angle pdb=" O3'   A R  36 "
        pdb=" P     U R  37 "
        pdb=" O5'   U R  37 "
      ideal   model   delta    sigma   weight residual
     104.00   98.30    5.70 1.50e+00 4.44e-01 1.44e+01
  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 1.00e+00 1.00e+00 1.37e+01
  angle pdb=" O3'   A R   4 "
        pdb=" P     A R   5 "
        pdb=" O5'   A R   5 "
      ideal   model   delta    sigma   weight residual
     104.00   98.80    5.20 1.50e+00 4.44e-01 1.20e+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: 706
       0.110 -    0.219: 118
       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:             1.160
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.700
  Find NCS groups from input model:        0.010
  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:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.960
-------------------------------------------------------------------------------
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= 0.404
  Angle     :  0.949   8.537   7079  Z= 0.559
  Chirality :  0.100   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        0.00612 /  0.40 ( 4966)
  covalent geometry    : angle       0.94945 /  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  : 0.084 
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: 0.0989
  time to fit residues: 9.7084
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  : 0.150 
-------------------------------------------------------------------------------
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 = 0.4610 r_free = 0.4610 target = 0.139684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.116622 restraints weight = 31737.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.115689 restraints weight = 32903.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.115689 restraints weight = 33037.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.115689 restraints weight = 33037.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.115689 restraints weight = 33037.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5578
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074   4966  Z= 0.224
  Angle     :  0.689   7.160   7079  Z= 0.390
  Chirality :  0.042   0.225    857
  Planarity :  0.007   0.052    632
  Dihedral  : 20.992 117.010   1622
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 16.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  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: -0.08 (0.40), residues: 405
  helix:  3.17 (1.49), residues: 11
  sheet:  0.81 (0.38), residues: 178
  loop : -1.02 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  18 
 TYR   0.020   0.002   TYR A  60 
 PHE   0.028   0.003   PHE A 169 
 TRP   0.018   0.002   TRP C  90 
 HIS   0.004   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00462 /  0.22 ( 4966)
  covalent geometry    : angle       0.68869 /  0.39 ( 7079)
  hydrogen bonds       : bond        0.06165 /  4.19 (  180)
  hydrogen bonds       : angle       4.69804 /  3.37 (  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  : 0.135 
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   68 ILE cc_start: 0.5887 (mt) cc_final: 0.5500 (mt)
REVERT: A  166 ARG cc_start: 0.8075 (mpt180) cc_final: 0.7053 (ptp90)
REVERT: A  173 LEU cc_start: 0.6075 (tp) cc_final: 0.5798 (mt)
REVERT: B   36 MET cc_start: 0.7447 (mmp) cc_final: 0.7242 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.0783
  time to fit residues: 4.6779
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  : 0.130 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 30 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 42 optimal weight:    8.9990
   chunk 17 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0170
   chunk 1 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   chunk 43 optimal weight:   10.0000
   chunk 11 optimal weight:    6.9990
   overall best weight:    3.2026

-------------------------------------------------------------------------------
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 = 0.4506 r_free = 0.4506 target = 0.130928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.102401 restraints weight = 34133.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.102261 restraints weight = 31063.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.102306 restraints weight = 29753.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.102306 restraints weight = 29379.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.102306 restraints weight = 29379.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.4102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5961
moved from start:          0.4633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.095   4966  Z= 0.249
  Angle     :  0.715   8.181   7079  Z= 0.406
  Chirality :  0.043   0.267    857
  Planarity :  0.007   0.064    632
  Dihedral  : 21.439 124.286   1622
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 19.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  3.79 %
    Favored  : 95.63 %
  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: -0.70 (0.40), residues: 405
  helix:  3.92 (1.43), residues: 11
  sheet:  0.20 (0.37), residues: 185
  loop : -1.34 (0.40), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.002   ARG B  18 
 TYR   0.034   0.004   TYR C  86 
 PHE   0.013   0.003   PHE B  31 
 TRP   0.025   0.004   TRP B 109 
 HIS   0.022   0.003   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00526 /  0.25 ( 4966)
  covalent geometry    : angle       0.71481 /  0.41 ( 7079)
  hydrogen bonds       : bond        0.06910 /  4.35 (  180)
  hydrogen bonds       : angle       5.14811 /  3.62 (  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
  49 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 0.132 
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: 0.8376 (mmt180) cc_final: 0.7568 (mmp-170)
REVERT: A  173 LEU cc_start: 0.6363 (tp) cc_final: 0.6038 (mt)
  outliers start: 2
  outliers final: 1
  residues processed: 49
  average time/residue: 0.0925
  time to fit residues: 5.4294
Evaluate side-chains
  35 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 34
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
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:    0.0370
   chunk 12 optimal weight:   40.0000
   chunk 0 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 19 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   overall best weight:    2.5664

-------------------------------------------------------------------------------
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 = 0.4480 r_free = 0.4480 target = 0.129064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.099377 restraints weight = 34700.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.099439 restraints weight = 32260.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.099439 restraints weight = 32140.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.099439 restraints weight = 32139.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.099439 restraints weight = 32139.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.4074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6052
moved from start:          0.5304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   4966  Z= 0.201
  Angle     :  0.652   7.670   7079  Z= 0.369
  Chirality :  0.041   0.302    857
  Planarity :  0.006   0.049    632
  Dihedral  : 21.552 121.955   1622
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 16.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  2.92 %
    Favored  : 96.79 %
  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: -0.50 (0.41), residues: 405
  helix:  4.15 (1.44), residues: 11
  sheet:  0.40 (0.38), residues: 173
  loop : -1.20 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  18 
 TYR   0.017   0.002   TYR B  62 
 PHE   0.017   0.002   PHE B  31 
 TRP   0.015   0.003   TRP B 109 
 HIS   0.003   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00437 /  0.20 ( 4966)
  covalent geometry    : angle       0.65204 /  0.37 ( 7079)
  hydrogen bonds       : bond        0.06032 /  3.95 (  180)
  hydrogen bonds       : angle       5.06275 /  3.59 (  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
  40 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.108 
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: 0.8391 (mmt180) cc_final: 0.7602 (mmp-170)
REVERT: A  173 LEU cc_start: 0.6580 (tp) cc_final: 0.6191 (mt)
REVERT: B   36 MET cc_start: 0.7686 (mmp) cc_final: 0.7401 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0948
  time to fit residues: 4.5317
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  : 0.083 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 23 optimal weight:    0.2980
   chunk 2 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 37 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   chunk 44 optimal weight:   20.0000
   chunk 5 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.131307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.101267 restraints weight = 34307.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.101537 restraints weight = 32941.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.101437 restraints weight = 32920.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.101669 restraints weight = 32298.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.101672 restraints weight = 31219.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.4100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5969
moved from start:          0.5351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   4966  Z= 0.122
  Angle     :  0.550   6.080   7079  Z= 0.306
  Chirality :  0.039   0.312    857
  Planarity :  0.005   0.041    632
  Dihedral  : 21.316 119.532   1622
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  2.04 %
    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: -0.26 (0.41), residues: 405
  helix:  4.35 (1.55), residues: 11
  sheet:  0.64 (0.39), residues: 175
  loop : -1.14 (0.40), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  53 
 TYR   0.013   0.001   TYR A  60 
 PHE   0.012   0.002   PHE B  70 
 TRP   0.012   0.002   TRP C  90 
 HIS   0.005   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.12 ( 4966)
  covalent geometry    : angle       0.54963 /  0.31 ( 7079)
  hydrogen bonds       : bond        0.04764 /  3.07 (  180)
  hydrogen bonds       : angle       4.91213 /  3.55 (  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  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 ARG cc_start: 0.8374 (mmt180) cc_final: 0.7673 (mmp-170)
REVERT: A  173 LEU cc_start: 0.6619 (tp) cc_final: 0.6232 (mt)
REVERT: B   36 MET cc_start: 0.7786 (mmp) cc_final: 0.7523 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0770
  time to fit residues: 3.8986
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  : 0.100 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 30 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0060
   chunk 40 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 19 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   chunk 21 optimal weight:    0.3980
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.7998

-------------------------------------------------------------------------------
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
** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.131024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.100792 restraints weight = 34519.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.101163 restraints weight = 33615.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 16)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.101716 restraints weight = 32406.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.101707 restraints weight = 29127.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.101707 restraints weight = 29477.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5962
moved from start:          0.5519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   4966  Z= 0.119
  Angle     :  0.550   5.797   7079  Z= 0.306
  Chirality :  0.037   0.233    857
  Planarity :  0.005   0.041    632
  Dihedral  : 21.163 118.895   1622
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  2.04 %
    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: -0.15 (0.42), residues: 405
  helix:  4.23 (1.53), residues: 11
  sheet:  0.75 (0.39), residues: 173
  loop : -1.08 (0.41), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  18 
 TYR   0.012   0.001   TYR A  60 
 PHE   0.009   0.001   PHE A 169 
 TRP   0.012   0.002   TRP C  90 
 HIS   0.001   0.000   HIS A 104 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.12 ( 4966)
  covalent geometry    : angle       0.54968 /  0.31 ( 7079)
  hydrogen bonds       : bond        0.04735 /  3.06 (  180)
  hydrogen bonds       : angle       4.76965 /  3.45 (  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
  38 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 ARG cc_start: 0.8345 (mmt180) cc_final: 0.7681 (mmp-170)
REVERT: B   36 MET cc_start: 0.7707 (mmp) cc_final: 0.7496 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0706
  time to fit residues: 3.2653
Evaluate side-chains
  29 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 33 optimal weight:    0.0470
   chunk 10 optimal weight:    9.9990
   chunk 42 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 40 optimal weight:    8.9990
   chunk 45 optimal weight:   20.0000
   chunk 11 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 3 optimal weight:    0.4980
   overall best weight:    2.9084

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  80 ASN
** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 172 GLN
B  59 ASN
** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.123181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.093442 restraints weight = 33482.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.093689 restraints weight = 31320.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.094392 restraints weight = 30151.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.094505 restraints weight = 28951.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.094508 restraints weight = 28383.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6134
moved from start:          0.6601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   4966  Z= 0.211
  Angle     :  0.687   7.465   7079  Z= 0.388
  Chirality :  0.042   0.254    857
  Planarity :  0.006   0.067    632
  Dihedral  : 21.443 121.923   1622
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 21.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  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: -0.60 (0.42), residues: 405
  helix:  3.48 (1.39), residues: 11
  sheet:  0.31 (0.40), residues: 174
  loop : -1.23 (0.41), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.028   0.001   ARG A  55 
 TYR   0.027   0.004   TYR C  31 
 PHE   0.019   0.003   PHE A 108 
 TRP   0.023   0.003   TRP B 109 
 HIS   0.006   0.002   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00441 /  0.21 ( 4966)
  covalent geometry    : angle       0.68702 /  0.39 ( 7079)
  hydrogen bonds       : bond        0.07470 /  4.80 (  180)
  hydrogen bonds       : angle       5.23177 /  3.74 (  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
  35 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 ASP cc_start: 0.8980 (t0) cc_final: 0.8654 (m-30)
REVERT: A  166 ARG cc_start: 0.8266 (mmt180) cc_final: 0.7495 (mmp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0754
  time to fit residues: 3.2046
Evaluate side-chains
  25 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
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:    0.0370
   chunk 35 optimal weight:    6.9990
   chunk 15 optimal weight:   20.0000
   chunk 13 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0470
   chunk 42 optimal weight:   20.0000
   chunk 1 optimal weight:    8.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.7958

-------------------------------------------------------------------------------
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 ** 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 = 0.4462 r_free = 0.4462 target = 0.126472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.097146 restraints weight = 35198.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.097610 restraints weight = 32936.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.098094 restraints weight = 31788.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.098071 restraints weight = 29009.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.098071 restraints weight = 28986.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.4082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6043
moved from start:          0.6602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4966  Z= 0.122
  Angle     :  0.572   7.423   7079  Z= 0.317
  Chirality :  0.038   0.235    857
  Planarity :  0.005   0.041    632
  Dihedral  : 21.323 117.184   1622
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  0.58 %
    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: -0.47 (0.43), residues: 405
  helix:  3.90 (1.49), residues: 11
  sheet:  0.26 (0.40), residues: 177
  loop : -1.02 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 100 
 TYR   0.015   0.002   TYR A  60 
 PHE   0.009   0.002   PHE A 178 
 TRP   0.014   0.002   TRP C  90 
 HIS   0.002   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.12 ( 4966)
  covalent geometry    : angle       0.57236 /  0.32 ( 7079)
  hydrogen bonds       : bond        0.04999 /  3.18 (  180)
  hydrogen bonds       : angle       4.98162 /  3.58 (  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
  37 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 ASP cc_start: 0.8964 (t0) cc_final: 0.8668 (m-30)
REVERT: A  166 ARG cc_start: 0.8324 (mmt180) cc_final: 0.7653 (mmp-170)
REVERT: C   37 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8923 (pp30)
  outliers start: 1
  outliers final: 0
  residues processed: 37
  average time/residue: 0.0973
  time to fit residues: 4.3165
Evaluate side-chains
  28 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 30 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 22 optimal weight:    0.1980
   chunk 13 optimal weight:    1.9990
   chunk 43 optimal weight:   20.0000
   chunk 8 optimal weight:    9.9990
   chunk 28 optimal weight:    6.9990
   chunk 37 optimal weight:   10.0000
   chunk 38 optimal weight:    0.6980
   chunk 35 optimal weight:    0.2980
   overall best weight:    1.0384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 ** 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 = 0.4464 r_free = 0.4464 target = 0.126800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.098032 restraints weight = 33950.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.097763 restraints weight = 31933.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.098122 restraints weight = 30314.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 15)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.098121 restraints weight = 28732.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.098121 restraints weight = 28735.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5990
moved from start:          0.6726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4966  Z= 0.120
  Angle     :  0.548   7.874   7079  Z= 0.307
  Chirality :  0.037   0.224    857
  Planarity :  0.005   0.043    632
  Dihedral  : 21.170 116.001   1622
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 16.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  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: -0.51 (0.42), residues: 405
  helix:  3.79 (1.49), residues: 11
  sheet:  0.09 (0.39), residues: 179
  loop : -0.92 (0.42), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  21 
 TYR   0.015   0.002   TYR A  60 
 PHE   0.011   0.002   PHE A 178 
 TRP   0.015   0.002   TRP C  90 
 HIS   0.001   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.12 ( 4966)
  covalent geometry    : angle       0.54839 /  0.31 ( 7079)
  hydrogen bonds       : bond        0.05243 /  3.34 (  180)
  hydrogen bonds       : angle       4.88754 /  3.51 (  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  : 0.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 ARG cc_start: 0.8246 (mmt180) cc_final: 0.7478 (mmp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0959
  time to fit residues: 4.1624
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  : 0.128 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 25 optimal weight:    8.9990
   chunk 35 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9990
   chunk 44 optimal weight:   20.0000
   chunk 15 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 7 optimal weight:   10.0000
   overall best weight:    1.1786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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  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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.125975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.096601 restraints weight = 34434.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.097053 restraints weight = 31754.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.097439 restraints weight = 30193.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.097595 restraints weight = 29455.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.097738 restraints weight = 28850.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.4087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5980
moved from start:          0.6947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4966  Z= 0.131
  Angle     :  0.590  10.554   7079  Z= 0.326
  Chirality :  0.038   0.223    857
  Planarity :  0.005   0.047    632
  Dihedral  : 21.128 115.811   1622
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 17.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  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 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: -0.65 (0.42), residues: 405
  helix:  3.77 (1.48), residues: 11
  sheet: -0.16 (0.38), residues: 180
  loop : -0.85 (0.43), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.001   ARG A 136 
 TYR   0.015   0.002   TYR A  60 
 PHE   0.028   0.002   PHE B  70 
 TRP   0.014   0.002   TRP C  90 
 HIS   0.001   0.001   HIS A 160 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.13 ( 4966)
  covalent geometry    : angle       0.58956 /  0.33 ( 7079)
  hydrogen bonds       : bond        0.05376 /  3.41 (  180)
  hydrogen bonds       : angle       5.07340 /  3.65 (  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
  36 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 ARG cc_start: 0.8180 (mmt180) cc_final: 0.7419 (mmp-170)
REVERT: B   75 ASP cc_start: 0.6298 (p0) cc_final: 0.6098 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0845
  time to fit residues: 3.7461
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  : 0.080 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 40 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 20 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 41 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 18 optimal weight:    0.0970
   chunk 29 optimal weight:    8.9990
   overall best weight:    1.4980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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  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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.124601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.095161 restraints weight = 34562.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.095517 restraints weight = 32014.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.095960 restraints weight = 30457.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.096529 restraints weight = 29819.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.096466 restraints weight = 27596.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6029
moved from start:          0.7273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4966  Z= 0.140
  Angle     :  0.575  10.319   7079  Z= 0.323
  Chirality :  0.038   0.222    857
  Planarity :  0.006   0.096    632
  Dihedral  : 21.107 115.752   1622
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 18.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  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 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 (0.42), residues: 405
  helix:  3.49 (1.40), residues: 11
  sheet: -0.28 (0.37), residues: 181
  loop : -0.85 (0.43), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 136 
 TYR   0.017   0.002   TYR A  60 
 PHE   0.014   0.002   PHE A 178 
 TRP   0.014   0.002   TRP C  90 
 HIS   0.002   0.001   HIS A 160 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.14 ( 4966)
  covalent geometry    : angle       0.57484 /  0.32 ( 7079)
  hydrogen bonds       : bond        0.05723 /  3.59 (  180)
  hydrogen bonds       : angle       5.21009 /  3.70 (  429)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1098.48 seconds
wall clock time: 19 minutes 33.28 seconds (1173.28 seconds total)