Starting phenix.real_space_refine
on Fri Aug 22 14:48:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yr6_34047/08_2025/7yr6_34047.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yr6_34047/08_2025/7yr6_34047.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yr6_34047/08_2025/7yr6_34047.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yr6_34047/08_2025/7yr6_34047.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yr6_34047/08_2025/7yr6_34047.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yr6_34047/08_2025/7yr6_34047.cif"
  }
  resolution = 4.8
  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=   0.004 sd=   0.039
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     118      5.49       5
     S       8      5.16       5
     C    2197      2.51       5
     N     797      2.21       5
     O    1128      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4248
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "E"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 426
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 6
    Chain: "C"
      Number of atoms: 425
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 425
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 426
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 6
    Chain: "A"
      Number of atoms: 2547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 2547
          Classifications: {'RNA': 118}
          Modifications used: {'rna2p_pur': 20, 'rna2p_pyr': 7, 'rna3p_pur': 52, 'rna3p_pyr': 39}
          Link IDs: {'rna2p': 26, 'rna3p': 91}
  Time building chain proxies: 1.05, per 1000 atoms: 0.25
  Number of scatterers: 4248
  At special positions: 0
  Unit cell: (84.15, 91.8, 101.15, 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       8     16.00
     P     118     15.00
     O    1128      8.00
     N     797      7.00
     C    2197      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: 0.31
  Conformation dependent library (CDL) restraints added in 75.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  398

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 3 sheets defined
      14.1% alpha, 14.1% beta
      30 base pairs and 49 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'E' and resid 48 through 55
    Processing helix  chain 'D' and resid 47 through 55
    Processing helix  chain 'C' and resid 46 through 54
    Processing helix  chain 'B' and resid 45 through 49
    Processing sheet with id=AA1, first strand: chain 'E' and resid 2 through 7
      removed outlier: 3.787A  pdb=" N   GLY D  33 " --> pdb=" O   THR D  21 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 20 through 26
      removed outlier: 5.104A  pdb=" N   VAL C  22 " --> pdb=" O   GLY C  33 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   GLY C  33 " --> pdb=" O   VAL C  22 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   VAL C  30 " --> pdb=" O   ARG B   6 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ARG B   6 " --> pdb=" O   VAL C  30 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 21 through 25
      removed outlier: 3.744A  pdb=" N   THR B  21 " --> pdb=" O   GLY B  33 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY B  33 " --> pdb=" O   THR B  21 " (cutoff:3.500A)
      removed outlier: 5.288A  pdb=" N   ARG B  31 " --> pdb=" O   LEU B  23 " (cutoff:3.500A)

    28 hydrogen bonds defined for protein.
    72 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      82 hydrogen bonds
      160 hydrogen bond angles
      0 basepair planarities
      30 basepair parallelities
      49 stacking parallelities
  Total time for adding SS restraints: 0.61

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 672
        1.33 -     1.45: 1678
        1.45 -     1.57: 1962
        1.57 -     1.69: 235
        1.69 -     1.80: 16
  Bond restraints: 4563
  Sorted by residual:
  bond pdb=" O3'   C A  15 "
       pdb=" P     G A  16 "
    ideal  model  delta    sigma   weight residual
    1.607  1.666 -0.059 1.50e-02 4.44e+03 1.54e+01
  bond pdb=" O3'   G A  57 "
       pdb=" P     A A  58 "
    ideal  model  delta    sigma   weight residual
    1.607  1.656 -0.049 1.50e-02 4.44e+03 1.05e+01
  bond pdb=" O3'   C A  61 "
       pdb=" P     C A  62 "
    ideal  model  delta    sigma   weight residual
    1.607  1.651 -0.044 1.50e-02 4.44e+03 8.77e+00
  bond pdb=" N   VAL D  40 "
       pdb=" CA  VAL D  40 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.037 1.27e-02 6.20e+03 8.30e+00
  bond pdb=" O3'   A A  63 "
       pdb=" P     U A  64 "
    ideal  model  delta    sigma   weight residual
    1.607  1.641 -0.034 1.50e-02 4.44e+03 5.28e+00
  ... (remaining 4558 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 6451
        2.00 -     4.01: 267
        4.01 -     6.01: 29
        6.01 -     8.01: 6
        8.01 -    10.01: 3
  Bond angle restraints: 6756
  Sorted by residual:
  angle pdb=" O3'   C A  61 "
        pdb=" C3'   C A  61 "
        pdb=" C2'   C A  61 "
      ideal   model   delta    sigma   weight residual
     109.50  119.51  -10.01 1.50e+00 4.44e-01 4.46e+01
  angle pdb=" N   ILE D  47 "
        pdb=" CA  ILE D  47 "
        pdb=" C   ILE D  47 "
      ideal   model   delta    sigma   weight residual
     113.71  109.21    4.50 9.50e-01 1.11e+00 2.25e+01
  angle pdb=" C   ILE E  47 "
        pdb=" N   TYR E  48 "
        pdb=" CA  TYR E  48 "
      ideal   model   delta    sigma   weight residual
     121.54  130.25   -8.71 1.91e+00 2.74e-01 2.08e+01
  angle pdb=" O3'   G A  81 "
        pdb=" C3'   G A  81 "
        pdb=" C2'   G A  81 "
      ideal   model   delta    sigma   weight residual
     109.50  115.96   -6.46 1.50e+00 4.44e-01 1.85e+01
  angle pdb=" N   LEU E  23 "
        pdb=" CA  LEU E  23 "
        pdb=" C   LEU E  23 "
      ideal   model   delta    sigma   weight residual
     110.88  116.23   -5.35 1.28e+00 6.10e-01 1.75e+01
  ... (remaining 6751 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.86: 2492
       35.86 -    71.71: 367
       71.71 -   107.57: 49
      107.57 -   143.42: 3
      143.42 -   179.28: 2
  Dihedral angle restraints: 2913
    sinusoidal: 2295
      harmonic: 618
  Sorted by residual:
  dihedral pdb=" O4'   U A  60 "
           pdb=" C1'   U A  60 "
           pdb=" N1    U A  60 "
           pdb=" C2    U A  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   53.25  146.75     1      1.50e+01 4.44e-03 7.83e+01
  dihedral pdb=" O4'   G A  39 "
           pdb=" C1'   G A  39 "
           pdb=" N9    G A  39 "
           pdb=" C4    G A  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
      68.00  153.16  -85.16     1      1.70e+01 3.46e-03 3.04e+01
  dihedral pdb=" CA  VAL D  18 "
           pdb=" C   VAL D  18 "
           pdb=" N   THR D  19 "
           pdb=" CA  THR D  19 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.48  -27.52     0      5.00e+00 4.00e-02 3.03e+01
  ... (remaining 2910 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.105: 822
       0.105 -    0.210: 46
       0.210 -    0.316: 6
       0.316 -    0.421: 1
       0.421 -    0.526: 1
  Chirality restraints: 876
  Sorted by residual:
  chirality pdb=" C3'   C A  61 "
            pdb=" C4'   C A  61 "
            pdb=" O3'   C A  61 "
            pdb=" C2'   C A  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.22   -0.53 2.00e-01 2.50e+01 6.92e+00
  chirality pdb=" CB  ILE C  32 "
            pdb=" CA  ILE C  32 "
            pdb=" CG1 ILE C  32 "
            pdb=" CG2 ILE C  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.35 2.00e-01 2.50e+01 3.06e+00
  chirality pdb=" P     G A  57 "
            pdb=" OP1   G A  57 "
            pdb=" OP2   G A  57 "
            pdb=" O5'   G A  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.72   -0.31 2.00e-01 2.50e+01 2.34e+00
  ... (remaining 873 not shown)

  Planarity restraints: 413
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A  35 "   -0.022 2.00e-02 2.50e+03   1.05e-02 3.31e+00
        pdb=" N9    G A  35 "    0.027 2.00e-02 2.50e+03
        pdb=" C8    G A  35 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    G A  35 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G A  35 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    G A  35 "   -0.005 2.00e-02 2.50e+03
        pdb=" O6    G A  35 "   -0.004 2.00e-02 2.50e+03
        pdb=" N1    G A  35 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    G A  35 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G A  35 "    0.006 2.00e-02 2.50e+03
        pdb=" N3    G A  35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    G A  35 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U A  91 "    0.021 2.00e-02 2.50e+03   1.08e-02 2.63e+00
        pdb=" N1    U A  91 "   -0.022 2.00e-02 2.50e+03
        pdb=" C2    U A  91 "   -0.003 2.00e-02 2.50e+03
        pdb=" O2    U A  91 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    U A  91 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    U A  91 "   -0.001 2.00e-02 2.50e+03
        pdb=" O4    U A  91 "    0.009 2.00e-02 2.50e+03
        pdb=" C5    U A  91 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    U A  91 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR E  48 "   -0.008 2.00e-02 2.50e+03   1.54e-02 2.37e+00
        pdb=" C   TYR E  48 "    0.027 2.00e-02 2.50e+03
        pdb=" O   TYR E  48 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   GLN E  49 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 410 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1060
        2.81 -     3.33: 3678
        3.33 -     3.86: 8638
        3.86 -     4.38: 9229
        4.38 -     4.90: 12472
  Nonbonded interactions: 35077
  Sorted by model distance:
  nonbonded pdb=" O2'   G A  50 "
            pdb=" O4'   G A  51 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O2'   A A  41 "
            pdb=" O5'   G A  43 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" O   GLU B  10 "
            pdb=" OG1 THR B  21 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" O   VAL E  40 "
            pdb=" N1    G A  10 "
     model   vdw
     2.370 3.120
  nonbonded pdb=" O   VAL B  42 "
            pdb=" N2    G A  39 "
     model   vdw
     2.397 3.120
  ... (remaining 35072 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ 
e N or name CA or name C or name O )) or resid 25 through 55))
  selection = (chain 'C' and (resid 1 through 22 or (resid 23 through 24 and (name N or name C \ 
A or name C or name O )) or resid 25 or (resid 26 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 27 through 55))
  selection = (chain 'D' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ 
e N or name CA or name C or name O )) or resid 25 through 55))
  selection = (chain 'E' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 18 through 25 or (resid 26 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 27 through 55))
}

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:             0.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.770
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   4563  Z= 0.257
  Angle     :  0.883  10.014   6756  Z= 0.497
  Chirality :  0.055   0.526    876
  Planarity :  0.004   0.028    413
  Dihedral  : 26.030 179.280   2515
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.09 %
    Favored  : 84.91 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 12.09 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.39 (0.42), residues: 212
  helix: -3.34 (0.76), residues: 24
  sheet: -3.13 (0.95), residues: 29
  loop : -4.07 (0.34), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  44 
 TYR   0.008   0.001   TYR B  48 
 HIS   0.004   0.001   HIS B  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 4563)
  covalent geometry    : angle       0.88334 ( 6756)
  hydrogen bonds       : bond        0.13349 (  110)
  hydrogen bonds       : angle       5.47836 (  232)

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

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

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.076 
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: E   13 MET cc_start: 0.9402 (tmm) cc_final: 0.9171 (tmm)
REVERT: E   46 GLU cc_start: 0.9307 (tp30) cc_final: 0.8712 (tp30)
REVERT: E   47 ILE cc_start: 0.8852 (mt) cc_final: 0.8353 (mp)
REVERT: C   43 HIS cc_start: 0.9032 (m-70) cc_final: 0.8789 (m90)
  outliers start: 6
  outliers final: 3
  residues processed: 84
  average time/residue: 0.1125
  time to fit residues: 10.9139
Evaluate side-chains
  59 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 12 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 13 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 30 optimal weight:   30.0000
   chunk 16 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 29 optimal weight:    9.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** E  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  52 GLN
** C  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  35 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.069194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.054010 restraints weight = 36987.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.055731 restraints weight = 21114.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.056887 restraints weight = 14163.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.057668 restraints weight = 10619.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.058246 restraints weight = 8600.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4563  Z= 0.227
  Angle     :  0.692   6.184   6756  Z= 0.363
  Chirality :  0.040   0.196    876
  Planarity :  0.005   0.029    413
  Dihedral  : 26.967 172.961   2095
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 24.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.23 %
    Favored  : 78.77 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 11.54 %
    Favored  : 87.91 %
  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 aren not related in a simple way.
  whole: -5.19 (0.47), residues: 212
  helix: -2.56 (0.89), residues: 28
  sheet: -2.95 (1.06), residues: 22
  loop : -4.07 (0.38), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  31 
 TYR   0.004   0.001   TYR D  48 
 HIS   0.007   0.003   HIS B  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 4563)
  covalent geometry    : angle       0.69190 ( 6756)
  hydrogen bonds       : bond        0.07906 (  110)
  hydrogen bonds       : angle       4.70837 (  232)

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

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

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.062 
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: E   13 MET cc_start: 0.9534 (tmm) cc_final: 0.9208 (tmm)
REVERT: E   44 ARG cc_start: 0.8796 (mtp180) cc_final: 0.8288 (mtt-85)
REVERT: E   47 ILE cc_start: 0.8823 (mt) cc_final: 0.8482 (mp)
REVERT: C    2 LEU cc_start: 0.8141 (mm) cc_final: 0.7912 (mm)
REVERT: B    1 MET cc_start: 0.7158 (mpp) cc_final: 0.6633 (mpp)
  outliers start: 1
  outliers final: 1
  residues processed: 57
  average time/residue: 0.1129
  time to fit residues: 7.3944
Evaluate side-chains
  46 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 22 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 4 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 30 optimal weight:   30.0000
   chunk 11 optimal weight:    0.9980
   chunk 23 optimal weight:    7.9990
   overall best weight:    3.3786

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

Flipped N/Q/H residues before XYZ refinement:
** E  52 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 = 0.3455 r_free = 0.3455 target = 0.069462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.054834 restraints weight = 40200.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.056379 restraints weight = 23445.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.057447 restraints weight = 15826.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.058205 restraints weight = 11888.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.058633 restraints weight = 9677.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4563  Z= 0.180
  Angle     :  0.642   5.599   6756  Z= 0.338
  Chirality :  0.039   0.172    876
  Planarity :  0.004   0.031    413
  Dihedral  : 26.992 170.561   2095
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 21.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.75 %
    Favored  : 79.25 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  9.34 %
    Favored  : 90.11 %
  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 aren not related in a simple way.
  whole: -4.88 (0.50), residues: 212
  helix: -2.04 (0.94), residues: 28
  sheet: -2.68 (1.08), residues: 22
  loop : -3.91 (0.41), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  31 
 TYR   0.004   0.001   TYR E  48 
 HIS   0.006   0.002   HIS B  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 4563)
  covalent geometry    : angle       0.64230 ( 6756)
  hydrogen bonds       : bond        0.05930 (  110)
  hydrogen bonds       : angle       4.45904 (  232)

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

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

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.127 
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: E    1 MET cc_start: 0.9411 (ptt) cc_final: 0.9127 (ppp)
REVERT: E   13 MET cc_start: 0.9541 (tmm) cc_final: 0.9183 (tmm)
REVERT: E   44 ARG cc_start: 0.8778 (mtp180) cc_final: 0.8273 (mtt-85)
REVERT: E   47 ILE cc_start: 0.8695 (mt) cc_final: 0.8334 (mp)
REVERT: B    1 MET cc_start: 0.7135 (mpp) cc_final: 0.6918 (mpp)
REVERT: B    4 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7990 (pp)
  outliers start: 1
  outliers final: 0
  residues processed: 56
  average time/residue: 0.1141
  time to fit residues: 7.3877
Evaluate side-chains
  48 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 17 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 1 optimal weight:    8.9990
   chunk 26 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
** E  52 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 = 0.3453 r_free = 0.3453 target = 0.069063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.054402 restraints weight = 39504.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.055964 restraints weight = 23081.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.057092 restraints weight = 15648.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.057721 restraints weight = 11651.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.058294 restraints weight = 9616.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.3413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4563  Z= 0.166
  Angle     :  0.633   7.172   6756  Z= 0.330
  Chirality :  0.038   0.171    876
  Planarity :  0.004   0.037    413
  Dihedral  : 26.979 168.384   2095
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 21.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.34 %
    Favored  : 80.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.80 (0.50), residues: 212
  helix: -2.24 (0.84), residues: 28
  sheet: -2.40 (1.17), residues: 22
  loop : -3.83 (0.43), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C   6 
 TYR   0.010   0.001   TYR C  48 
 HIS   0.007   0.002   HIS B  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 4563)
  covalent geometry    : angle       0.63314 ( 6756)
  hydrogen bonds       : bond        0.05590 (  110)
  hydrogen bonds       : angle       4.27604 (  232)

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

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

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.081 
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: E    1 MET cc_start: 0.9390 (ptt) cc_final: 0.9088 (ppp)
REVERT: E   13 MET cc_start: 0.9540 (tmm) cc_final: 0.9163 (tmm)
REVERT: E   44 ARG cc_start: 0.8778 (mtp180) cc_final: 0.8349 (mtt-85)
REVERT: E   47 ILE cc_start: 0.8726 (mt) cc_final: 0.8380 (mp)
REVERT: B    1 MET cc_start: 0.7226 (mpp) cc_final: 0.6961 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1157
  time to fit residues: 7.7275
Evaluate side-chains
  50 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 8 optimal weight:    0.0030
   chunk 18 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 27 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   overall best weight:    3.5394

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

Flipped N/Q/H residues before XYZ refinement:
** E  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.067299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.052679 restraints weight = 40112.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.054320 restraints weight = 23317.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.055405 restraints weight = 15750.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.056057 restraints weight = 11856.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.056621 restraints weight = 9754.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.3903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4563  Z= 0.190
  Angle     :  0.660   5.920   6756  Z= 0.343
  Chirality :  0.039   0.173    876
  Planarity :  0.005   0.033    413
  Dihedral  : 27.111 166.865   2095
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 24.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.87 %
    Favored  : 81.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.79 %
    Favored  : 91.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.47 %

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 aren not related in a simple way.
  whole: -4.79 (0.52), residues: 212
  helix: -2.27 (0.85), residues: 28
  sheet: -2.35 (1.20), residues: 22
  loop : -3.83 (0.44), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C   6 
 TYR   0.017   0.002   TYR B  48 
 HIS   0.011   0.004   HIS B  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 4563)
  covalent geometry    : angle       0.66034 ( 6756)
  hydrogen bonds       : bond        0.06487 (  110)
  hydrogen bonds       : angle       4.41529 (  232)

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

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

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.104 
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: E    1 MET cc_start: 0.9360 (ptt) cc_final: 0.9038 (ptt)
REVERT: E   13 MET cc_start: 0.9551 (tmm) cc_final: 0.9238 (tmm)
REVERT: E   44 ARG cc_start: 0.8885 (mtp180) cc_final: 0.8374 (mtt-85)
REVERT: E   47 ILE cc_start: 0.8801 (mt) cc_final: 0.8437 (mp)
REVERT: C    2 LEU cc_start: 0.8244 (mm) cc_final: 0.8034 (mm)
REVERT: C   31 ARG cc_start: 0.9224 (mtt180) cc_final: 0.9015 (ttt180)
REVERT: B    1 MET cc_start: 0.7470 (mpp) cc_final: 0.7242 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1212
  time to fit residues: 7.9946
Evaluate side-chains
  48 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 12 optimal weight:    7.9990
   chunk 4 optimal weight:    0.5980
   chunk 13 optimal weight:    6.9990
   chunk 14 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    4.1188

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

Flipped N/Q/H residues before XYZ refinement:
** E  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  35 ASN
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.066064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.051504 restraints weight = 41913.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.053064 restraints weight = 24056.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.054143 restraints weight = 16191.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.054808 restraints weight = 12152.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.055388 restraints weight = 9957.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.4383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4563  Z= 0.213
  Angle     :  0.681   5.874   6756  Z= 0.356
  Chirality :  0.041   0.215    876
  Planarity :  0.005   0.024    413
  Dihedral  : 27.273 167.194   2095
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 25.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.23 %
    Favored  : 78.77 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  7.69 %
    Favored  : 91.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.47 %

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 aren not related in a simple way.
  whole: -4.77 (0.52), residues: 212
  helix: -2.22 (0.83), residues: 28
  sheet: -2.38 (1.19), residues: 22
  loop : -3.82 (0.45), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C   6 
 TYR   0.012   0.001   TYR C  48 
 HIS   0.008   0.003   HIS B  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 4563)
  covalent geometry    : angle       0.68088 ( 6756)
  hydrogen bonds       : bond        0.07341 (  110)
  hydrogen bonds       : angle       4.41484 (  232)

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

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

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.9264 (ptt) cc_final: 0.8937 (ptt)
REVERT: E   13 MET cc_start: 0.9590 (tmm) cc_final: 0.9258 (tmm)
REVERT: E   46 GLU cc_start: 0.9390 (tp30) cc_final: 0.9138 (tp30)
REVERT: D   48 TYR cc_start: 0.9114 (t80) cc_final: 0.8872 (t80)
REVERT: C    2 LEU cc_start: 0.8170 (mm) cc_final: 0.7948 (mm)
REVERT: B    1 MET cc_start: 0.7446 (mpp) cc_final: 0.6944 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1209
  time to fit residues: 8.5080
Evaluate side-chains
  52 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 16 optimal weight:    8.9990
   chunk 11 optimal weight:    0.6980
   chunk 1 optimal weight:    7.9990
   chunk 17 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 8 optimal weight:   20.0000
   chunk 0 optimal weight:    4.9990
   chunk 15 optimal weight:    8.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
** E  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.067543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.052698 restraints weight = 40841.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.054362 restraints weight = 23633.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.055540 restraints weight = 15838.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.056297 restraints weight = 11766.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.056739 restraints weight = 9605.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.4430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4563  Z= 0.173
  Angle     :  0.653   6.380   6756  Z= 0.344
  Chirality :  0.040   0.245    876
  Planarity :  0.004   0.027    413
  Dihedral  : 27.118 166.514   2095
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 22.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.81 %
    Favored  : 80.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.47 %

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 aren not related in a simple way.
  whole: -5.00 (0.50), residues: 212
  helix: -3.18 (0.66), residues: 28
  sheet: -2.86 (1.43), residues: 12
  loop : -3.75 (0.44), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  50 
 TYR   0.009   0.001   TYR C  48 
 HIS   0.006   0.002   HIS B  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 4563)
  covalent geometry    : angle       0.65278 ( 6756)
  hydrogen bonds       : bond        0.05982 (  110)
  hydrogen bonds       : angle       4.59079 (  232)

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

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

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.098 
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: E    1 MET cc_start: 0.9238 (ptt) cc_final: 0.8909 (ptt)
REVERT: E   13 MET cc_start: 0.9603 (tmm) cc_final: 0.9251 (tmm)
REVERT: D   48 TYR cc_start: 0.9303 (t80) cc_final: 0.9088 (t80)
REVERT: B    1 MET cc_start: 0.7202 (mpp) cc_final: 0.6937 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.1180
  time to fit residues: 8.0877
Evaluate side-chains
  49 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 10 optimal weight:   20.0000
   chunk 19 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   chunk 7 optimal weight:    0.3980
   chunk 9 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   chunk 24 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    4.6788

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

Flipped N/Q/H residues before XYZ refinement:
** E  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.065175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.050358 restraints weight = 40006.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.051882 restraints weight = 22783.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.052990 restraints weight = 15378.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.053660 restraints weight = 11569.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.054208 restraints weight = 9498.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.4889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   4563  Z= 0.236
  Angle     :  0.738   6.120   6756  Z= 0.386
  Chirality :  0.042   0.262    876
  Planarity :  0.005   0.031    413
  Dihedral  : 27.293 166.999   2095
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 30.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 22.64 %
    Favored  : 77.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.47 %

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 aren not related in a simple way.
  whole: -5.27 (0.48), residues: 212
  helix: -3.49 (0.64), residues: 28
  sheet: -2.98 (1.43), residues: 12
  loop : -3.94 (0.42), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C   6 
 TYR   0.010   0.001   TYR C  48 
 HIS   0.008   0.003   HIS B  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 4563)
  covalent geometry    : angle       0.73805 ( 6756)
  hydrogen bonds       : bond        0.07949 (  110)
  hydrogen bonds       : angle       4.51350 (  232)

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

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

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  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: E    1 MET cc_start: 0.9285 (ptt) cc_final: 0.9014 (ptt)
REVERT: E   13 MET cc_start: 0.9598 (tmm) cc_final: 0.9279 (tmm)
REVERT: E   46 GLU cc_start: 0.9290 (tp30) cc_final: 0.8586 (tp30)
REVERT: E   47 ILE cc_start: 0.8771 (mp) cc_final: 0.8239 (mp)
REVERT: E   50 ARG cc_start: 0.9475 (pmt170) cc_final: 0.9188 (pmt170)
REVERT: D   48 TYR cc_start: 0.9245 (t80) cc_final: 0.9018 (t80)
REVERT: B    1 MET cc_start: 0.7553 (mpp) cc_final: 0.7304 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1145
  time to fit residues: 7.5153
Evaluate side-chains
  48 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 6 optimal weight:    0.2980
   chunk 12 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 30 optimal weight:   30.0000
   chunk 19 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 26 optimal weight:    9.9990
   chunk 25 optimal weight:    8.9990
   chunk 23 optimal weight:   10.0000
   overall best weight:    3.6386

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

Flipped N/Q/H residues before XYZ refinement:
** E  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.066287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.051354 restraints weight = 40839.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.052967 restraints weight = 23545.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.054100 restraints weight = 15891.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.054857 restraints weight = 11845.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.055316 restraints weight = 9646.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.4997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4563  Z= 0.193
  Angle     :  0.688   7.044   6756  Z= 0.361
  Chirality :  0.041   0.266    876
  Planarity :  0.004   0.035    413
  Dihedral  : 27.194 166.387   2095
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 25.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.70 %
    Favored  : 78.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.47 %

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 aren not related in a simple way.
  whole: -5.35 (0.48), residues: 212
  helix: -3.55 (0.63), residues: 28
  sheet: -3.15 (1.38), residues: 12
  loop : -3.99 (0.42), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C   6 
 TYR   0.010   0.001   TYR C  48 
 HIS   0.006   0.002   HIS B  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 4563)
  covalent geometry    : angle       0.68825 ( 6756)
  hydrogen bonds       : bond        0.06784 (  110)
  hydrogen bonds       : angle       4.43402 (  232)

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

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

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.112 
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: E    1 MET cc_start: 0.9253 (ptt) cc_final: 0.8995 (ptt)
REVERT: E   13 MET cc_start: 0.9623 (tmm) cc_final: 0.9269 (tmm)
REVERT: E   46 GLU cc_start: 0.9448 (tp30) cc_final: 0.8754 (tp30)
REVERT: E   47 ILE cc_start: 0.8518 (mp) cc_final: 0.8177 (mp)
REVERT: E   50 ARG cc_start: 0.9540 (pmt170) cc_final: 0.9269 (pmt170)
REVERT: D   48 TYR cc_start: 0.9275 (t80) cc_final: 0.9035 (t80)
REVERT: C   31 ARG cc_start: 0.9144 (mtt180) cc_final: 0.8876 (ttt180)
REVERT: B    1 MET cc_start: 0.7162 (mpp) cc_final: 0.6891 (mpp)
REVERT: B    4 LEU cc_start: 0.7858 (pp) cc_final: 0.7573 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.1199
  time to fit residues: 7.7307
Evaluate side-chains
  47 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 8 optimal weight:    0.1980
   chunk 22 optimal weight:   10.0000
   chunk 26 optimal weight:    9.9990
   chunk 6 optimal weight:   30.0000
   chunk 29 optimal weight:   10.0000
   chunk 14 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    4.2388

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

Flipped N/Q/H residues before XYZ refinement:
** E  52 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 = 0.3374 r_free = 0.3374 target = 0.064981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.050302 restraints weight = 41446.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.051882 restraints weight = 23961.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.052968 restraints weight = 16142.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.053718 restraints weight = 12056.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.054170 restraints weight = 9819.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.5320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4563  Z= 0.221
  Angle     :  0.735   7.289   6756  Z= 0.386
  Chirality :  0.042   0.264    876
  Planarity :  0.005   0.038    413
  Dihedral  : 27.290 167.384   2095
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 30.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 25.00 %
    Favored  : 75.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.47 %

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 aren not related in a simple way.
  whole: -5.39 (0.49), residues: 212
  helix: -3.70 (0.63), residues: 28
  sheet: -3.10 (1.42), residues: 12
  loop : -4.00 (0.42), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  44 
 TYR   0.011   0.002   TYR C  48 
 HIS   0.007   0.002   HIS B  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 4563)
  covalent geometry    : angle       0.73496 ( 6756)
  hydrogen bonds       : bond        0.07793 (  110)
  hydrogen bonds       : angle       4.75365 (  232)

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

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

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  424 Ramachandran restraints generated.
    212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.062 
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: E    1 MET cc_start: 0.9246 (ptt) cc_final: 0.9007 (ptt)
REVERT: E   13 MET cc_start: 0.9637 (tmm) cc_final: 0.9340 (tmm)
REVERT: E   46 GLU cc_start: 0.9439 (tp30) cc_final: 0.9171 (tp30)
REVERT: D   50 ARG cc_start: 0.9474 (ptm160) cc_final: 0.9217 (ptt180)
REVERT: C   31 ARG cc_start: 0.9192 (mtt180) cc_final: 0.8948 (ttt180)
REVERT: B    1 MET cc_start: 0.7306 (mpp) cc_final: 0.6989 (mpp)
REVERT: B    4 LEU cc_start: 0.7918 (pp) cc_final: 0.7698 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.1190
  time to fit residues: 7.5279
Evaluate side-chains
  45 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 4 optimal weight:   20.0000
   chunk 17 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 5 optimal weight:   20.0000
   chunk 23 optimal weight:   10.0000
   chunk 30 optimal weight:   30.0000
   chunk 19 optimal weight:    1.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** E  52 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 = 0.3414 r_free = 0.3414 target = 0.067796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.052621 restraints weight = 38559.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.054297 restraints weight = 22114.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.055441 restraints weight = 14917.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.056190 restraints weight = 11116.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.056636 restraints weight = 9057.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.5260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4563  Z= 0.158
  Angle     :  0.657   8.358   6756  Z= 0.345
  Chirality :  0.039   0.235    876
  Planarity :  0.004   0.038    413
  Dihedral  : 26.977 166.302   2095
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 20.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.28 %
    Favored  : 79.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  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 aren not related in a simple way.
  whole: -5.26 (0.51), residues: 212
  helix: -3.93 (0.58), residues: 28
  sheet: -3.03 (1.40), residues: 12
  loop : -3.83 (0.45), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  44 
 TYR   0.009   0.001   TYR C  48 
 HIS   0.005   0.002   HIS B  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 4563)
  covalent geometry    : angle       0.65704 ( 6756)
  hydrogen bonds       : bond        0.05771 (  110)
  hydrogen bonds       : angle       4.52629 (  232)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 854.86 seconds
wall clock time: 15 minutes 23.67 seconds (923.67 seconds total)